##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_61.variant23 sample.vcf #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample_61.variant23 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 0/1:121,195:316:99:4152,0,2237:58,63,99,96 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 0/1:121,200:321:99:5348,0,2260:55,66,95,105 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 0/1:261,58:319:99:538,0,8686:117,144,28,30 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 0/1:179,49:228:99:598,0,4335:70,109,21,28 chr1 15820 . G T 112.71 PASS AC=1;AF=0.714;AN=2;DP=55;set=variant14-variant19-variant23-variant25-variant33-variant34-variant37 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:29:130,0,29:1,1,3,2 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 0/1:73,18:91:99:243,0,1937:50,23,12,6 chr1 17538 . C A 373.32 PASS AC=1;AF=0.5;AN=2;DP=2172;set=variant-filterInvariant2-variant3-variant4-filterInvariant5-filterInvariant8-variant9-variant11-variant12-variant13-filterInvariant22-variant23-variant26-variant27-variant29-filterInvariant31-filterInvariant32-filterInvariant34-filterInvariant36-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:98,24:122:99:295,0,2369:53,45,7,17 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 1/1:0,6:6:18:133,18,0:0,0,3,3 chr1 137825 . G A 202.81 DRAGENHardSNP AC=2;AF=0.548;AN=2;DP=674;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:531,63,0:0,0,12,9 chr1 137923 . C T 136.65 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=73;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:6,10:16:92:192,0,92:2,4,6,4 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 1/1:0,3:3:9:76,9,0:0,0,0,3 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 1/1:0,5:5:15:124,15,0:0,0,3,2 chr1 664468 . G T 343.75 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=3234;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:93,17:110:99:107,0,1961:47,46,8,9 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 1/1:0,8:8:24:282,24,0:0,0,0,8 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 1/1:0,20:20:60:796,60,0:0,0,20,0 chr1 762273 . G A 1157.09 PASS AC=2;AF=0.841;AN=2;DP=5222;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2736,262,0:0,0,29,59 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 1/1:0,47:47:99:2185,147,0:0,0,14,33 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 1/1:0,48:48:99:2149,144,0:0,0,16,32 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 1/1:0,43:43:99:1980,132,0:0,0,13,30 chr1 762632 . T A 137.73 PASS AC=2;AF=0.852;AN=2;DP=1189;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:801,75,0:0,0,9,16 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 1/1:0,26:26:78:792,78,0:0,0,17,9 chr1 792480 . C T 3383.51 PASS AC=2;AF=0.966;AN=2;DP=4598;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2664,264,0:0,0,43,45 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 1/1:0,4:4:12:168,12,0:0,0,1,3 chr1 808631 . G A 199.97 PASS AC=1;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 0/1:8,17:25:99:553,0,216:7,1,13,4 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 1/1:0,177:177:99:6862,530,0:0,0,103,74 chr1 808928 . C T 1200.84 PASS AC=1;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 0/1:89,96:185:99:2261,0,2543:55,34,53,43 chr1 809319 . C T 623.84 PASS AC=1;AF=0.5;AN=2;DP=1524;set=variant14-filterInvariant15-filterInvariant18-filterInvariant21-filterInvariant23-filterInvariant27-filterInvariant37 GT:AD:DP:GQ:PL:SB 0/1:173,24:197:81:81,0,4584:77,96,7,17 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 1/1:0,16:16:48:582,48,0:0,0,14,2 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 1/1:0,14:14:41:542,41,0:0,0,0,14 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 1/1:0,38:38:99:1122,114,0:0,0,24,14 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 1/1:0,13:13:39:584,39,0:0,0,0,13 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 1/1:0,40:40:99:1290,120,0:0,0,13,27 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 0/1:25,25:50:99:932,0,3326:9,16,11,14 chr1 876499 . A G 1882.55 PASS AC=1;AF=0.955;AN=2;DP=2368;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:22,25:47:99:606,0,521:13,9,15,10 chr1 877715 . C G 143.34 PASS AC=1;AF=0.932;AN=2;DP=898;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:247,0,353:6,6,5,5 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 1/1:0,29:29:87:1082,87,0:0,0,14,15 chr1 879676 . G A 1408.37 PASS AC=1;AF=0.943;AN=2;DP=1667;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:15,17:32:99:545,0,525:0,15,3,14 chr1 879687 . T C 1236.05 PASS AC=1;AF=0.955;AN=2;DP=1367;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:11,14:25:99:448,0,326:1,10,3,11 chr1 880238 . A G 3393.3 PASS AC=1;AF=0.955;AN=2;DP=4666;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:40,63:103:99:1447,0,949:19,21,32,31 chr1 881627 . G A 2994.94 PASS AC=1;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 0/1:46,67:113:99:1769,0,1105:28,18,43,24 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 1/1:0,114:114:99:3320,341,0:0,0,57,57 chr1 884091 . C G,CACCCTGGTCCCCCTGGTCCCTTTGGCCCTGCACCTGGCTGG 5001.48 PASS AC=0,1;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 0/2:117:99:17,40,19,41 chr1 886788 . G A 2211.72 PASS AC=1;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 0/1:42,18:60:99:484,0,1125:14,28,5,13 chr1 886817 . C T,CATTTT 2829.07 PASS AC=1,0;AF=0.852,0.102;AN=2;DP=2251;MQ=60;set=Intersection GT:DP:GQ:SB 0/1:51:99:12,25,5,9 chr1 886827 . G A 298.35 PASS AC=1;AF=0.5;AN=2;DP=41;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.167;QD=7.28;ReadPosRankSum=0.805;SOR=0.563;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:31,10:41:99:327,0,1717:9,22,3,7 chr1 887560 . A C 1452.03 PASS AC=1;AF=0.955;AN=2;DP=6243;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:54,59:113:99:1478,0,1318:23,31,33,26 chr1 887801 . A G 4434.03 PASS AC=1;AF=0.966;AN=2;DP=8622;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:72,96:168:99:2713,0,1652:38,34,55,41 chr1 888639 . T C 4516.36 PASS AC=1;AF=0.966;AN=2;DP=12259;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:158,134:292:99:3215,0,3784:71,87,70,64 chr1 888659 . T C 4816.6 PASS AC=1;AF=0.966;AN=2;DP=12310;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:153,136:289:99:3309,0,3634:66,87,67,69 chr1 889158 . G C 373.04 PASS AC=1;AF=0.955;AN=2;DP=1550;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:599,0,519:10,3,13,2 chr1 889159 . A C 373.04 PASS AC=1;AF=0.955;AN=2;DP=1561;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:14,16:30:99:599,0,519:10,4,13,3 chr1 889238 . G A 648.16 PASS AC=1;AF=0.5;AN=2;DP=220;FractionInformativeReads=1;MQ=60;set=variant23-variant33-variant42 GT:AD:DP:GQ:PL:SB 0/1:33,29:62:99:676,0,862:20,13,17,12 chr1 889638 . G C 595.76 PASS AC=1;AF=0.943;AN=2;DP=1606;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:14,15:29:99:373,0,432:2,12,6,9 chr1 892745 . G A 1918.45 PASS AC=1;AF=0.966;AN=2;DP=3748;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:22,46:68:99:1098,0,524:8,14,20,26 chr1 894573 . G A 2989.22 PASS AC=1;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 0/1:107,109:216:99:2815,0,2553:44,63,40,69 chr1 897325 . G C 2862.26 PASS AC=1;AF=0.92;AN=2;DP=14802;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:154,125:279:99:2826,0,3700:71,83,57,68 chr1 897459 . CA C 1658.48 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=128;FS=325.353;FractionInformativeReads=0.992;MQ=60;MQRankSum=-1.176;QD=12.96;ReadPosRankSum=-0.998;SOR=7.824;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:78,49:127:99:1696,0,3446:2,76,49,0 chr1 897464 . CA C 1639.74 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=125;FS=333.288;FractionInformativeReads=1;MQ=60;MQRankSum=0.383;QD=13.12;ReadPosRankSum=-2.942;SOR=7.784;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:77,48:125:99:1677,0,3715:1,76,48,0 chr1 897470 . A C 1260.65 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=3038;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:89,48:137:99:1650,0,4074:10,79,48,0 chr1 897474 . CAGTCTTTGTCTTTGACT C 1432.45 PASS AC=1;AF=0.5;AN=2;DP=195;FS=183.823;FractionInformativeReads=1;MQ=60;MQRankSum=1.805;QD=7.35;ReadPosRankSum=2.36;SOR=7.742;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:148,47:195:99:1470,0,6594:47,101,47,0 chr1 897494 . CGA C 1370.26 PASS AC=1;AF=0.5;AN=2;DP=200;FS=153.704;FractionInformativeReads=1;MQ=60;MQRankSum=-0.7;QD=6.85;ReadPosRankSum=-6.628;SOR=7.614;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:156,44:200:99:1408,0,6966:58,98,44,0 chr1 897501 . G C 679.01 PASS AC=1;AF=0.5;AN=2;DP=178;FS=50.823;FractionInformativeReads=1;MQ=60;MQRankSum=1.755;QD=3.81;ReadPosRankSum=-4.869;SOR=5.28;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:165,13:178:99:707,0,7010:63,102,13,0 chr1 897564 . T C 2909.93 PASS AC=1;AF=0.932;AN=2;DP=11047;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:114,115:229:99:2926,0,2971:61,53,54,61 chr1 897738 . C T 2735.42 PASS AC=1;AF=0.5;AN=2;DP=1696;MQ=60;set=variant-variant13-variant20-variant23-variant33-variant42 GT:AD:DP:GQ:PL:SB 0/1:105,148:253:99:3816,0,2552:47,58,66,82 chr1 898323 . T C 4219.65 PASS AC=1;AF=0.977;AN=2;DP=5091;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:58,46:104:99:1131,0,1502:28,30,21,25 chr1 898467 . C T 2627.08 PASS AC=1;AF=0.5;AN=2;DP=768;MQ=60;set=variant20-variant23-variant33-variant42 GT:AD:DP:GQ:PL:SB 0/1:93,109:202:99:2564,0,2010:48,45,54,55 chr1 899928 . G C 3748.18 PASS AC=1;AF=0.967;AN=2;DP=2449;set=variant2-variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,24:58:99:818,0,3824:13,21,6,18 chr1 899937 . G T 3318.78 PASS AC=1;AF=0.967;AN=2;DP=2028;FractionInformativeReads=1;set=variant2-variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,19:49:99:683,0,3785:9,21,4,15 chr1 899938 . G C 3284.59 PASS AC=1;AF=0.967;AN=2;DP=1968;FractionInformativeReads=1;set=variant2-variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,19:49:99:686,0,3764:9,21,4,15 chr1 899942 . G A 2961.37 PASS AC=1;AF=0.967;AN=2;DP=2062;FractionInformativeReads=1;set=variant2-variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,33:60:99:670,0,3575:8,19,10,23 chr1 900285 . C T 474.01 PASS AC=1;AF=0.92;AN=2;DP=2618;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:21,12:33:99:421,0,1177:16,5,9,3 chr1 900286 . A G 1388.37 PASS AC=1;AF=0.955;AN=2;DP=2675;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:20,12:32:99:421,0,1177:15,5,9,3 chr1 900717 . CTTAT C 1579.23 PASS AC=1;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 0/1:11,6:17:99:216,0,1055:6,5,2,4 chr1 900730 . G A 310.68 PASS AC=1;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 0/1:11,6:17:99:219,0,996:7,4,2,4 chr1 900972 . T G 2315.01 PASS AC=1;AF=0.955;AN=2;DP=3339;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:18,37:55:99:910,0,394:7,11,17,20 chr1 901023 . T C 1702.94 PASS AC=1;AF=0.943;AN=2;DP=2741;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:16,33:49:99:883,0,361:6,10,13,20 chr1 906272 . A C 1484.62 PASS AC=1;AF=0.5;AN=2;DP=918;MQ=60;set=variant8-variant23-variant25-variant31-variant36-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:68,49:117:99:1132,0,1411:29,39,20,29 chr1 909419 . C T 2026.38 PASS AC=1;AF=0.6;AN=2;DP=491;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant10-variant22-variant23-variant24-variant28-variant30-variant33-variant36 GT:AD:DP:GQ:PL:SB 0/1:31,22:53:99:507,0,695:15,16,10,12 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 1/1:2,181:183:99:5315,511,0:1,1,76,105 chr1 910394 . C T 2195.44 PASS AC=1;AF=0.615;AN=2;DP=2163;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant15-variant19-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,40:74:99:1491,0,1237:14,20,18,22 chr1 910409 . T C 721.47 PASS AC=1;AF=0.5;AN=2;DP=947;MQ=60;set=variant-variant3-variant6-variant10-variant18-variant23-variant24-variant25-variant28-variant30-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:31,40:71:99:1445,0,1175:13,18,18,22 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 1/1:0,51:51:99:1696,153,0:0,0,19,32 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 1/1:0,60:60:99:1934,180,0:0,0,31,29 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 1/1:0,150:150:99:4612,449,0:0,0,71,79 chr1 912049 . T C 213.23 PASS AC=1;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 0/1:12,18:30:99:521,0,288:3,9,5,13 chr1 912103 . G A 121.67 PASS AC=2;AF=0.81;AN=2;DP=145;FS=0;FractionInformativeReads=1;set=variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant14-variant17-variant21-variant23-variant24-variant26-variant28-variant29-variant32-variant34-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,0,3 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 1/1:0,34:34:99:1100,102,0:0,0,20,14 chr1 914333 . C G 1672.94 PASS AC=1;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 0/1:55,59:114:99:1525,0,1266:34,21,34,25 chr1 914852 . G C 2797.3 PASS AC=1;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 0/1:89,78:167:99:1875,0,2270:47,42,41,37 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 1/1:0,196:196:99:7057,589,0:0,0,101,95 chr1 914940 . T C 3310.69 PASS AC=1;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 0/1:124,126:250:99:2876,0,2786:62,62,63,63 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 1/1:0,132:132:99:4357,396,0:0,0,71,61 chr1 916549 . A G 815.56 PASS AC=1;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 0/1:39,45:84:99:1166,0,891:20,19,18,27 chr1 916590 . G A 964.77 PASS AC=1;AF=0.55;AN=2;DP=750;MQ=60;set=variant-variant5-variant10-variant18-variant22-variant23-variant24-variant28-variant30-variant33 GT:AD:DP:GQ:PL:SB 0/1:34,27:61:99:688,0,910:14,20,11,16 chr1 917640 . G A 365.81 PASS AC=1;AF=0.536;AN=2;DP=604;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant10-variant18-variant22-variant23-variant24-variant25-variant28-variant30-variant33-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,16:42:99:338,0,652:10,16,6,10 chr1 935459 . A G 693.98 PASS AC=1;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 0/1:40,18:58:99:480,0,917:19,21,13,5 chr1 935492 . G T 799.7 PASS AC=1;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 0/1:42,21:63:99:465,0,1030:21,21,13,8 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 1/1:0,14:14:42:393,42,0:0,0,9,5 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 1/1:0,101:101:99:4612,313,0:0,0,60,41 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 1/1:0,120:120:99:5097,361,0:0,0,70,50 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 1/1:0,144:144:99:4312,431,0:0,0,77,67 chr1 949608 . G A 2587.39 PASS AC=2;AF=0.648;AN=2;DP=8690;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant13-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,270:270:99:8292,807,0:0,0,135,135 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 1/1:0,264:264:99:8215,789,0:0,0,131,133 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 1/1:0,39:39:99:1286,117,0:0,0,14,25 chr1 955597 . G T 235.36 PASS AC=2;AF=0.659;AN=2;DP=775;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant18-variant19-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant33-variant34-variant36-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1029,116,0:0,0,21,18 chr1 957898 . G T 199.44 PASS AC=2;AF=0.667;AN=2;DP=806;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant13-variant18-variant19-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant33-variant34-variant36-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1589,135,0:0,0,11,34 chr1 970561 . GGT G 62.28 PASS AC=1;AF=0.5;AN=2;DP=20;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant23 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:71:71,0,187:2,0,2,0 chr1 970573 . T G 33.26 PASS AC=1;AF=0.5;AN=2;DP=11;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.354;QD=3.02;ReadPosRankSum=0.118;SOR=0.132;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:9,2:11:61:61,0,342:7,2,1,1 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 1/1:0,23:23:67:666,67,0:0,0,17,6 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 1/1:0,96:96:99:2980,288,0:0,0,60,36 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 1/1:0,62:62:99:2003,185,0:0,0,20,42 chr1 978603 . CCT C 1953.61 PASS AC=1;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 0/1:69,77:146:99:3016,0,2776:45,24,49,28 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 1/1:0,21:21:63:672,63,0:0,0,14,7 chr1 980948 . C T 3717.87 PASS AC=1;AF=0.5;AN=2;DP=1030;MQ=60;set=variant23-variant29-variant39 GT:AD:DP:GQ:PL:SB 0/1:165,146:311:99:3746,0,4329:83,82,66,80 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 1/1:0,341:341:99:10527,1021,0:0,0,173,168 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 1/1:0,126:126:99:4247,377,0:0,0,63,63 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 1/1:0,255:255:99:7847,763,0:0,0,129,126 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 1/1:0,220:220:99:6806,658,0:0,0,99,121 chr1 984147 . CAAAAAAAAAAA C,CAAAAAAAAAA,CAAAAAA 457.58 PASS AC=1,0,0;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 0/1:8:99:2,1,3,2 chr1 984171 . CAG C 496.56 PASS AC=1;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 0/1:8,5:13:99:186,0,677:5,3,3,2 chr1 984302 . T C 572.85 PASS AC=1;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 0/1:12,11:23:99:224,0,267:7,5,5,6 chr1 985266 . C T 1809.38 PASS AC=1;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 0/1:119,91:210:99:2043,0,2934:62,57,47,44 chr1 985443 . AG A 455.27 PASS AC=1;AF=0.7;AN=2;DP=725;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-filterInvariant15-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant30-variant33-variant34-variant36-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,5:16:99:181,0,421:4,7,2,3 chr1 985446 . G T 777.49 PASS AC=1;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 0/1:8,11:19:99:345,0,261:3,5,5,6 chr1 985449 . G A 473.22 PASS AC=1;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 0/1:8,11:19:99:342,0,288:4,4,5,6 chr1 985450 . G A 463.86 PASS AC=1;AF=0.694;AN=2;DP=620;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-filterInvariant15-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant30-variant33-variant34-variant36-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,7:19:99:208,0,418:5,7,4,3 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 1/1:0,108:108:99:3398,323,0:0,0,53,55 chr1 986541 . T G 189.54 PASS AC=1;AF=0.5;AN=2;DP=62;FS=53.462;FractionInformativeReads=1;MQ=60;MQRankSum=-0.311;QD=3.06;ReadPosRankSum=-3.943;SOR=5.279;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:49,13:62:99:218,0,1911:34,15,0,13 chr1 986549 . T G 227.18 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=133;FractionInformativeReads=1;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:43,14:57:99:255,0,1773:33,10,0,14 chr1 986554 . C G 233.2 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=127;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:40,15:55:99:261,0,1689:31,9,0,15 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 1/1:0,123:123:99:4180,369,0:0,0,67,56 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 1/1:0,69:69:99:2102,207,0:0,0,29,40 chr1 990280 . C T 868.79 PASS AC=1;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 0/1:28,27:55:99:695,0,711:14,14,13,14 chr1 990380 . C T 393.14 PASS AC=1;AF=0.583;AN=2;DP=1808;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant13-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,29:58:99:829,0,749:12,17,15,14 chr1 990417 . T C 939.82 PASS AC=1;AF=0.597;AN=2;DP=2479;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,39:72:99:1115,0,895:18,15,26,13 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 1/1:0,123:123:99:3553,368,0:0,0,63,60 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 1/1:0,80:80:99:2301,238,0:0,0,40,40 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 1/1:0,80:80:99:2445,239,0:0,0,37,43 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 1/1:0,136:136:99:4196,408,0:0,0,65,71 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 1/1:0,59:59:99:2111,177,0:0,0,43,16 chr1 1007222 . G T 1165.39 PASS AC=1;AF=0.583;AN=2;DP=1269;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant19-variant20-variant21-variant23-variant24-variant27-variant29-variant34-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:36,44:80:99:1113,0,1044:28,8,28,16 chr1 1007432 . G A 2492.6 PASS AC=1;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 0/1:89,105:194:99:2570,0,3223:42,47,56,49 chr1 1007448 . G T 2154.04 PASS AC=1;AF=0.5;AN=2;DP=199;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.512;QD=10.82;ReadPosRankSum=-2.249;SOR=0.719;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:109,90:199:99:2182,0,4181:55,54,46,44 chr1 1017170 . C G 247.35 PASS AC=1;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 0/1:17,15:32:99:376,0,421:11,6,9,6 chr1 1017197 . C T 440.11 PASS AC=1;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 0/1:21,21:42:99:488,0,582:14,7,12,9 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 1/1:0,90:90:99:2638,269,0:0,0,45,45 chr1 1017587 . C T 382.69 PASS AC=1;AF=0.583;AN=2;DP=1115;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant19-variant20-variant21-variant23-variant24-variant27-variant29-variant34-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:26,34:60:99:929,0,650:12,14,12,22 chr1 1018144 . T C 3254.98 PASS AC=1;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 0/1:101,132:233:99:3136,0,2178:47,54,68,64 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 1/1:0,54:54:99:2157,165,0:0,0,32,22 chr1 1019180 . T C 703.91 PASS AC=1;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 0/1:30,27:57:99:731,0,797:18,12,16,11 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 1/1:0,19:19:56:658,56,0:0,0,16,3 chr1 1021346 . A G 1387.07 PASS AC=1;AF=0.565;AN=2;DP=3691;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant13-variant14-variant19-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant34-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:65,69:134:99:1534,0,1370:27,38,35,34 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 1/1:0,49:49:99:1675,147,0:0,0,15,34 chr1 1023145 . G A 394.12 PASS AC=1;AF=0.594;AN=2;DP=899;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant10-variant14-variant19-variant21-variant23-variant27-variant29-variant34-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:25,29:54:99:767,0,705:6,19,9,20 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 0/1:32,68:100:99:1664,0,702:21,11,38,30 chr1 1026801 . T A 2434.16 PASS AC=2;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 1/1:0,163:163:99:4755,487,0:0,0,82,81 chr1 1027310 . AAG A 6224.88 PASS AC=1;AF=0.75;AN=2;DP=256;MQ=60;MQRankSum=-0.994;ReadPosRankSum=0.759;set=variant6-variant23 GT:AD:DP:GQ:PL:SB 0/1:55,60:115:99:2324,0,2027:32,23,37,23 chr1 1109104 . G T 166.66 PASS AC=1;AF=0.5;AN=2;DP=51;FractionInformativeReads=1;MQ=60;set=variant10-variant15-variant18-variant23 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:66:66,0,123:3,1,1,1 chr1 1109195 . A G 510.74 PASS AC=1;AF=0.5;AN=2;DP=207;FractionInformativeReads=1;MQ=60;set=variant10-variant15-variant18-variant20-variant23 GT:AD:DP:GQ:PL:SB 0/1:22,12:34:99:277,0,547:15,7,8,4 chr1 1109252 . A G 1162.79 PASS AC=1;AF=0.563;AN=2;DP=1257;MQ=60;set=variant-variant2-variant7-variant8-variant10-variant11-variant13-variant15-variant18-variant19-variant20-variant23-variant26-variant27-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:44,32:76:99:713,0,1032:24,20,19,13 chr1 1109311 . G A 1611.8 PASS AC=1;AF=0.5;AN=2;DP=348;MQ=60;set=variant10-variant15-variant18-variant20-variant23 GT:AD:DP:GQ:PL:SB 0/1:40,37:77:99:1401,0,1547:18,22,17,20 chr1 1109315 . C G 1672.18 PASS AC=1;AF=0.5;AN=2;DP=346;MQ=60;set=variant10-variant15-variant18-variant20-variant23 GT:AD:DP:GQ:PL:SB 0/1:40,36:76:99:1370,0,1550:18,22,16,20 chr1 1109376 . G A 419.42 PASS AC=1;AF=0.5;AN=2;DP=223;MQ=60;set=variant10-variant15-variant18-variant20-variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:21,17:38:99:450,0,641:7,14,7,10 chr1 1109653 . G A 400.04 PASS AC=1;AF=0.5;AN=2;DP=170;FractionInformativeReads=1;MQ=60;set=variant10-variant15-variant18-variant20-variant23 GT:AD:DP:GQ:PL:SB 0/1:11,16:27:99:412,0,325:8,3,11,5 chr1 1109903 . C T 167.84 PASS AC=1;AF=0.5;AN=2;DP=101;FractionInformativeReads=1;MQ=60;set=variant10-variant15-variant18-variant20-variant23 GT:AD:DP:GQ:PL:SB 0/1:15,7:22:99:160,0,412:5,10,2,5 chr1 1110987 . T TC 2335.57 PASS AC=1;AF=0.5;AN=2;DP=581;MQ=60;set=variant10-variant15-variant18-variant20-variant23 GT:AD:DP:GQ:PL:SB 0/1:47,76:123:99:1863,0,2500:26,21,41,35 chr1 1110991 . G C 2341.58 PASS AC=1;AF=0.5;AN=2;DP=580;MQ=60;set=variant10-variant15-variant18-variant20-variant23 GT:AD:DP:GQ:PL:SB 0/1:47,77:124:99:1863,0,2500:26,21,41,36 chr1 1111212 . G GAGAGGCTGCCGCTGTGCCGGTGGAGAGGCTGCCGCCGTGCAGGTGGAA 1330.96 PASS AC=1;AF=0.5;AN=2;DP=417;set=variant15-variant18-variant20-variant23 GT:AD:DP:GQ:PL:SB 0/1:20,37:57:99:1751,0,592:7,13,15,22 chr1 1111423 . G GGA 48.65 PASS AC=1;AF=0.5;AN=2;DP=162;set=filterInvariant18-variant23 GT:AD:DP:GQ:PL:SB 0/1:43,9:52:99:188,0,1769:19,24,7,2 chr1 1111444 . G C 430.21 PASS AC=1;AF=0.5;AN=2;DP=167;FractionInformativeReads=1;set=variant18-variant23 GT:AD:DP:GQ:PL:SB 0/1:38,9:47:99:261,0,1636:18,20,7,2 chr1 1111458 . C A 736.17 PASS AC=1;AF=0.5;AN=2;DP=166;set=variant18-variant23 GT:AD:DP:GQ:PL:SB 0/1:33,9:42:99:303,0,1475:16,17,7,2 chr1 1111465 . G A 827.58 PASS AC=1;AF=0.5;AN=2;DP=189;set=variant18-variant23 GT:AD:DP:GQ:PL:SB 0/1:56,10:66:99:297,0,1634:30,26,7,3 chr1 1111469 . G C 867.2 PASS AC=1;AF=0.5;AN=2;DP=195;set=variant18-variant23 GT:AD:DP:GQ:PL:SB 0/1:56,11:67:99:300,0,1592:31,25,8,3 chr1 1114668 . G A 902.88 PASS AC=1;AF=0.5;AN=2;DP=775;FractionInformativeReads=1;MQ=60;set=variant10-variant15-variant18-variant20-variant23 GT:AD:DP:GQ:PL:SB 0/1:87,73:160:99:1570,0,2132:47,40,39,34 chr1 1116311 . A G 148.51 PASS AC=1;AF=0.694;AN=2;DP=127;FS=0;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant11-variant13-variant14-variant15-variant19-variant20-variant23-variant26-variant33-variant34-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:1,6:7:25:211,0,25:0,1,0,6 chr1 1117398 . A G 381.22 PASS AC=1;AF=0.625;AN=2;DP=467;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant20-variant23-variant26-variant27-variant28-variant33-variant34-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:9,5:14:99:142,0,248:2,7,1,4 chr1 1118212 . T C 1032.79 PASS AC=1;AF=0.568;AN=2;DP=2081;MQ=60;set=variant-variant3-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant18-variant20-variant23-variant26-variant27-variant28-variant33-variant34-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:60,29:89:99:690,0,1361:30,30,20,9 chr1 1120307 . G A 495.11 PASS AC=2;AF=0.611;AN=2;DP=1403;set=variant-variant2-variant8-variant9-variant11-variant12-variant15-variant18-variant19-variant20-variant23-variant24-variant26-variant31-variant33-variant34-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2525,240,0:0,0,53,27 chr1 1121014 . G A 828.1 PASS AC=1;AF=0.536;AN=2;DP=932;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant11-variant12-variant19-variant23-variant24-variant26-variant31-variant33-variant34-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,40:75:99:949,0,789:18,17,19,21 chr1 1121341 . C T 97.67 PASS AC=1;AF=0.688;AN=2;DP=45;FractionInformativeReads=1;MQ=60;set=variant9-variant11-variant23-variant26-variant31-variant34-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:30:82,0,30:0,1,1,2 chr1 1132785 . C T 148.59 PASS AC=1;AF=0.538;AN=2;DP=217;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant11-variant12-variant19-variant23-variant24-variant26-variant31-variant33-variant34-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,11:15:85:307,0,85:2,2,5,6 chr1 1132938 . G A 725.11 PASS AC=1;AF=0.538;AN=2;DP=1070;MQ=60;set=variant8-variant9-variant11-variant12-variant19-variant23-variant24-variant26-variant31-variant33-variant34-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:33,25:58:99:476,0,652:17,16,11,14 chr1 1132966 . C A 755.31 PASS AC=1;AF=0.538;AN=2;DP=857;MQ=60;set=variant8-variant9-variant11-variant12-variant19-variant23-variant24-variant26-variant31-variant33-variant34-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,22:49:99:443,0,597:13,14,10,12 chr1 1133077 . A G 337.18 PASS AC=2;AF=0.595;AN=2;DP=1102;MQ=60;set=variant-variant2-variant7-variant8-variant9-variant11-variant12-variant15-variant18-variant19-variant20-variant23-variant24-variant26-variant31-variant33-variant34-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,30:31:47:1065,47,0:1,0,23,7 chr1 1133254 . G A 3608.71 PASS AC=1;AF=0.538;AN=2;DP=2247;MQ=60;set=variant8-variant9-variant11-variant12-variant19-variant23-variant24-variant26-variant31-variant33-variant34-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:66,76:142:99:1754,0,1610:34,32,41,35 chr1 1133273 . T C 2712.9 PASS AC=2;AF=0.6;AN=2;DP=3744;MQ=60;set=variant-variant2-variant7-variant8-variant9-variant11-variant12-variant15-variant18-variant19-variant20-variant23-variant24-variant26-variant31-variant33-variant34-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,146:146:99:5335,438,0:0,0,74,72 chr1 1147243 . A C 1283.02 PASS AC=1;AF=0.5;AN=2;DP=502;MQ=60;set=variant-variant15-variant18-variant20-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:34,30:64:99:842,0,934:14,20,11,19 chr1 1147297 . G A 1414.39 PASS AC=1;AF=0.5;AN=2;DP=540;MQ=60;set=variant-variant15-variant18-variant20-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:28,36:64:99:1089,0,679:15,13,19,17 chr1 1147422 . C T 3190.76 PASS AC=1;AF=0.524;AN=2;DP=4746;MQ=60;set=variant-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant26-variant28-variant31-variant34-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:103,93:196:99:2049,0,2207:56,47,50,43 chr1 1148753 . T C 461.48 PASS AC=1;AF=0.5;AN=2;DP=55;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.499;QD=8.39;ReadPosRankSum=-1.496;SOR=0.713;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:35,20:55:99:490,0,905:19,16,11,9 chr1 1152631 . C A 1998.68 PASS AC=1;AF=0.5;AN=2;DP=1563;MQ=60;set=variant14-variant15-variant16-variant20-variant23-variant27-variant33-variant41 GT:AD:DP:GQ:PL:SB 0/1:111,68:179:99:1386,0,2733:52,59,32,36 chr1 1153113 . G A 3291.63 PASS AC=1;AF=0.556;AN=2;DP=2142;MQ=60;set=variant-variant14-variant15-variant16-variant18-variant20-variant23-variant27-variant33 GT:AD:DP:GQ:PL:SB 0/1:99,123:222:99:2695,0,2133:43,56,53,70 chr1 1156131 . T C 1820.91 PASS AC=1;AF=0.545;AN=2;DP=1509;FractionInformativeReads=1;MQ=60;set=variant7-variant10-variant14-variant15-variant19-variant22-variant23-variant28-variant33-variant34-variant40 GT:AD:DP:GQ:PL:SB 0/1:56,63:119:99:1532,0,1335:23,33,31,32 chr1 1158534 . G GAC 762.4 PASS AC=1;AF=0.5;AN=2;DP=256;set=variant15-variant18-variant20-variant23-variant27-variant33-variant41 GT:AD:DP:GQ:PL:SB 0/1:17,17:34:99:579,0,579:13,4,13,4 chr1 1158562 . AAC A 1230.76 PASS AC=1;AF=0.5;AN=2;DP=410;MQ=60;set=variant15-variant18-variant20-variant23-variant27-variant33-variant41 GT:AD:DP:GQ:PL:SB 0/1:25,21:46:99:776,0,907:17,8,15,6 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 1/1:0,130:130:99:3993,390,0:0,0,76,54 chr1 1159485 . C T 327.04 PASS AC=1;AF=0.5;AN=2;DP=143;FractionInformativeReads=1;MQ=60;set=variant15-variant18-variant20-variant23-variant27-variant33-variant41 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:163,0,340:2,8,1,5 chr1 1163804 . C T 1785.41 PASS AC=1;AF=0.545;AN=2;DP=1667;MQ=60;set=variant8-variant11-variant15-variant16-variant18-variant20-variant23-variant26-variant27-variant33-variant40 GT:AD:DP:GQ:PL:SB 0/1:55,61:116:99:1340,0,1492:36,19,38,23 chr1 1167796 . C T 299.8 PASS AC=1;AF=0.563;AN=2;DP=138;FractionInformativeReads=1;MQ=60;set=variant15-variant16-variant18-variant20-variant23-variant27-variant33-variant41 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:88:88,0,189:3,4,2,2 chr1 1177918 . CT C 4163.26 PASS AC=1;AF=0.5;AN=2;DP=940;MQ=60;set=variant15-variant23-variant27-variant33 GT:AD:DP:GQ:PL:SB 0/1:84,87:171:99:2907,0,2783:54,30,53,34 chr1 1178245 . C T 2858.61 PASS AC=1;AF=0.5;AN=2;DP=826;MQ=60;set=variant15-variant23-variant27-variant33 GT:AD:DP:GQ:PL:SB 0/1:95,96:191:99:2194,0,2406:54,41,55,41 chr1 1178482 . A G 2176.53 PASS AC=1;AF=0.5;AN=2;DP=1262;MQ=60;set=variant15-variant23-variant27-variant31-variant33 GT:AD:DP:GQ:PL:SB 0/1:132,79:211:99:1709,0,3471:47,85,28,51 chr1 1178925 . G A 1956.99 PASS AC=1;AF=0.5;AN=2;DP=662;MQ=60;set=variant15-variant23-variant27-variant33 GT:AD:DP:GQ:PL:SB 0/1:66,68:134:99:1631,0,1532:25,41,27,41 chr1 1179030 . G A 388.24 PASS AC=1;AF=0.5;AN=2;DP=94;FractionInformativeReads=1;MQ=60;set=variant15-variant23-variant27-variant33 GT:AD:DP:GQ:PL:SB 0/1:3,11:14:95:392,0,95:0,3,2,9 chr1 1179309 . G A 812.04 PASS AC=1;AF=0.5;AN=2;DP=276;MQ=60;set=variant15-variant23-variant27-variant33 GT:AD:DP:GQ:PL:SB 0/1:30,42:72:99:915,0,818:22,8,22,20 chr1 1179800 . G A 1535.2 PASS AC=1;AF=0.5;AN=2;DP=539;FractionInformativeReads=1;MQ=60;set=variant15-variant23-variant27-variant33 GT:AD:DP:GQ:PL:SB 0/1:73,49:122:99:1158,0,1852:36,37,25,24 chr1 1179983 . G A 346.54 PASS AC=1;AF=0.5;AN=2;DP=98;FractionInformativeReads=1;MQ=60;set=variant15-variant23-variant27-variant33 GT:AD:DP:GQ:PL:SB 0/1:9,12:21:99:379,0,326:0,9,3,9 chr1 1181751 . T C 230.56 PASS AC=1;AF=0.5;AN=2;DP=74;FS=0;FractionInformativeReads=1;MQ=60;set=variant15-variant23-variant27-variant33-variant41 GT:AD:DP:GQ:PL:SB 0/1:10,3:13:96:96,0,343:7,3,2,1 chr1 1192787 . C A 49.78 PASS AC=2;AF=1;AN=2;DP=3;FS=0;FractionInformativeReads=1;MQ=60;QD=16.59;SOR=2.833;set=variant23 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:78,9,0:0,0,0,3 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 1/1:0,34:34:99:1303,102,0:0,0,5,29 chr1 1223465 . GC G 279.8 PASS AC=1;AF=0.5;AN=2;DP=58;MQ=60;set=variant15-variant23-variant33 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:245,0,319:4,6,2,6 chr1 1225641 . C A 2307.28 PASS AC=1;AF=0.5;AN=2;DP=851;MQ=60;set=variant11-variant15-variant23-variant26-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,64:113:99:1627,0,1198:28,21,36,28 chr1 1226221 . A G 556.27 PASS AC=1;AF=0.5;AN=2;DP=563;MQ=60;set=variant6-variant8-variant11-variant13-variant15-variant23-variant26-variant27-variant28-variant29-variant33-variant34-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:22,20:42:99:605,0,574:11,11,11,9 chr1 1226348 . C G 756.77 PASS AC=1;AF=0.5;AN=2;DP=1171;MQ=60;set=variant8-variant11-variant13-variant14-variant15-variant23-variant24-variant26-variant27-variant28-variant31-variant33-variant34-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:39,29:68:99:844,0,934:20,19,18,11 chr1 1226690 . C T 1232.8 PASS AC=1;AF=0.5;AN=2;DP=277;FractionInformativeReads=1;MQ=60;set=variant15-variant23-variant27-variant33 GT:AD:DP:GQ:PL:SB 0/1:27,28:55:99:653,0,704:15,12,15,13 chr1 1227664 . TTGAG T 115.64 PASS AC=1;AF=0.5;AN=2;DP=131;MQ=60;set=variant14-variant15-variant23-variant24-variant27-variant31-variant33-variant34-variant41 GT:AD:DP:GQ:PL:SB 0/1:9,3:12:99:99,0,487:6,3,1,2 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 1/1:10:29:0,0,5,5 chr1 1229680 . G T 6334.85 PASS AC=2;AF=0.977;AN=2;DP=8725;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,164:164:99:5330,489,0:0,0,75,89 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 1/1:0,8:8:24:261,24,0:0,0,2,6 chr1 1238492 . G A 1180.32 PASS AC=1;AF=0.5;AN=2;DP=395;MQ=60;set=variant15-variant23-variant25-variant27-variant28-variant33 GT:AD:DP:GQ:PL:SB 0/1:27,17:44:99:380,0,749:15,12,11,6 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 1/1:1,91:92:99:3573,230,0:1,0,79,12 chr1 1242707 . A G 1082.04 PASS AC=2;AF=0.886;AN=2;DP=3710;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2436,225,0:0,0,26,49 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 1/1:0,14:14:42:558,42,0:0,0,12,2 chr1 1243929 . G T 139.03 PASS AC=2;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 1/1:0,20:20:66:858,66,0:0,0,14,6 chr1 1243932 . GGA G 153.56 PASS AC=1;AF=0.556;AN=2;DP=188;set=variant3-variant4-variant12-variant17-variant23-variant24-variant32-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,11:16:68:208,0,68:4,1,8,3 chr1 1245368 . G A 1846.94 PASS AC=1;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 0/1:31,31:62:99:782,0,942:7,24,11,20 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 1/1:0,119:119:99:3520,355,0:0,0,69,50 chr1 1247494 . T C 1685.79 PASS AC=1;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 0/1:42,19:61:99:413,0,1273:17,25,10,9 chr1 1247578 . T TGGGGGGGGGG,TGGGGG,TGGGG,TGG,TGGGGGGGGG 263.17 PASS AC=0,1,0,1,0;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 4/2:14:99:1,0,12,1 chr1 1247589 . C G 131.56 PASS AC=1;AF=0.5;AN=2;DP=204;MQ=60;set=variant2-filterInvariant8-variant12-filterInvariant14-variant18-variant19-variant23-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,8:21:99:252,0,425:11,2,6,2 chr1 1249187 . G A 9794.83 PASS AC=1;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 0/1:174,166:340:99:3947,0,4252:82,92,81,85 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 1/1:0,37:37:99:1233,111,0:0,0,25,12 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 1/1:0,137:137:99:6197,418,0:0,0,69,68 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 1/1:0,141:141:99:6289,427,0:0,0,70,71 chr1 1254841 . C G 3017.72 PASS AC=2;AF=0.909;AN=2;DP=6951;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3755,353,0:0,0,50,68 chr1 1257282 . A C 1386.68 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=13223;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:195,76:271:99:689,0,5280:42,153,71,5 chr1 1257286 . A C 934.06 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=12942;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:191,80:271:99:656,0,2887:39,152,72,8 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 1/1:2,14:16:38:431,38,0:0,2,10,4 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 1/1:0,203:203:99:5829,605,0:0,0,119,84 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 1/1:0,184:184:99:5583,549,0:0,0,101,83 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 1/1:0,186:186:99:5622,555,0:0,0,87,99 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 1/1:0,138:138:99:4267,411,0:0,0,71,67 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 1/1:0,176:176:99:5448,528,0:0,0,91,85 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 1/1:0,286:286:99:8404,856,0:0,0,131,155 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 1/1:0,238:238:99:7297,712,0:0,0,135,103 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 1/1:0,50:50:99:1744,150,0:0,0,30,20 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 1/1:0,57:57:99:2025,171,0:0,0,36,21 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 1/1:0,46:46:99:1425,138,0:0,0,21,25 chr1 1271924 . G A 335.55 PASS AC=1;AF=0.5;AN=2;DP=49;FractionInformativeReads=1;MQ=60;set=variant15-variant23 GT:AD:DP:GQ:PL:SB 0/1:9,14:23:99:315,0,217:3,6,5,9 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 1/1:1,136:137:99:4040,399,0:1,0,59,77 chr1 1273278 . A G 827.3 PASS AC=1;AF=0.875;AN=2;DP=1356;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:235,0,318:8,2,9,1 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 0/1:53,13:66:95:95,0,2578:10,43,13,0 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 0/1:56,11:67:70:70,0,2673:12,44,11,0 chr1 1275264 . A ACAGCCGCATGTCCCCCAGCAGCCCCCACAGACCCACCCG,ACAGCCGCATGTCCCCCAGCAGCCCCCGCAGACCCACCCG 1606.88 PASS AC=2,0;AF=0.966,0.017;AN=2;DP=1771;FS=0;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant2-variant36 GT:DP:GQ:SB 1/1:24:61:0,0,1,23 chr1 1276930 . GCA G 1430.05 PASS AC=1;AF=0.5;AN=2;DP=507;MQ=60;set=variant15-variant23-variant25-variant27-variant28-variant33-variant34 GT:AD:DP:GQ:PL:SB 0/1:25,31:56:99:1117,0,838:19,6,19,12 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 1/1:0,102:102:99:4590,307,0:0,0,65,37 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 1/1:0,112:112:99:3619,336,0:0,0,40,72 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 1/1:0,64:64:99:2036,192,0:0,0,18,46 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 1/1:0,72:72:99:2175,213,0:0,0,21,51 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 1/1:0,60:60:99:1811,180,0:0,0,33,27 chr1 1288471 . C T 4023.57 PASS AC=2;AF=0.932;AN=2;DP=5852;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3568,327,0:0,0,68,41 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 1/1:0,163:163:99:5207,488,0:0,0,87,76 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 1/1:0,62:62:99:1959,185,0:0,0,24,38 chr1 1289043 . G C 1084.3 PASS AC=1;AF=0.75;AN=2;DP=178;FractionInformativeReads=1;MQ=60;MQRankSum=-1.65;ReadPosRankSum=-0.875;set=variant23-variant32 GT:AD:DP:GQ:PL:SB 0/1:29,45:74:99:1113,0,700:18,11,21,24 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 1/1:0,125:125:99:5495,376,0:0,0,64,61 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 1/1:0,93:93:99:2741,276,0:0,0,31,62 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 1/1:0,11:11:33:394,33,0:0,0,7,4 chr1 1293764 . G C 3070.36 PASS AC=1;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 0/1:41,52:93:99:1495,0,983:25,16,35,17 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 1/1:0,154:154:99:4896,460,0:0,0,62,92 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 1/1:0,112:112:99:3569,336,0:0,0,61,51 chr1 1297059 . G A 2773.48 PASS AC=1;AF=0.886;AN=2;DP=4188;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:50,57:107:99:1302,0,1918:20,30,27,30 chr1 1297065 . C T 633.82 PASS AC=1;AF=0.5;AN=2;DP=842;MQ=60;set=variant14-variant15-variant23-variant25-variant27-variant28-variant33-variant34-variant42 GT:AD:DP:GQ:PL:SB 0/1:52,50:102:99:1260,0,2057:22,30,20,30 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 1/1:0,25:25:75:1094,75,0:0,0,10,15 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 1/1:0,23:23:72:1059,72,0:0,0,9,14 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 1/1:0,4:4:12:162,12,0:0,0,4,0 chr1 1309885 . A G 1053.84 PASS AC=1;AF=0.5;AN=2;DP=717;FractionInformativeReads=1;MQ=60;set=variant14-variant15-variant23-variant25-variant27-variant28-variant33-variant34-variant41 GT:AD:DP:GQ:PL:SB 0/1:39,29:68:99:685,0,997:20,19,14,15 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 1/1:0,168:168:99:4807,501,0:0,0,92,76 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 1/1:0,153:153:99:4828,458,0:0,0,80,73 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 1/1:0,31:31:93:1102,93,0:0,0,7,24 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 1/1:0,11:11:33:449,33,0:0,0,1,10 chr1 1323078 . A G 1444.77 PASS AC=1;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 0/1:26,25:51:99:729,0,751:11,15,7,18 chr1 1323143 . CCT C 1128.68 PASS AC=1;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 0/1:25,21:46:99:797,0,1030:15,10,9,12 chr1 1323945 . GTC G,GTCTC 536.31 PASS AC=1,0;AF=0.795,0.045;AN=2;DP=2179;MQ=60;set=Intersection GT:DP:GQ:SB 0/1:28:99:9,10,6,3 chr1 1323963 . CTA C 507.58 PASS AC=1;AF=0.5;AN=2;DP=368;MQ=60;set=variant14-variant15-variant19-variant23-variant27-variant6-variant33 GT:AD:DP:GQ:PL:SB 0/1:17,19:36:99:441,0,317:8,9,9,10 chr1 1330726 . A G 893.46 PASS AC=1;AF=0.536;AN=2;DP=578;FractionInformativeReads=1;MQ=60;set=variant8-variant11-variant14-variant15-variant23-variant25-variant26-variant27-variant28-variant33-variant34-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,13:33:99:374,0,552:13,7,10,3 chr1 1333598 . C A 1900.23 PASS AC=1;AF=0.5;AN=2;DP=1038;MQ=60;set=variant15-variant23-variant25-variant27-variant28-variant33-variant34 GT:AD:DP:GQ:PL:SB 0/1:55,75:130:99:1808,0,1247:29,26,42,33 chr1 1335790 . A G 2153.31 PASS AC=1;AF=0.536;AN=2;DP=1968;MQ=60;set=variant8-variant11-variant14-variant15-variant23-variant25-variant26-variant27-variant28-variant33-variant34-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:46,74:120:99:2294,0,1250:25,21,36,38 chr1 1336136 . GGA G 4133.24 PASS AC=1;AF=0.5;AN=2;DP=1330;MQ=60;set=variant15-variant23-variant25-variant27-variant28-variant33-variant34 GT:AD:DP:GQ:PL:SB 0/1:87,87:174:99:3354,0,3504:37,50,43,44 chr1 1337334 . G T 753.66 PASS AC=1;AF=0.5;AN=2;DP=326;MQ=60;set=variant15-variant23-variant25-variant27-variant28-variant33-variant34 GT:AD:DP:GQ:PL:SB 0/1:23,27:50:99:660,0,637:15,8,17,10 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 0/1:101,94:195:99:2200,0,2496:43,58,41,53 chr1 1361555 . T C 774.01 PASS AC=1;AF=0.643;AN=2;DP=509;FractionInformativeReads=1;MQ=60;set=variant14-variant23-variant26-variant32-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:45,39:84:99:852,0,1134:18,27,19,20 chr1 1361633 . G A 884.14 PASS AC=1;AF=0.5;AN=2;DP=389;FractionInformativeReads=1;MQ=60;set=variant15-variant17-variant23-variant27-variant28-variant33-variant34-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,23:41:99:802,0,668:6,12,9,14 chr1 1361641 . C T 471.25 PASS AC=1;AF=0.577;AN=2;DP=559;FractionInformativeReads=1;MQ=60;set=variant14-variant15-variant17-variant23-variant26-variant27-variant28-variant33-variant34-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:19,16:35:99:604,0,698:7,12,7,9 chr1 1374834 . A G 535.53 PASS AC=1;AF=0.536;AN=2;DP=786;MQ=60;set=variant13-variant14-variant15-variant17-variant23-variant26-variant27-variant28-variant33-variant34-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,17:43:99:527,0,617:10,16,5,12 chr1 1375185 . G C 81.24 PASS AC=1;AF=0.5;AN=2;DP=98;FS=0;FractionInformativeReads=1;MQ=60;set=variant15-variant17-variant23-variant27-variant28-variant33-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:190,0,192:3,5,4,4 chr1 1375810 . C G 1548.31 PASS AC=1;AF=0.536;AN=2;DP=1517;FractionInformativeReads=1;MQ=60;set=variant7-variant13-variant14-variant15-variant17-variant23-variant26-variant27-variant28-variant33-variant34-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:44,52:96:99:1271,0,1081:20,24,22,30 chr1 1376214 . C G 983.49 PASS AC=1;AF=0.533;AN=2;DP=966;MQ=60;set=variant7-variant13-variant14-variant15-variant17-variant23-variant26-variant27-variant28-variant33-variant34-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:29,25:54:99:702,0,762:11,18,16,9 chr1 1376567 . A G 1087.51 PASS AC=1;AF=0.538;AN=2;DP=1927;MQ=60;set=variant13-variant14-variant15-variant17-variant23-variant26-variant27-variant28-variant33-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:86,63:149:99:1544,0,1984:39,47,33,30 chr1 1378173 . G A 837.17 PASS AC=1;AF=0.5;AN=2;DP=332;MQ=60;set=variant15-variant17-variant23-variant27-variant28-variant33 GT:AD:DP:GQ:PL:SB 0/1:32,25:57:99:629,0,831:17,15,11,14 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 1/1:0,539:539:99:16139,1615,0:0,0,275,264 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 0/1:16:93:3,5,1,7 chr1 1417474 . T C 671.62 PASS AC=1;AF=0.75;AN=2;DP=156;MQRankSum=0.906;ReadPosRankSum=-1.073;set=variant23-variant32 GT:AD:DP:GQ:PL:SB 0/1:75,29:104:99:700,0,1835:44,31,11,18 chr1 1417696 . C G 195.72 PASS AC=1;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 0/1:55,30:85:99:844,0,1719:28,27,18,12 chr1 1418531 . G A 64.78 PASS AC=2;AF=1;AN=2;DP=176;FS=0;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:161,15,0:0,0,1,4 chr1 1460793 . CTT CT,CTTT,C 116.63 PASS AC=0,1,0;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 0/2:27:99:2,14,4,7 chr1 1469263 . G T 507.88 PASS AC=1;AF=0.5;AN=2;DP=617;FractionInformativeReads=1;set=variant13-variant14-variant15-variant16-variant23-variant26-variant34-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:31,34:65:99:678,0,764:17,14,22,12 chr1 1469546 . G A 786.13 PASS AC=1;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 0/1:86,92:178:99:2546,0,2182:44,42,46,46 chr1 1469787 . C T 1823.9 PASS AC=1;AF=0.5;AN=2;DP=135;FS=0;FractionInformativeReads=1;MQ=57.62;MQRankSum=-3.448;QD=13.51;ReadPosRankSum=-0.825;SOR=0.656;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:67,68:135:99:1852,0,1786:25,42,26,42 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 0/1:47,44:91:99:1125,0,1182:29,18,26,18 chr1 1477578 . G A 823.55 PASS AC=1;AF=0.75;AN=2;DP=150;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.438;ReadPosRankSum=1.688;set=variant23-variant32 GT:AD:DP:GQ:PL:SB 0/1:43,36:79:99:852,0,1035:17,26,15,21 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 0/1:37,31:68:99:705,0,917:18,19,17,14 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 0/1:13,5:18:90:90,0,405:8,5,3,2 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 0/1:23,14:37:99:280,0,668:10,13,5,9 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 0/1:6,7:13:99:276,0,334:5,1,5,2 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 0/1:17,13:30:99:259,0,347:10,7,7,6 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 0/1:78,93:171:99:2292,0,1547:40,38,56,37 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 0/1:34,34:68:99:1297,0,1309:14,20,10,24 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 0/1:10,8:18:99:184,0,348:1,9,3,5 chr1 1534614 . T C 3678.6 PASS AC=1;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 0/1:90,86:176:99:2036,0,2018:47,43,48,38 chr1 1550702 . A G 1419.51 PASS AC=1;AF=0.756;AN=2;DP=1476;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-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,17:27:99:419,0,194:4,6,11,6 chr1 1551249 . C T 755.59 PASS AC=1;AF=0.756;AN=2;DP=759;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-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,6:22:99:155,0,475:10,6,4,2 chr1 1551428 . C T 1666.45 PASS AC=1;AF=0.589;AN=2;DP=1949;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,41:84:99:817,0,1046:19,24,22,19 chr1 1551927 . T C 3368.42 PASS AC=1;AF=0.75;AN=2;DP=4423;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,46:93:99:1125,0,1129:26,21,26,20 chr1 1558792 . T C 2624.05 PASS AC=2;AF=0.966;AN=2;DP=4846;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2607,255,0:0,0,54,31 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 1/1:0,15:15:45:542,45,0:0,0,12,3 chr1 1560100 . G A 2903.84 PASS AC=1;AF=0.603;AN=2;DP=3468;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,53:118:99:1235,0,2495:39,26,32,21 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 0/1:56,64:120:99:1481,0,2057:32,24,39,25 chr1 1562437 . C G 2896.53 PASS AC=1;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 0/1:69,62:131:99:1798,0,2016:22,47,23,39 chr1 1562536 . G A 2477.35 PASS AC=1;AF=0.5;AN=2;DP=1204;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant15-variant23-variant26-variant34-variant40 GT:AD:DP:GQ:PL:SB 0/1:72,69:141:99:1777,0,1938:40,32,40,29 chr1 1563789 . C A 5485.86 PASS AC=1;AF=0.607;AN=2;DP=5365;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:96,98:194:99:2461,0,2315:42,54,48,50 chr1 1564704 . A ACGG 1964.88 PASS AC=1;AF=0.5;AN=2;DP=245;MQ=60;set=variant8-variant23 GT:AD:DP:GQ:PL:SB 0/1:56,49:105:99:1820,0,2392:27,29,24,25 chr1 1564952 . TG T 2995.53 PASS AC=1;AF=0.607;AN=2;DP=3632;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:54,59:113:99:1520,0,1349:31,23,31,28 chr1 1566068 . A G 791.3 PASS AC=2;AF=0.841;AN=2;DP=1734;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:948,81,0:0,0,6,21 chr1 1572939 . T C 1036.73 PASS AC=1;AF=0.542;AN=2;DP=3060;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:68,48:116:99:1450,0,1866:18,50,10,38 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 0/1:31,37:68:99:733,0,637:12,19,16,21 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 0/1:18,24:42:99:584,0,435:4,14,6,18 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 1/1:0,51:51:99:1435,153,0:0,0,37,14 chr1 1575836 . C G 2109.87 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=11550;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:203,117:320:99:1928,0,4390:85,118,62,55 chr1 1580738 . T A 148 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=8719;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:88,81:169:99:1700,0,1828:34,54,25,56 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 1/1:0,8:8:24:298,24,0:0,0,0,8 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 1/1:0,6:6:18:204,18,0:0,0,1,5 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 0/1:84,29:113:99:571,0,2077:48,36,20,9 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 0/1:53,28:81:99:604,0,1351:21,32,10,18 chr1 1582106 . T C 2887.64 PASS AC=2;AF=0.977;AN=2;DP=5193;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,112:112:99:3069,335,0:0,0,65,47 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 0/1:102,96:198:99:2024,0,2155:51,51,47,49 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 1/1:0,16:16:47:508,47,0:0,0,13,3 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 0/1:7,7:14:99:302,0,261:4,3,4,3 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 0/1:7,8:15:99:302,0,261:4,3,4,4 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 0/1:21,34:55:99:797,0,529:16,5,21,13 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 0/1:113,45:158:99:857,0,2530:56,57,27,18 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 0/1:106,66:172:99:1171,0,2386:56,50,31,35 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 1/1:0,18:18:54:714,54,0:0,0,1,17 chr1 1585597 . A G 1221.47 PASS AC=1;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 0/1:48,32:80:99:704,0,1154:27,21,18,14 chr1 1585642 . G T 1183.17 PASS AC=1;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 0/1:54,44:98:99:1006,0,1304:24,30,22,22 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 1/1:0,76:76:99:2523,228,0:0,0,56,20 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 0/1:39,20:59:99:487,0,1129:26,13,14,6 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 0/1:65,29:94:99:465,0,1705:39,26,15,14 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 0/1:78,28:106:99:941,0,3171:44,34,14,14 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 0/1:81,28:109:99:936,0,3357:45,36,14,14 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 0/1:87,29:116:99:921,0,3500:49,38,14,15 chr1 1591401 . A C 137.19 PASS AC=1;AF=0.5;AN=2;DP=238;FractionInformativeReads=1;set=variant-filterInvariant4-variant7-filterInvariant8-filterInvariant13-filterInvariant20-filterInvariant21-filterInvariant23-variant24-filterInvariant29-filterInvariant40-filterInvariant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:111,0,191:7,0,4,1 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 1/1:0,50:50:99:1454,150,0:0,0,28,22 chr1 1596500 . C T 991.36 PASS AC=1;AF=0.523;AN=2;DP=1878;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,34:71:99:897,0,907:20,17,19,15 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 1/1:0,111:111:99:3381,331,0:0,0,53,58 chr1 1597020 . C G 1031.47 PASS AC=1;AF=0.522;AN=2;DP=2295;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,50:93:99:1394,0,992:19,24,23,27 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 0/1:33,5:38:77:77,0,957:25,8,5,0 chr1 1599888 . A G 2767.6 PASS AC=1;AF=0.568;AN=2;DP=5891;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:32,83:115:99:2128,0,432:16,16,50,33 chr1 1599981 . C T 1237.66 PASS AC=1;AF=0.523;AN=2;DP=3062;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:53,43:96:99:1044,0,1552:20,33,14,29 chr1 1601052 . G A 54.21 PASS AC=1;AF=0.6;AN=2;DP=87;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant22-variant23-variant24-variant27-variant28-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:37:78,0,37:1,1,2,0 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 1/1:0,45:45:99:1353,134,0:0,0,27,18 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 1/1:0,197:197:99:5586,589,0:0,0,111,86 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 1/1:0,206:206:99:6143,616,0:0,0,110,96 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 1/1:0,147:147:99:4617,438,0:0,0,70,77 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 1/1:0,298:298:99:9148,891,0:0,0,137,161 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 1/1:0,100:100:99:3074,300,0:0,0,59,41 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 1/1:0,10:10:30:334,30,0:0,0,0,10 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 1/1:0,6:6:18:202,18,0:0,0,0,6 chr1 1639801 . T C 132.2 PASS AC=1;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 0/1:8,5:13:93:93,0,277:2,6,2,3 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 1/1:0,15:15:45:525,45,0:0,0,6,9 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 1/1:0,11:11:33:354,33,0:0,0,2,9 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 1/1:0,6:6:18:270,18,0:0,0,6,0 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 1/1:0,7:7:21:295,21,0:0,0,6,1 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 1/1:1,22:23:24:594,24,0:0,1,8,14 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 1/1:0,12:12:36:394,36,0:0,0,3,9 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 1/1:0,7:7:21:192,21,0:0,0,2,5 chr1 1646574 . T C 136.3 PASS AC=2;AF=1;AN=2;DP=19;FS=0;FractionInformativeReads=1;set=variant7-filterInvariant9-variant14-variant19-variant20-variant23-variant27-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:78,6,0:0,0,1,1 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 1/1:1,4:5:5:83,5,0:1,0,3,1 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 1/1:0,21:21:63:688,63,0:0,0,13,8 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 0/1:23,20:43:99:813,0,1278:21,2,18,2 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 0/1:25,21:46:99:801,0,1525:22,3,19,2 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 0/1:25,21:46:99:801,0,1525:22,3,19,2 chr1 1647729 . C T 1090 PASS AC=1;AF=0.511;AN=2;DP=2995;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:28,21:49:99:822,0,1631:25,3,19,2 chr1 1647730 . A G 1090 PASS AC=1;AF=0.511;AN=2;DP=3071;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:30,22:52:99:822,0,1631:27,3,20,2 chr1 1647745 . G A 1900.84 PASS AC=1;AF=0.511;AN=2;DP=4407;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:39,39:78:99:1553,0,1969:32,7,29,10 chr1 1647753 . C T 2022.4 PASS AC=1;AF=0.511;AN=2;DP=5070;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:44,42:86:99:1590,0,2017:34,10,30,12 chr1 1647778 . C G 2535.07 PASS AC=1;AF=0.511;AN=2;DP=7411;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:72,69:141:99:1816,0,1829:47,25,45,24 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 0/1:107,103:210:99:2436,0,2651:62,45,63,40 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 0/1:161,127:288:99:2867,0,3653:78,83,59,68 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 0/1:144,110:254:99:4145,0,5683:63,81,47,63 chr1 1647968 . C CAT 2494.68 PASS AC=1;AF=0.511;AN=2;DP=5490;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:75,50:125:99:1843,0,2950:25,50,10,40 chr1 1647971 . G A 2343.37 PASS AC=1;AF=0.511;AN=2;DP=4943;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:71,47:118:99:1790,0,2956:23,48,9,38 chr1 1647983 . T A 1606.07 PASS AC=1;AF=0.511;AN=2;DP=3799;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:54,32:86:99:1121,0,2097:15,39,7,25 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 0/1:48,27:75:99:1061,0,1988:14,34,6,21 chr1 1648002 . C T 1117.93 PASS AC=1;AF=0.511;AN=2;DP=2554;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:34,21:55:99:780,0,1074:7,27,3,18 chr1 1648018 . C T 652.33 PASS AC=1;AF=0.511;AN=2;DP=1789;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:24,13:37:99:516,0,649:6,18,0,13 chr1 1648027 . T C 966.69 PASS AC=2;AF=0.955;AN=2;DP=1376;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:970,75,0:0,0,3,22 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 0/1:39,35:74:99:1374,0,1529:23,16,19,16 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 0/1:41,37:78:99:1456,0,1691:25,16,21,16 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 0/1:44,35:79:99:1369,0,1739:27,17,20,15 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 0/1:39,47:86:99:1253,0,1415:20,19,29,18 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 0/1:53,40:93:99:965,0,1400:32,21,22,18 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 0/1:44,57:101:99:1461,0,1025:24,20,32,25 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 0/1:97,14:111:99:111,0,5210:40,57,6,8 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 0/1:51,40:91:99:1526,0,3951:19,32,17,23 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 0/1:50,40:90:99:1526,0,3951:18,32,17,23 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 0/1:42,30:72:99:1133,0,3607:13,29,13,17 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 0/1:41,28:69:99:1052,0,3571:13,28,12,16 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 0/1:30,20:50:99:678,0,1829:9,21,7,13 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 0/1:28,17:45:99:638,0,1801:8,20,4,13 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 1/1:0,114:114:99:3511,341,0:0,0,73,41 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 1/1:0,137:137:99:3923,411,0:0,0,73,64 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 1/1:0,2:2:6:72,6,0:0,0,2,0 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 1/1:0,15:15:45:472,45,0:0,0,11,4 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 1/1:0,22:22:69:1035,69,0:0,0,16,6 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 1/1:0,23:23:72:1045,72,0:0,0,17,6 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 1/1:0,24:24:72:1045,72,0:0,0,17,7 chr1 1657021 . T C 241.7 DRAGENHardSNP AC=2;AF=0.879;AN=2;DP=291;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:250,24,0:0,0,1,7 chr1 1661704 . A G 932.32 PASS AC=1;AF=0.56;AN=2;DP=3458;set=variant2-variant3-variant4-variant5-variant7-filterInvariant9-variant11-variant12-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:123,42:165:99:798,0,3135:73,50,27,15 chr1 1661844 . G C 1130.11 PASS AC=1;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 0/1:161,89:250:99:1743,0,3827:70,91,42,47 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 1/1:0,3:3:9:100,9,0:0,0,3,0 chr1 1663831 . C T 1396.96 PASS AC=1;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 0/1:64,56:120:99:1266,0,2519:39,25,30,26 chr1 1663851 . G C 2528.42 PASS AC=1;AF=0.6;AN=2;DP=3844;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,69:127:99:2459,0,2286:30,28,40,29 chr1 1663861 . G A 2777.97 PASS AC=1;AF=0.6;AN=2;DP=3742;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,60:116:99:2330,0,2126:31,25,33,27 chr1 1663960 . G A 1628.75 PASS AC=1;AF=0.5;AN=2;DP=263;FractionInformativeReads=1;MQ=60;set=variant21-variant23 GT:AD:DP:GQ:PL:SB 0/1:61,52:113:99:1189,0,1496:28,33,25,27 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 1/1:0,92:92:99:2892,275,0:0,0,37,55 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 1/1:0,40:40:99:1286,120,0:0,0,15,25 chr1 1666175 . C T 286.66 PASS AC=1;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 0/1:21,7:28:99:100,0,495:13,8,4,3 chr1 1666251 . G A 939.61 PASS AC=1;AF=0.517;AN=2;DP=2172;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-filterInvariant14-filterInvariant15-variant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,25:50:99:571,0,456:12,13,19,6 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 1/1:0,46:46:99:1425,137,0:0,0,21,25 chr1 1669646 . ACT A 1144.37 PASS AC=1;AF=0.6;AN=2;DP=1443;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,16:34:99:600,0,701:14,4,13,3 chr1 1669734 . G T 2187.53 PASS AC=1;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 0/1:78,87:165:99:2183,0,2983:51,27,60,27 chr1 1669748 . A G 1698.37 PASS AC=1;AF=0.6;AN=2;DP=6161;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:102,82:184:99:1574,0,3673:63,39,52,30 chr1 1669964 . G A 94.16 PASS AC=1;AF=0.604;AN=2;DP=349;FS=0;FractionInformativeReads=1;set=variant2-filterInvariant3-filterInvariant4-variant5-variant7-variant9-variant11-variant12-variant16-variant18-variant19-filterInvariant21-variant23-variant24-variant25-variant26-filterInvariant28-filterInvariant29-filterInvariant30-variant33-filterInvariant37-variant40-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:124,0,238:0,7,0,6 chr1 1670570 . T C 78.15 PASS AC=1;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 0/1:4,3:7:76:76,0,97:2,2,0,3 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 0/1:86,67:153:99:1673,0,2081:50,36,42,25 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 0/1:12,27:39:99:803,0,306:7,5,11,16 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 0/1:26,39:65:99:914,0,646:16,10,21,18 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 0/1:99,72:171:99:2564,0,3915:55,44,40,32 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 0/1:98,99:197:99:1988,0,2450:37,61,44,55 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 1/1:0,15:15:45:555,45,0:0,0,4,11 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 0/1:28,43:71:99:1668,0,5838:16,12,33,10 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 0/1:123,91:214:99:1945,0,2946:70,53,48,43 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 0/1:11,20:31:99:722,0,715:3,8,7,13 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 0/1:9,13:22:99:519,0,654:3,6,3,10 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 0/1:12,9:21:99:262,0,340:11,1,7,2 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 1/1:0,42:42:99:1450,126,0:0,0,24,18 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 1/1:0,7:7:21:315,21,0:0,0,0,7 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 0/1:1,3:4:34:123,0,34:0,1,1,2 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 0/1:19,16:35:99:350,0,465:14,5,9,7 chr1 1690126 . A AAC 124.67 PASS AC=2;AF=0.92;AN=2;DP=685;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:613,42,0:0,0,3,11 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 0/1:11,20:31:99:653,0,322:2,9,2,18 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 0/1:7,5:12:99:148,0,215:3,4,1,4 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 1/1:0,14:14:42:586,42,0:0,0,13,1 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 0/1:5,4:9:80:80,0,82:3,2,2,2 chr1 1710229 . C A 710.23 PASS AC=1;AF=0.5;AN=2;DP=132;FractionInformativeReads=1;MQ=60;set=variant4-variant23-variant40 GT:AD:DP:GQ:PL:SB 0/1:12,26:38:99:608,0,244:6,6,13,13 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 0/1:9,24:33:99:771,0,260:5,4,14,10 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 1/1:0,78:78:99:2530,234,0:0,0,34,44 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 0/1:38,37:75:99:1017,0,889:18,20,20,17 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 0/1:48,51:99:99:1395,0,1275:23,25,23,28 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 0/1:37,53:90:99:1243,0,835:17,20,26,27 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 0/1:65,64:129:99:1589,0,1618:40,25,43,21 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 0/1:59,79:138:99:2085,0,1528:28,31,39,40 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 1/1:0,10:10:30:325,30,0:0,0,4,6 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 0/1:70,43:113:99:1137,0,1913:39,31,23,20 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 0/1:35,25:60:99:585,0,765:20,15,14,11 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 0/1:24:99:6,8,2,8 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 1/1:0,11:11:36:530,36,0:0,0,9,2 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 0/1:58,31:89:99:603,0,1444:28,30,17,14 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 0/1:12,14:26:99:441,0,324:5,7,9,5 chr1 1855450 . A G 93.15 PASS AC=2;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 1/1:0,13:13:39:423,39,0:0,0,3,10 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 0/1:6,7:13:99:154,0,194:2,4,4,3 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 0/1:142,110:252:99:2601,0,3593:61,81,56,54 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 0/1:20,12:32:99:421,0,726:1,19,0,12 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 0/1:32,30:62:99:715,0,860:18,14,17,13 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 0/1:89,76:165:99:1696,0,2110:52,37,42,34 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 0/1:24,22:46:99:617,0,694:6,18,6,16 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 0/1:16,5:21:99:121,0,451:11,5,4,1 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 0/1:21,13:34:99:321,0,586:14,7,7,6 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 0/1:26,13:39:99:303,0,720:17,9,7,6 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 0/1:23,19:42:99:718,0,1349:9,14,9,10 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 0/1:23,18:41:99:718,0,1349:9,14,9,9 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 0/1:58,45:103:99:1704,0,3097:31,27,24,21 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 0/1:58,45:103:99:1704,0,3097:31,27,24,21 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 0/1:16,18:34:99:556,0,434:4,12,4,14 chr1 1886519 . C CGGCTCACACCGGAAGTGAGGCTCACACCGGAAGTGA,CTCACACCGGAAGTGA 691.67 PASS AC=1,0;AF=0.5,0.042;AN=2;DP=865;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant31-variant33-variant36-variant38-variant40 GT:DP:GQ:SB 0/1:38:99:20,3,15,0 chr1 1887019 . A G 1667.8 PASS AC=1;AF=0.768;AN=2;DP=5879;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-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,62:106:99:1613,0,1015:21,23,25,37 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 0/1:55,70:125:99:1827,0,1268:23,32,31,39 chr1 1895177 . C T 914.61 PASS AC=1;AF=0.559;AN=2;DP=1294;MQ=60;set=variant2-variant5-variant8-variant10-variant14-variant15-variant18-variant19-variant22-variant23-variant28-variant34-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:46,36:82:99:864,0,1285:31,15,26,10 chr1 1896440 . G A 942.84 PASS AC=1;AF=0.559;AN=2;DP=2579;MQ=60;set=variant2-variant5-variant8-variant10-variant14-variant15-variant18-variant19-variant22-variant23-variant28-variant34-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:94,51:145:99:1047,0,2286:45,49,23,28 chr1 1896553 . C T 475.21 PASS AC=1;AF=0.559;AN=2;DP=1397;MQ=60;set=variant2-variant5-variant8-variant10-variant14-variant15-variant18-variant19-variant22-variant23-variant28-variant34-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:41,36:77:99:784,0,1177:10,31,14,22 chr1 1897753 . C G 499.21 PASS AC=1;AF=0.559;AN=2;DP=1010;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant8-variant10-variant14-variant15-variant18-variant19-variant22-variant23-variant28-variant34-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:22,36:58:99:941,0,522:15,7,22,14 chr1 1900024 . TG T 801.34 PASS AC=1;AF=0.559;AN=2;DP=863;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant8-variant10-variant14-variant15-variant18-variant19-variant22-variant23-variant28-variant34-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,32:57:99:1117,0,846:15,10,23,9 chr1 1900106 . T TCTC 1502.49 PASS AC=1;AF=0.529;AN=2;DP=2089;MQ=60;set=variant2-variant5-variant8-variant10-variant14-variant15-variant18-variant19-variant22-variant23-variant28-variant34-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:57,43:100:99:1673,0,2225:32,25,24,19 chr1 1900232 . T C 1328.25 PASS AC=1;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 0/1:65,53:118:99:1253,0,1704:31,34,26,27 chr1 1900332 . A G 503.92 PASS AC=1;AF=0.567;AN=2;DP=714;set=variant2-variant5-variant8-variant10-variant14-variant15-variant18-variant19-variant23-variant28-variant34-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:30,15:45:99:468,0,1254:12,18,7,8 chr1 1900339 . A G 506.47 PASS AC=1;AF=0.559;AN=2;DP=729;set=variant2-variant5-variant8-variant10-variant14-variant15-variant18-variant19-variant22-variant23-variant28-variant34-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:29,11:40:99:350,0,1259:11,18,6,5 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 0/1:12,8:20:99:259,0,319:8,4,7,1 chr1 1905790 . A G 348.68 PASS AC=1;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 0/1:6,4:10:99:139,0,155:1,5,0,4 chr1 1918191 . A G 54.14 PASS AC=1;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 0/1:4,5:9:99:104,0,110:3,1,3,2 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 1/1:0,202:202:99:6100,606,0:0,0,119,83 chr1 1957037 . T C 3027.07 PASS AC=1;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 0/1:170,190:360:99:4456,0,3728:83,87,92,98 chr1 1960674 . C T 2018.12 PASS AC=1;AF=0.5;AN=2;DP=2445;MQ=60;set=variant2-variant3-variant5-variant13-variant18-variant20-variant21-variant23-variant30-variant34-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:81,79:160:99:1643,0,1997:34,47,37,42 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 1/1:0,30:30:90:1143,90,0:0,0,26,4 chr1 1961408 . C T 1547.34 PASS AC=1;AF=0.5;AN=2;DP=1466;MQ=60;set=variant2-variant3-variant5-variant13-variant18-variant20-variant21-variant23-variant30-variant34-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:53,65:118:99:1385,0,1162:32,21,36,29 chr1 1981836 . C T 70.68 PASS AC=1;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 0/1:1,2:3:16:75,0,16:0,1,0,2 chr1 1986754 . G T 493.04 PASS AC=1;AF=0.583;AN=2;DP=208;MQ=60;set=variant4-variant12-variant20-variant23-variant28-variant32 GT:AD:DP:GQ:PL:SB 0/1:16,14:30:99:343,0,376:9,7,10,4 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 1/1:0,59:59:99:1900,176,0:0,0,20,39 chr1 2036263 . G A 2418.21 PASS AC=2;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 1/1:1,79:80:99:2074,225,0:0,1,33,46 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 0/1:16,11:27:99:318,0,437:11,5,8,3 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 0/1:24,24:48:99:581,0,709:8,16,9,15 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 0/1:12,12:24:99:468,0,938:1,11,1,11 chr1 2082505 . C T 518.75 PASS AC=1;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 0/1:12,10:22:99:384,0,944:1,11,0,10 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 0/1:37,51:88:99:1217,0,817:16,21,21,30 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 0/1:27,12:39:99:287,0,750:8,19,4,8 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 1/1:0,17:17:51:737,51,0:0,0,0,17 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 1/1:0,3:3:9:128,9,0:0,0,0,3 chr1 2116287 . C T 1456.56 PASS AC=1;AF=0.5;AN=2;DP=85;FS=4.87;FractionInformativeReads=1;MQ=60;MQRankSum=0.058;QD=17.14;ReadPosRankSum=-2.192;SOR=1.35;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:36,49:85:99:1485,0,1012:24,12,38,11 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 0/1:47,78:125:99:1933,0,1173:19,28,32,46 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 1/1:0,25:25:75:772,75,0:0,0,16,9 chr1 2121118 . C T 2926.23 PASS AC=2;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 1/1:0,214:214:99:6005,637,0:0,0,121,93 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 0/1:66,56:122:99:1578,0,1818:34,32,23,33 chr1 2125976 . C A 83.27 PASS AC=1;AF=0.542;AN=2;DP=85;MQ=60;set=variant-variant2-variant6-variant9-variant15-variant16-variant17-variant21-variant23-variant29-variant33-variant40 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:73:150,0,73:2,0,4,0 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 1/1:0,8:8:24:214,24,0:0,0,3,5 chr1 2144788 . A G 4672.92 PASS AC=2;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 1/1:0,144:144:99:4356,432,0:0,0,74,70 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 1/1:0,83:83:99:2318,246,0:0,0,30,53 chr1 2160390 . C G 2356.25 PASS AC=1;AF=0.5;AN=2;DP=1286;MQ=60;set=variant-variant2-variant6-variant17-variant23-variant28-variant33 GT:AD:DP:GQ:PL:SB 0/1:82,102:184:99:2399,0,1977:44,38,58,44 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 0/1:9,6:15:99:205,0,275:6,3,6,0 chr1 2240006 . T C 7534.4 PASS AC=1;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 0/1:113,106:219:99:2455,0,2884:64,49,57,49 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 0/1:61,61:122:99:1394,0,1768:36,25,34,27 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 1/1:0,57:57:99:1807,171,0:0,0,21,36 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 0/1:25,32:57:99:1023,0,659:16,9,14,18 chr1 2304000 . G T 1086.61 PASS AC=1;AF=0.5;AN=2;DP=97;FS=4.071;FractionInformativeReads=1;MQ=60;MQRankSum=-2.456;QD=11.2;ReadPosRankSum=-1.313;SOR=0.379;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:52,45:97:99:1115,0,1542:15,37,17,28 chr1 2322726 . G A 695.67 PASS AC=1;AF=0.55;AN=2;DP=519;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant11-variant23-variant26-variant29-variant32-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,15:42:99:350,0,681:16,11,11,4 chr1 2325544 . A G 880.71 PASS AC=1;AF=0.5;AN=2;DP=55;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.875;QD=16.01;ReadPosRankSum=0.979;SOR=0.77;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:21,34:55:99:909,0,420:9,12,14,20 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 0/1:44,27:71:99:657,0,1213:23,21,16,11 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 0/1:25,28:53:99:696,0,635:10,15,12,16 chr1 2326918 . G A 477.51 PASS AC=1;AF=0.611;AN=2;DP=1307;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant16-variant17-variant18-variant20-variant22-variant23-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:31,12:43:99:278,0,745:14,17,6,6 chr1 2327075 . C T 499.54 PASS AC=1;AF=0.615;AN=2;DP=1307;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant16-variant17-variant18-variant20-variant22-variant23-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:31,10:41:99:189,0,787:16,15,7,3 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 1/1:0,42:42:99:1501,126,0:0,0,9,33 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 0/1:57,66:123:99:1549,0,1414:29,28,33,33 chr1 2336210 . C T 370.84 PASS AC=1;AF=0.611;AN=2;DP=517;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-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,10:15:99:243,0,129:4,1,6,4 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 0/1:24,19:43:99:549,0,729:13,11,9,10 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 0/1:76,69:145:99:1530,0,1789:39,37,39,30 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 1/1:0,209:209:99:6314,625,0:0,0,108,101 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 0/1:15,13:28:99:466,0,1461:7,8,7,6 chr1 2399119 . A G 2255.79 PASS AC=1;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 0/1:80,65:145:99:2373,0,3342:37,43,28,37 chr1 2399149 . A G 2060.83 PASS AC=1;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 0/1:67,57:124:99:2226,0,3065:31,36,24,33 chr1 2409892 . A G 1373.09 PASS AC=2;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 1/1:0,119:119:99:3722,356,0:0,0,69,50 chr1 2410789 . C T 1165.85 PASS AC=2;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 1/1:0,70:70:99:2130,208,0:0,0,34,36 chr1 2411451 . A G 2087.81 PASS AC=2;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 1/1:0,114:114:99:3692,342,0:0,0,44,70 chr1 2418935 . C T 294.88 PASS AC=2;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 1/1:0,21:21:63:849,63,0:0,0,15,6 chr1 2420590 . T C 652.97 PASS AC=2;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 1/1:0,57:57:99:1803,170,0:0,0,40,17 chr1 2420913 . A G 74.46 PASS AC=2;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 1/1:0,28:28:84:1054,84,0:0,0,4,24 chr1 2422614 . G A 772.2 PASS AC=2;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 1/1:0,71:71:99:2071,211,0:0,0,44,27 chr1 2426766 . A G 211.39 PASS AC=2;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 1/1:0,21:21:63:703,63,0:0,0,14,7 chr1 2428874 . T C 439.37 PASS AC=2;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 1/1:0,59:59:99:1719,172,0:0,0,45,14 chr1 2430617 . C T 2186.62 PASS AC=2;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 1/1:0,245:245:99:6917,732,0:0,0,121,124 chr1 2433456 . C T 965.87 PASS AC=1;AF=0.5;AN=2;DP=72;FS=2.098;FractionInformativeReads=1;MQ=60;MQRankSum=-2.138;QD=13.41;ReadPosRankSum=-1.308;SOR=1.008;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:31,41:72:99:994,0,765:20,11,29,12 chr1 2433900 . C T 1513.56 PASS AC=2;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 1/1:0,118:118:99:3519,350,0:0,0,64,54 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 0/1:42,26:68:99:474,0,678:4,38,20,6 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 0/1:49,16:65:99:225,0,2501:4,45,16,0 chr1 2435356 . CACAGACA C 154.74 PASS AC=1;AF=0.5;AN=2;DP=2064;MQ=60;set=filterInvariant-variant2-variant4-filterInvariant5-variant7-variant9-variant10-variant11-variant12-filterInvariant15-variant16-variant18-variant19-variant21-variant22-variant23-variant25-filterInvariant28-variant30-variant34-variant41-filterInvariant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,15:68:99:210,0,2604:6,47,15,0 chr1 2444414 . G A 1373.04 PASS AC=2;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 1/1:0,122:122:99:3582,364,0:0,0,68,54 chr1 2452569 . T C 950.93 PASS AC=2;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 1/1:0,32:32:96:1016,96,0:0,0,19,13 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 1/1:0,18:18:54:698,54,0:0,0,15,3 chr1 2522392 . G A 2647.81 PASS AC=2;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 1/1:0,173:173:99:5293,518,0:0,0,82,91 chr1 2527678 . A G 509.75 PASS AC=2;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 1/1:0,35:35:99:1225,105,0:0,0,8,27 chr1 2528133 . T C 5016.85 PASS AC=2;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 1/1:0,196:196:99:5674,587,0:0,0,86,110 chr1 2530341 . A AG 811.16 PASS AC=2;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 1/1:0,17:17:51:636,51,0:0,0,2,15 chr1 2535566 . A C 280 PASS AC=1;AF=0.5;AN=2;DP=780;MQ=60;set=variant4-filterInvariant8-filterInvariant9-filterInvariant10-variant11-variant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-variant22-filterInvariant23-variant31-filterInvariant33-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,9:36:74:74,0,641:8,19,8,1 chr1 2560735 . A G 839.58 PASS AC=2;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 1/1:0,53:53:99:1683,159,0:0,0,37,16 chr1 2560882 . G A 2668.7 PASS AC=2;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 1/1:0,84:84:99:3505,257,0:0,0,40,44 chr1 2560903 . T G 2517.21 PASS AC=2;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 1/1:0,81:81:99:3386,243,0:0,0,36,45 chr1 2564183 . T C 1038.18 PASS AC=2;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 1/1:0,45:45:99:1570,135,0:0,0,29,16 chr1 2564465 . T C 1819.09 PASS AC=2;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 1/1:0,31:31:93:1137,93,0:0,0,11,20 chr1 2573199 . A G 3678.94 PASS AC=2;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 1/1:0,101:101:99:2990,300,0:0,0,49,52 chr1 2700117 . C G 1445.55 PASS AC=2;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 1/1:0,37:37:99:1367,111,0:0,0,30,7 chr1 2704471 . C T 401.14 PASS AC=2;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 1/1:0,7:7:21:304,21,0:0,0,1,6 chr1 2718025 . C T 219.45 PASS AC=1;AF=0.5;AN=2;DP=147;FractionInformativeReads=1;MQ=60;set=variant9-variant14-variant23-variant40 GT:AD:DP:GQ:PL:SB 0/1:21,22:43:99:673,0,609:15,6,19,3 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 0/1:56,72:128:99:1682,0,1347:25,31,35,37 chr1 2980878 . A C 327.99 PASS AC=1;AF=0.5;AN=2;DP=48;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.531;QD=6.83;ReadPosRankSum=-1.207;SOR=0.807;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:31,17:48:99:356,0,828:12,19,6,11 chr1 2983963 . G A 6949.55 PASS AC=2;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 1/1:1,193:194:99:5174,566,0:0,1,98,95 chr1 3310898 . G A 216.91 PASS AC=1;AF=0.5;AN=2;DP=19;FS=1.871;FractionInformativeReads=1;MQ=60;MQRankSum=1.184;QD=11.42;ReadPosRankSum=0.776;SOR=1.329;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:245,0,186:5,4,7,3 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 1/1:0,21:21:63:929,63,0:0,0,12,9 chr1 3311212 . C G 801.47 PASS AC=1;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 0/1:17,18:35:99:351,0,365:8,9,7,11 chr1 3311261 . C T 433.73 PASS AC=1;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 0/1:10,9:19:99:210,0,282:1,9,2,7 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 0/1:61,50:111:99:1176,0,1492:30,31,23,27 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 0/1:132,104:236:99:2489,0,3186:70,62,52,52 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 1/1:0,60:60:99:1836,180,0:0,0,36,24 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 1/1:0,155:155:99:5240,464,0:0,0,105,50 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 1/1:0,263:263:99:7885,787,0:0,0,111,152 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 1/1:0,184:184:99:5740,550,0:0,0,73,111 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 1/1:0,115:115:99:4112,345,0:0,0,37,78 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 1/1:55:99:0,1,28,26 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 1/1:0,58:58:99:2524,178,0:0,0,33,25 chr1 3352872 . A C 2009.51 PASS AC=1;AF=0.619;AN=2;DP=2591;MQ=60;set=variant-variant3-variant6-variant9-variant10-variant12-variant13-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant33-variant34-variant36-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:60,61:121:99:1459,0,1372:30,30,30,31 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 1/1:0,103:103:99:3121,309,0:0,0,45,58 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 1/1:0,76:76:99:2465,228,0:0,0,38,38 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 1/1:0,101:101:99:4341,307,0:0,0,53,48 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 1/1:0,99:99:99:4333,298,0:0,0,56,43 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 0/1:5,5:10:99:154,0,142:1,4,2,3 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 1/1:0,71:71:99:2133,213,0:0,0,38,33 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 1/1:0,122:122:99:3923,366,0:0,0,70,52 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 1/1:0,69:69:99:2329,206,0:0,0,22,47 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 0/1:11,17:28:99:476,0,403:8,3,14,3 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 0/1:19,14:33:99:334,0,733:16,3,10,4 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 1/1:0,100:100:99:2910,298,0:0,0,59,41 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 1/1:1,118:119:99:3383,344,0:0,1,59,59 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 1/1:0,118:118:99:3427,351,0:0,0,47,71 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 1/1:0,67:67:99:2579,201,0:0,0,42,25 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 1/1:0,125:125:99:3849,374,0:0,0,43,82 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 1/1:0,67:67:99:2305,201,0:0,0,16,51 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 1/1:2,280:282:99:8220,808,0:1,1,131,149 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 1/1:0,25:25:75:935,75,0:0,0,4,21 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 1/1:0,99:99:99:4308,298,0:0,0,58,41 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 1/1:0,24:24:72:966,72,0:0,0,2,22 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 1/1:0,135:135:99:4474,404,0:0,0,59,76 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 1/1:0,87:87:99:3815,262,0:0,0,36,51 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 1/1:0,78:78:99:2339,232,0:0,0,34,44 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 1/1:0,43:43:99:1267,129,0:0,0,18,25 chr1 3413426 . A G 611.72 PASS AC=1;AF=0.528;AN=2;DP=592;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant9-variant11-variant13-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant25-variant36-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,17:28:99:621,0,327:2,9,5,12 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 0/1:59,65:124:99:1463,0,1470:25,34,26,39 chr1 3416449 . C A 2846.6 PASS AC=1;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 0/1:43,20:63:99:601,0,1207:16,27,8,12 chr1 3417131 . A G 4143.91 PASS AC=1;AF=0.898;AN=2;DP=7206;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:88,60:148:99:1596,0,2263:45,43,35,25 chr1 3417960 . G A 2286.88 PASS AC=1;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 0/1:46,43:89:99:951,0,1180:18,28,18,25 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 1/1:0,34:34:99:1149,102,0:0,0,10,24 chr1 3418613 . CCG C 709.54 PASS AC=1;AF=0.523;AN=2;DP=699;set=variant-variant4-variant5-variant6-variant7-variant8-variant12-variant15-variant16-variant17-variant23-variant24-variant25-variant29-variant30-variant32-variant33-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,10:25:99:298,0,635:8,7,3,7 chr1 3418615 . G C 184.24 PASS AC=1;AF=0.5;AN=2;DP=26;FS=3.524;FractionInformativeReads=0.923;MQ=57.55;MQRankSum=-0.232;QD=7.09;ReadPosRankSum=-2.723;SOR=0.529;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:11,13:24:99:212,0,359:4,7,7,6 chr1 3418616 . G A 718.55 PASS AC=1;AF=0.5;AN=2;DP=689;set=variant-variant4-variant5-variant6-variant7-variant8-variant12-variant15-variant16-variant17-variant23-variant24-variant25-variant29-variant30-variant32-variant33-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,10:25:99:292,0,699:8,7,3,7 chr1 3418618 . G A 718.55 PASS AC=1;AF=0.5;AN=2;DP=704;set=variant-variant4-variant5-variant6-variant7-variant8-variant12-variant15-variant16-variant17-variant23-variant24-variant25-variant29-variant30-variant32-variant33-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,9:27:99:289,0,761:10,8,2,7 chr1 3418652 . CCCG C 264.41 PASS AC=1;AF=0.5;AN=2;DP=48;FS=0;set=variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:302,0,466:7,6,5,4 chr1 3421586 . C T 791.53 PASS AC=1;AF=0.5;AN=2;DP=401;MQ=60;set=variant6-variant10-variant23-variant25-variant30-variant33-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,31:43:99:904,0,396:10,2,21,10 chr1 3421600 . TCAAGGCAACACCGGTAG T 726.35 PASS AC=1;AF=0.5;AN=2;DP=435;MQ=60;set=variant10-variant13-variant23-variant30-variant33-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,31:51:99:1188,0,744:14,6,21,10 chr1 3421658 . A T 1856.48 PASS AC=1;AF=0.565;AN=2;DP=2247;MQ=60;set=variant3-variant6-variant7-variant8-variant10-variant11-variant13-variant15-variant16-variant19-variant21-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,46:90:99:1237,0,1142:27,17,28,18 chr1 3428160 . T G 1622.18 PASS AC=1;AF=0.565;AN=2;DP=2470;MQ=60;set=variant2-variant3-variant6-variant7-variant10-variant11-variant13-variant16-variant19-variant21-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,49:80:99:1185,0,813:20,11,29,20 chr1 3428424 . G T 555.31 PASS AC=1;AF=0.5;AN=2;DP=657;MQ=60;set=variant2-variant3-variant6-variant7-variant10-variant11-variant16-variant23-variant27-variant28-variant29-variant30-variant33-variant34-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,25:40:99:936,0,1004:4,11,6,19 chr1 3428428 . C T 521.78 PASS AC=1;AF=0.5;AN=2;DP=619;FractionInformativeReads=1;set=variant2-variant3-variant6-variant7-variant10-variant11-variant16-variant23-variant27-variant28-variant29-variant30-variant33-variant34-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,21:35:99:885,0,977:4,10,4,17 chr1 3428608 . G A 1492.52 PASS AC=1;AF=0.5;AN=2;DP=1197;MQ=60;set=variant6-variant10-variant23-variant27-variant30-variant33-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:55,75:130:99:1843,0,1388:34,21,45,30 chr1 3432278 . C G 332.99 PASS AC=1;AF=0.5;AN=2;DP=237;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant10-variant15-variant23-variant27-variant30-variant33-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,12:21:99:389,0,219:4,5,3,9 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 1/1:0,60:60:99:1907,180,0:0,0,37,23 chr1 3440943 . A C 104.17 PASS AC=1;AF=0.5;AN=2;DP=272;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant8-variant10-variant13-variant15-variant23-variant27-variant30-variant33-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,11:24:99:382,0,412:2,11,0,11 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 0/1:13,4:17:88:88,0,382:4,9,1,3 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 1/1:0,34:34:99:1194,102,0:0,0,24,10 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 1/1:0,101:101:99:3110,301,0:0,0,54,47 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 1/1:0,6:6:18:235,18,0:0,0,5,1 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 0/1:17,18:35:99:492,0,454:12,5,13,5 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 0/1:41,54:95:99:1426,0,987:16,25,22,32 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 1/1:0,67:67:99:2186,201,0:0,0,30,37 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 1/1:0,45:45:99:1351,135,0:0,0,15,30 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 0/1:66,76:142:99:1922,0,1625:30,36,35,41 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 0/1:49,96:145:99:3007,0,1279:17,32,39,57 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 1/1:0,71:71:99:3135,217,0:0,0,38,33 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 0/1:16,12:28:99:299,0,396:7,9,3,9 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 0/1:5,3:8:99:111,0,303:4,1,2,1 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 1/1:0,102:102:99:3236,306,0:0,0,42,60 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 0/1:10,9:19:99:261,0,319:2,8,2,7 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 0/1:28,16:44:99:500,0,717:19,9,15,1 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 0/1:29,37:66:99:933,0,604:13,16,15,22 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 0/1:11,12:23:99:406,0,375:1,10,2,10 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 0/1:63,54:117:99:2006,0,2429:25,38,23,31 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 1/1:0,42:42:99:1409,126,0:0,0,13,29 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 0/1:118,102:220:99:2460,0,2780:59,59,58,44 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 1/1:0,260:260:99:7514,776,0:0,0,119,141 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 1/1:0,22:22:64:679,64,0:0,0,7,15 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 1/1:0,12:12:36:531,36,0:0,0,4,8 chr1 3644085 . G A 465.42 PASS AC=1;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 0/1:12,18:30:99:593,0,380:10,2,15,3 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 1/1:0,84:84:99:2643,252,0:0,0,29,55 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 1/1:0,51:51:99:1778,153,0:0,0,12,39 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 1/1:0,12:12:39:560,39,0:0,0,8,4 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 1/1:0,18:18:54:686,54,0:0,0,12,6 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 1/1:0,121:121:99:3750,362,0:0,0,58,63 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 1/1:0,106:106:99:4502,319,0:0,0,48,58 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 1/1:0,95:95:99:4221,295,0:0,0,42,53 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 1/1:0,68:68:99:2201,204,0:0,0,33,35 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 1/1:0,27:27:81:952,81,0:0,0,19,8 chr1 3650317 . C A 377.98 PASS AC=1;AF=0.5;AN=2;DP=76;FractionInformativeReads=1;MQ=60;set=variant10-variant23 GT:AD:DP:GQ:PL:SB 0/1:24,18:42:99:433,0,694:12,12,10,8 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 0/1:20:73:4,4,4,8 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 1/1:0,77:77:99:2253,228,0:0,0,41,36 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 1/1:1,82:83:99:2681,238,0:0,1,43,39 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 1/1:0,94:94:99:3041,282,0:0,0,47,47 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 1/1:0,12:12:36:375,36,0:0,0,4,8 chr1 3659657 . G A 420.91 PASS AC=1;AF=0.568;AN=2;DP=1613;MQ=60;set=variant-variant3-variant7-variant8-variant10-variant12-variant13-variant14-variant18-variant20-variant23-variant25-variant27-variant28-variant29-variant30-variant34-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:41,34:75:99:802,0,1046:26,15,20,14 chr1 3662845 . A G 549.45 PASS AC=1;AF=0.64;AN=2;DP=1797;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant10-variant12-variant13-variant14-variant18-variant20-variant23-variant25-variant27-variant28-variant29-variant30-variant34-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:35,36:71:99:975,0,829:17,18,14,22 chr1 3669201 . A G 1559.32 PASS AC=1;AF=0.64;AN=2;DP=4054;set=variant-variant2-variant3-variant4-variant7-variant8-variant10-variant12-variant13-variant14-variant18-variant20-variant23-variant25-variant27-variant28-variant29-variant30-variant34-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:93,83:176:99:3151,0,4968:46,47,48,35 chr1 3669205 . C G 1610.47 PASS AC=1;AF=0.64;AN=2;DP=4024;set=variant-variant2-variant3-variant4-variant7-variant8-variant10-variant12-variant13-variant14-variant18-variant20-variant23-variant25-variant27-variant28-variant29-variant30-variant34-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:94,81:175:99:3115,0,4993:46,48,46,35 chr1 3672156 . C A 606.88 PASS AC=1;AF=0.605;AN=2;DP=933;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant10-variant12-variant13-variant14-variant18-variant20-variant23-variant25-variant27-variant28-variant30-variant34-variant37-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:28,18:46:99:510,0,924:4,24,4,14 chr1 3673496 . T G 319.16 PASS AC=1;AF=0.619;AN=2;DP=484;MQ=60;set=variant-variant3-variant7-variant10-variant12-variant13-variant14-variant18-variant20-variant23-variant25-variant27-variant28-variant29-variant30-variant34-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:240,0,491:1,12,2,7 chr1 3677933 . T C 675.53 PASS AC=1;AF=0.635;AN=2;DP=2086;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant10-variant12-variant13-variant14-variant18-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:42,39:81:99:894,0,1090:17,25,19,20 chr1 3679139 . T C 787.34 PASS AC=1;AF=0.673;AN=2;DP=1195;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant10-variant12-variant13-variant14-variant18-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,21:39:99:814,0,1010:12,6,10,11 chr1 3679146 . G A 809.06 PASS AC=1;AF=0.639;AN=2;DP=862;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant10-variant12-variant13-variant14-variant18-variant20-variant23-variant25-variant27-variant28-variant30-variant34-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:19,22:41:99:835,0,1007:12,7,10,12 chr1 3679307 . T C 88.49 PASS AC=1;AF=0.656;AN=2;DP=260;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant10-variant12-variant13-variant18-variant20-variant23-variant25-variant27-variant28-variant30-variant34-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:10,7:17:99:183,0,304:2,8,2,5 chr1 3679775 . C T 1403.89 PASS AC=1;AF=0.647;AN=2;DP=1443;MQ=60;set=variant-variant3-variant7-variant10-variant12-variant13-variant18-variant20-variant23-variant25-variant27-variant28-variant30-variant34-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:34,51:85:99:1224,0,835:20,14,27,24 chr1 3686318 . G A 1769.91 PASS AC=1;AF=0.5;AN=2;DP=196;FS=0.542;FractionInformativeReads=1;MQ=60;MQRankSum=1.032;QD=9.03;ReadPosRankSum=-0.113;SOR=0.613;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:117,79:196:99:1798,0,3026:69,48,45,34 chr1 3687889 . C T 865.29 PASS AC=1;AF=0.5;AN=2;DP=60;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.664;QD=14.42;ReadPosRankSum=1.04;SOR=0.727;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:27,33:60:99:894,0,595:17,10,21,12 chr1 3691770 . TGAG T 674.29 PASS AC=1;AF=0.5;AN=2;DP=30;FS=1.527;FractionInformativeReads=1;MQ=60;MQRankSum=0.445;QD=22.48;ReadPosRankSum=-0.826;SOR=0.439;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:12,18:30:99:712,0,595:9,3,12,6 chr1 3692240 . T C 635.35 PASS AC=1;AF=0.655;AN=2;DP=1571;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant30-variant31-variant32-variant33-variant36-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,27:58:99:734,0,713:13,18,11,16 chr1 3696761 . C CAG 333.96 PASS AC=1;AF=0.5;AN=2;DP=21;FS=6.69;FractionInformativeReads=1;MQ=60;MQRankSum=-0.106;QD=15.9;ReadPosRankSum=-0.669;SOR=0.061;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:11,10:21:99:371,0,1424:11,0,8,2 chr1 3696763 . C G 337 PASS AC=1;AF=0.5;AN=2;DP=22;FS=3.882;FractionInformativeReads=1;MQ=60;MQRankSum=-1.402;QD=15.32;ReadPosRankSum=0.534;SOR=0.098;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:365,0,1467:13,0,8,1 chr1 3696770 . T C 904.43 PASS AC=1;AF=0.5;AN=2;DP=383;FractionInformativeReads=1;MQ=60;set=variant7-variant9-variant13-variant15-variant17-variant23-variant24-variant25-variant33-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,10:25:99:371,0,1473:14,1,9,1 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 0/1:49,42:91:99:1138,0,1338:30,19,26,16 chr1 3697486 . C G 84.19 PASS AC=2;AF=0.583;AN=2;DP=50;FractionInformativeReads=1;MQ=60;set=variant7-variant13-variant17-variant23-variant25-variant33 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:181,15,0:0,0,3,2 chr1 3697538 . CA CAA,C 96.2 PASS AC=0,1;AF=0.5,0.063;AN=2;DP=97;MQ=60;set=variant7-variant9-variant13-variant17-variant23-variant25-variant33-variant43 GT:DP:GQ:SB 0/2:15:99:7,2,4,2 chr1 3698017 . G A 757.92 PASS AC=1;AF=0.5;AN=2;DP=419;FractionInformativeReads=1;MQ=60;set=variant7-variant9-variant13-variant15-variant17-variant23-variant24-variant25-variant33-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,22:43:99:596,0,533:11,10,8,14 chr1 3700618 . G A 2056.17 PASS AC=1;AF=0.5;AN=2;DP=145;FS=1.326;FractionInformativeReads=1;MQ=60;MQRankSum=-1.094;QD=14.18;ReadPosRankSum=-0.725;SOR=0.826;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:60,85:145:99:2084,0,1370:32,28,48,37 chr1 3700850 . C G 431.87 PASS AC=1;AF=0.5;AN=2;DP=22;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.668;QD=19.63;ReadPosRankSum=1.402;SOR=0.352;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:9,13:22:99:460,0,333:0,9,1,12 chr1 3701490 . C T 199.63 PASS AC=1;AF=0.5;AN=2;DP=14;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.485;QD=14.26;ReadPosRankSum=1.614;SOR=0.804;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:228,0,296:5,3,4,2 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 0/1:8,6:14:99:228,0,296:5,3,4,2 chr1 3701580 . G C 740.29 PASS AC=1;AF=0.5;AN=2;DP=434;MQ=60;set=variant7-variant9-variant13-variant15-variant23-variant24-variant25-variant33-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,13:36:99:283,0,666:15,8,8,5 chr1 3701663 . T C 1011.44 PASS AC=1;AF=0.5;AN=2;DP=780;MQ=60;set=variant7-variant9-variant13-variant15-variant23-variant24-variant25-variant33-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,27:60:99:586,0,682:17,16,14,13 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 0/1:11,11:22:99:307,0,339:9,2,8,3 chr1 3703903 . C T 754.51 PASS AC=1;AF=0.5;AN=2;DP=66;FS=0.984;FractionInformativeReads=1;MQ=60;MQRankSum=-0.2;QD=11.43;ReadPosRankSum=-2.35;SOR=0.837;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:36,30:66:99:783,0,1017:12,24,9,21 chr1 3712513 . G C 4045.99 PASS AC=1;AF=0.5;AN=2;DP=330;FS=2.385;FractionInformativeReads=0.997;MQ=60;MQRankSum=3.279;QD=12.26;ReadPosRankSum=3.373;SOR=0.56;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:154,175:329:99:4074,0,3775:90,64,96,79 chr1 3713247 . G A 351.31 PASS AC=1;AF=0.5;AN=2;DP=25;FS=1.76;FractionInformativeReads=1;MQ=60;MQRankSum=-1.311;QD=14.05;ReadPosRankSum=1.369;SOR=1.371;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:8,17:25:99:380,0,196:4,4,6,11 chr1 3713269 . A G 280.25 PASS AC=1;AF=0.5;AN=2;DP=17;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.845;QD=16.49;ReadPosRankSum=1.845;SOR=0.418;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:5,12:17:99:308,0,132:1,4,4,8 chr1 3729567 . A C 116.05 PASS AC=1;AF=0.5;AN=2;DP=18;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.288;QD=6.45;ReadPosRankSum=-1.2;SOR=0.693;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:144,0,241:5,5,4,4 chr1 3729796 . T C 342.55 PASS AC=1;AF=0.5;AN=2;DP=19;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=2.65;QD=18.03;ReadPosRankSum=1.15;SOR=0.61;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:4,15:19:83:371,0,83:1,3,5,10 chr1 3729818 . CT CTT,C 53.66 PASS AC=1,0;AF=0.646,0.021;AN=2;DP=413;MQ=60;set=variant2-variant3-variant4-variant6-variant8-variant10-variant12-variant14-variant17-variant20-variant21-variant22-variant23-variant26-variant27-variant30-variant31-variant33-variant34-variant36-variant39-variant40-variant41-variant42 GT:DP:GQ:SB 0/1:9:25:0,2,1,6 chr1 3731020 . G C 554.43 PASS AC=1;AF=0.5;AN=2;DP=45;FS=2.555;FractionInformativeReads=1;MQ=60;MQRankSum=-1.138;QD=12.32;ReadPosRankSum=-0.885;SOR=0.957;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:19,26:45:99:583,0,513:10,9,11,15 chr1 3731617 . G C 701.78 PASS AC=1;AF=0.5;AN=2;DP=66;FS=1.986;FractionInformativeReads=1;MQ=60;MQRankSum=-0.449;QD=10.63;ReadPosRankSum=-0.834;SOR=0.834;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:33,33:66:99:730,0,849:16,17,18,15 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 0/1:39,34:73:99:1151,0,1340:20,19,19,15 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 0/1:60,35:95:99:866,0,1577:35,25,18,17 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 0/1:29,13:42:99:409,0,882:18,11,10,3 chr1 3743186 . C T 1094.91 PASS AC=1;AF=0.5;AN=2;DP=98;FS=0.778;FractionInformativeReads=1;MQ=60;MQRankSum=0.59;QD=11.17;ReadPosRankSum=-0.839;SOR=0.823;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:51,47:98:99:1123,0,1294:31,20,30,17 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 0/1:48,30:78:99:731,0,1196:21,27,11,19 chr1 3743433 . T TG 2718.13 PASS AC=2;AF=0.909;AN=2;DP=2689;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1589,135,0:0,0,14,31 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 0/1:15,19:34:99:492,0,370:9,6,11,8 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 0/1:38,38:76:99:883,0,860:21,17,20,18 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 1/1:0,11:11:33:483,33,0:0,0,11,0 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 0/1:28,19:47:99:692,0,1119:9,19,5,14 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 0/1:18,28:46:99:1097,0,705:5,13,9,19 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 1/1:0,43:43:99:1966,132,0:0,0,14,29 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 0/1:5,9:14:99:282,0,174:5,0,7,2 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 1/1:0,20:20:60:716,60,0:0,0,16,4 chr1 3752868 . CAAAA CAA,CA,C,CAAA 200.71 PASS AC=0,1,0,0;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 0/2:8:99:3,2,3,0 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 0/1:39,31:70:99:874,0,936:16,23,15,16 chr1 3753315 . G C 113.93 PASS AC=1;AF=0.5;AN=2;DP=18;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.774;QD=6.33;ReadPosRankSum=-1.676;SOR=1.179;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:13,5:18:99:142,0,444:2,11,0,5 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 1/1:0,130:130:99:4105,393,0:0,0,53,77 chr1 3756074 . C A 582.25 PASS AC=1;AF=0.5;AN=2;DP=31;FS=1.951;FractionInformativeReads=1;MQ=60;MQRankSum=-0.31;QD=18.78;ReadPosRankSum=-0.723;SOR=1.609;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:11,20:31:99:610,0,277:8,3,17,3 chr1 3756120 . A G 2938.76 PASS AC=2;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 1/1:0,69:69:99:2082,206,0:0,0,46,23 chr1 3756155 . T C 1407.58 PASS AC=1;AF=0.5;AN=2;DP=88;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.03;QD=16;ReadPosRankSum=1.271;SOR=0.685;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:32,56:88:99:1436,0,693:19,13,33,23 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 1/1:0,124:124:99:3655,371,0:0,0,50,74 chr1 3759889 . TA TAA,T,TAAA 95.89 PASS AC=1,0,1;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 1/3:16:99:0,2,5,9 chr1 3759940 . A C 30.74 PASS AC=2;AF=1;AN=2;DP=3;FS=0;FractionInformativeReads=1;MQ=60;QD=10.25;SOR=1.179;set=variant23 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:59,9,0:0,0,1,2 chr1 3761262 . C CAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAA,CAAAAAAAAAAAAA,CAAAAAAAAAAAA,CAAAAAAAAAAA,CAAAAAAAAAAAAAAAA 142.73 PASS AC=2,0,0,0,0,0;AF=0.267,0.133,0.4,0.067,0.067,0.067;AN=2;DP=51;FS=0;set=variant2-variant3-variant4-variant6-variant10-variant14-variant18-variant23-variant25-variant28-variant29-variant31-variant33-variant42-variant43 GT:DP:GQ:SB 1/1:5:30:0,0,5,0 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 1/1:0,12:12:36:355,36,0:0,0,11,1 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 0/1:84,45:129:99:940,0,2204:39,45,23,22 chr1 3761650 . A G 1165.07 PASS AC=2;AF=0.989;AN=2;DP=1621;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1793,171,0:0,0,23,34 chr1 3765055 . C T 573.93 PASS AC=1;AF=0.545;AN=2;DP=218;FS=0;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant19-variant20-variant21-variant23-variant24-variant25-variant29-variant31-variant33-variant36-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:33:123,0,33:1,0,3,0 chr1 3765095 . CA CAAAA,C,CAA,CAAAAAAA,CAAAAAA,CAAAAA,CAAAAAAAAAA 207.8 PASS AC=0,0,1,0,0,0,0;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 0/3:7:11:2,0,3,2 chr1 3765386 . G A 416.66 PASS AC=1;AF=0.5;AN=2;DP=46;FS=2.838;FractionInformativeReads=1;MQ=60;MQRankSum=-0.979;QD=9.06;ReadPosRankSum=-0.956;SOR=1.215;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:29,17:46:99:445,0,793:10,19,4,13 chr1 3765424 . G GT 243.25 PASS AC=1;AF=0.5;AN=2;DP=84;MQ=60;set=variant17-variant23-variant39 GT:AD:DP:GQ:PL:SB 0/1:10,14:24:99:430,0,275:2,8,5,9 chr1 3768815 . C T 328.55 PASS AC=1;AF=0.5;AN=2;DP=35;FS=1.939;FractionInformativeReads=1;MQ=60;MQRankSum=0.017;QD=9.39;ReadPosRankSum=-0.191;SOR=1.179;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:23,12:35:99:357,0,756:19,4,11,1 chr1 3769033 . A T 4280.97 PASS AC=1;AF=0.542;AN=2;DP=2238;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant31-variant33-variant36-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,39:81:99:1470,0,2286:15,27,14,25 chr1 3769034 . A T 4280.97 PASS AC=1;AF=0.542;AN=2;DP=2204;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant31-variant33-variant36-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,37:79:99:1470,0,2286:15,27,13,24 chr1 3773380 . GCCCGCGC G 1007.69 PASS AC=1;AF=0.542;AN=2;DP=463;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant31-variant33-variant36-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:195,0,395:2,3,3,2 chr1 3773546 . A C 1251.05 PASS AC=1;AF=0.542;AN=2;DP=889;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant31-variant33-variant36-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,20:31:99:610,0,239:7,4,12,8 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 0/1:30,17:47:99:400,0,723:17,13,11,6 chr1 3773718 . A G 2671.87 PASS AC=2;AF=0.989;AN=2;DP=4568;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:3237,278,0:0,0,48,44 chr1 3773733 . C A 4705.16 PASS AC=1;AF=0.542;AN=2;DP=2621;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant31-variant33-variant36-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,42:85:99:934,0,1009:23,20,20,22 chr1 3774130 . A G 8615.2 PASS AC=1;AF=0.542;AN=2;DP=4802;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant31-variant33-variant36-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:96,80:176:99:3024,0,4993:48,48,40,40 chr1 3774138 . T C 8733.54 PASS AC=1;AF=0.542;AN=2;DP=4983;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant31-variant33-variant36-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:97,80:177:99:3009,0,5010:50,47,42,38 chr1 3774296 . A G 2248.58 PASS AC=1;AF=0.542;AN=2;DP=1669;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant31-variant33-variant36-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,34:68:99:912,0,968:8,26,10,24 chr1 3774312 . T C 1700.61 PASS AC=1;AF=0.542;AN=2;DP=1229;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant31-variant33-variant36-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,29:54:99:774,0,723:5,20,7,22 chr1 3775226 . G A 2350.44 PASS AC=1;AF=0.5;AN=2;DP=213;FS=3.128;FractionInformativeReads=1;MQ=60;MQRankSum=-1.708;QD=11.03;ReadPosRankSum=3.092;SOR=0.499;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:111,102:213:99:2379,0,2751:68,43,57,45 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 1/1:0,84:84:99:2697,252,0:0,0,29,55 chr1 3775507 . C T 371.5 PASS AC=1;AF=0.5;AN=2;DP=32;FS=0;FractionInformativeReads=0.969;MQ=60;MQRankSum=0.466;QD=11.61;ReadPosRankSum=1.683;SOR=0.556;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:19,12:31:99:400,0,649:3,16,2,10 chr1 3782608 . C T 1645.17 PASS AC=1;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 0/1:24,18:42:99:385,0,600:13,11,11,7 chr1 3786189 . G A 2788.78 PASS AC=2;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 1/1:1,77:78:99:2201,221,0:0,1,49,28 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 1/1:0,5:5:15:181,15,0:0,0,3,2 chr1 3788968 . G A 1284.06 PASS AC=1;AF=0.563;AN=2;DP=766;MQ=60;set=variant-variant4-variant9-variant11-variant14-variant17-variant23-variant26-variant27-variant31-variant32-variant34-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,18:44:99:429,0,537:16,10,13,5 chr1 3789194 . G GCGGCCC 1728.27 PASS AC=2;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 1/1:0,68:68:99:2880,214,0:0,0,23,45 chr1 3789195 . T TGTCCCTGCCGC,TGTCCCTGCCAC 1728.27 PASS AC=2,0;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 1/1:58:99:0,0,19,39 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 1/1:0,191:191:99:5927,572,0:0,0,99,92 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 1/1:0,98:98:99:2966,293,0:0,0,35,63 chr1 3801611 . T C 669.28 PASS AC=1;AF=0.5;AN=2;DP=257;MQ=60;set=variant-variant9-variant14-variant23-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,8:33:99:186,0,603:14,11,6,2 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 1/1:0,79:79:99:2381,237,0:0,0,38,41 chr1 3809299 . T A 1212.43 PASS AC=1;AF=0.5;AN=2;DP=552;FractionInformativeReads=1;MQ=60;set=variant-variant23-variant27-variant34-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:55,33:88:99:792,0,1480:34,21,17,16 chr1 3816892 . TCCCC TCC,TCCC,TC,T,TCCCCC,TTCCCCC,TTCCCCCCCCCCCCCC,TTCCCCCC 1597.52 PASS AC=1,0,0,0,0,0,0,0;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 0/1:44:99:7,20,1,16 chr1 3816893 . C T 67.08 PASS AC=1;AF=0.5;AN=2;DP=463;MQ=60;set=filterInvariant9-variant11-filterInvariant19-variant23-filterInvariant26-variant28 GT:AD:DP:GQ:PL:SB 0/1:19,19:38:99:229,0,461:2,17,6,13 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 0/1:31,13:44:99:125,0,675:7,24,1,12 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 0/1:65,18:83:99:312,0,1634:35,30,9,9 chr1 4772053 . T C 2461.02 PASS AC=2;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 1/1:0,219:219:99:6467,656,0:0,0,99,120 chr1 4772717 . G A 1872.01 PASS AC=2;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 1/1:0,87:87:99:2656,258,0:0,0,29,58 chr1 4842980 . C T 1016.16 PASS AC=1;AF=0.563;AN=2;DP=594;MQ=60;set=variant13-variant17-variant18-variant23-variant29-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,26:54:99:662,0,857:19,9,13,13 chr1 4843283 . AT A 1177.82 PASS AC=1;AF=0.632;AN=2;DP=1323;MQ=60;set=variant2-variant9-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant22-variant23-variant29-variant30-variant33-variant34-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,12:39:99:326,0,878:13,14,5,7 chr1 4843531 . G A 115.27 PASS AC=2;AF=0.921;AN=2;DP=85;FS=0;MQ=60;set=variant3-variant4-variant6-variant7-variant9-variant11-variant15-variant16-variant17-variant22-variant23-variant24-variant25-variant26-variant28-variant33-variant34-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:80,6,0:0,0,0,2 chr1 4847845 . G A 3069.62 PASS AC=1;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 0/1:143,167:310:99:4268,0,3467:63,80,73,94 chr1 5623965 . C T 360.77 PASS AC=2;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 1/1:0,46:46:99:1427,138,0:0,0,24,22 chr1 5716287 . GA G 127.06 PASS AC=2;AF=0.767;AN=2;DP=111;FS=0;MQ=60;set=variant3-variant6-variant9-variant12-variant16-variant23-variant24-variant27-variant29-variant32-variant33-variant36-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:111,9,0:0,0,3,0 chr1 5873771 . A G 121.45 PASS AC=2;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 1/1:0,9:9:27:284,27,0:0,0,5,4 chr1 5924360 . C T 1017.55 PASS AC=1;AF=0.5;AN=2;DP=68;FS=0.98;FractionInformativeReads=1;MQ=60;MQRankSum=-0.233;QD=14.96;ReadPosRankSum=0.902;SOR=0.497;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:26,42:68:99:1046,0,732:17,9,25,17 chr1 5934490 . A G 2104.42 PASS AC=1;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 0/1:84,69:153:99:1634,0,2000:50,34,41,28 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 0/1:20,10:30:99:300,0,600:13,7,6,4 chr1 5935162 . A T 617.04 PASS AC=1;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 0/1:46,31:77:99:803,0,1191:19,27,12,19 chr1 5935222 . T C 527.56 PASS AC=1;AF=0.648;AN=2;DP=1618;MQ=60;set=variant4-variant6-variant7-variant8-variant9-variant14-variant15-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,17:44:99:427,0,785:8,19,6,11 chr1 5937091 . T C 1532.33 PASS AC=2;AF=0.943;AN=2;DP=3168;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2111,204,0:0,0,40,28 chr1 5937168 . G A 1023.47 PASS AC=1;AF=0.617;AN=2;DP=3485;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant31-variant33-variant34-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,63:121:99:1589,0,1377:35,23,38,25 chr1 5937391 . C T 842.69 PASS AC=2;AF=0.845;AN=2;DP=4673;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2637,261,0:0,0,38,49 chr1 5937413 . A C 864.78 PASS AC=1;AF=0.609;AN=2;DP=2792;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant33-variant34-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,44:68:99:1147,0,530:8,16,17,27 chr1 5939544 . T G 1909.86 PASS AC=2;AF=0.845;AN=2;DP=5640;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3415,346,0:0,0,59,57 chr1 5948677 . G A 533.39 PASS AC=2;AF=0.845;AN=2;DP=3461;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:1897,192,0:0,0,31,33 chr1 5964991 . T C 549.75 PASS AC=2;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 1/1:0,58:58:99:2303,174,0:0,0,10,48 chr1 6027167 . C A 563.35 PASS AC=2;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 1/1:0,24:24:71:765,71,0:0,0,14,10 chr1 6027252 . A G 1369.9 PASS AC=2;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 1/1:0,56:56:99:1914,168,0:0,0,39,17 chr1 6029086 . CAA CA,C,CAAA 233.73 PASS AC=2,0,0;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 1/1:37:48:2,1,24,10 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 1/1:1,33:34:97:1189,97,0:1,0,6,27 chr1 6052581 . G A 974.21 PASS AC=1;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 0/1:50,41:91:99:1115,0,1278:26,24,22,19 chr1 6094450 . AG A 652.69 PASS AC=1;AF=0.595;AN=2;DP=1780;MQ=60;set=variant8-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,46:87:99:1457,0,1271:29,12,27,19 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 1/1:0,115:115:99:3705,344,0:0,0,52,63 chr1 6094800 . G A 1844.69 PASS AC=1;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 0/1:19,30:49:99:753,0,407:7,12,10,20 chr1 6100458 . G A 1410.29 PASS AC=1;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 0/1:11,9:20:99:247,0,286:6,5,6,3 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 0/1:24,25:49:99:728,0,765:4,20,5,20 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 0/1:24,14:38:99:322,0,785:6,18,5,9 chr1 6155332 . T C 367.85 PASS AC=1;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 0/1:13,17:30:99:437,0,251:8,5,12,5 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 0/1:61,23:84:99:562,0,1146:20,41,22,1 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 0/1:67,20:87:99:311,0,2998:24,43,20,0 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 0/1:24,27:51:99:818,0,769:20,4,23,4 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 0/1:114,134:248:99:3185,0,2721:58,56,70,64 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 0/1:37,49:86:99:1277,0,807:19,18,27,22 chr1 6158562 . A G 5872.58 PASS AC=1;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 0/1:103,85:188:99:2067,0,2552:54,49,44,41 chr1 6159032 . A G 3269.35 PASS AC=1;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 0/1:47,55:102:99:1333,0,1165:25,22,27,28 chr1 6160563 . A G 4220.84 PASS AC=1;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 0/1:67,55:122:99:1350,0,1917:29,38,28,27 chr1 6160692 . G GC 4464.14 PASS AC=1;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 0/1:56,51:107:99:1989,0,2714:26,30,24,27 chr1 6160698 . A G 4546.86 PASS AC=1;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 0/1:58,53:111:99:2022,0,2711:26,32,25,28 chr1 6160876 . A G 3566.83 PASS AC=1;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 0/1:47,49:96:99:1225,0,1040:25,22,23,26 chr1 6160958 . A G 2786.05 PASS AC=1;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 0/1:33,31:64:99:740,0,926:18,15,13,18 chr1 6161075 . T A 1882.89 PASS AC=1;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 0/1:36,27:63:99:743,0,917:16,20,14,13 chr1 6161100 . T TA 1835.83 PASS AC=1;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 0/1:46,26:72:99:679,0,1292:21,25,14,12 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 0/1:51,35:86:99:936,0,1256:24,27,10,25 chr1 6162583 . G A 2927.62 PASS AC=1;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 0/1:81,53:134:99:1161,0,1998:38,43,21,32 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 0/1:54,38:92:99:1444,0,2785:28,26,23,15 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 0/1:54,39:93:99:1444,0,2797:28,26,23,16 chr1 6163584 . C T 3165.44 PASS AC=1;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 0/1:79,43:122:99:1066,0,1920:40,39,19,24 chr1 6163925 . C T 2031 PASS AC=1;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 0/1:20,22:42:99:681,0,520:13,7,11,11 chr1 6164550 . A AGG 4096.8 PASS AC=1;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 0/1:50,38:88:99:1447,0,1912:25,25,18,20 chr1 6164689 . A C 124.38 PASS AC=1;AF=0.5;AN=2;DP=322;MQ=60;set=variant-variant6-filterInvariant10-filterInvariant19-variant23-variant28-filterInvariant38 GT:AD:DP:GQ:PL:SB 0/1:24,11:35:99:152,0,426:2,22,9,2 chr1 6172344 . G A 1031.28 PASS AC=1;AF=0.5;AN=2;DP=116;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.218;QD=8.89;ReadPosRankSum=1.525;SOR=0.671;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:66,50:116:99:1060,0,1615:30,36,23,27 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 1/1:0,25:25:75:898,75,0:0,0,4,21 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 1/1:0,64:64:99:2397,193,0:0,0,41,23 chr1 6257826 . T C 637.54 PASS AC=1;AF=0.571;AN=2;DP=848;MQ=60;set=variant3-variant6-variant7-variant8-variant14-variant16-variant21-variant23-variant28-variant30-variant34-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,30:52:99:691,0,533:11,11,17,13 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 1/1:0,56:56:99:1617,168,0:0,0,25,31 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 1/1:0,45:45:99:1456,135,0:0,0,23,22 chr1 6269120 . T TGGGGGGGG 70.45 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=38;FS=0;FractionInformativeReads=0.895;MQ=60;MQRankSum=-1.529;QD=1.85;ReadPosRankSum=-1.529;SOR=1.393;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:33,1:34:99:108,0,1486:29,4,0,1 chr1 6269126 . C G 82.17 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=45;FS=52.24;FractionInformativeReads=1;MQ=60;MQRankSum=-0.965;QD=1.83;ReadPosRankSum=-3.369;SOR=4.395;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:37,8:45:99:110,0,1517:32,5,0,8 chr1 6295100 . C G 414.95 PASS AC=1;AF=0.5;AN=2;DP=30;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.561;QD=13.83;ReadPosRankSum=-3.139;SOR=0.602;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:14,16:30:99:443,0,378:4,10,5,11 chr1 6305292 . C A 2193.57 PASS AC=2;AF=0.708;AN=2;DP=2194;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:1752,191,0:0,0,30,34 chr1 6305303 . C A 2287.38 PASS AC=2;AF=0.708;AN=2;DP=2149;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1730,180,0:0,0,26,34 chr1 6307389 . C T 381.21 PASS AC=2;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 1/1:0,24:24:72:726,72,0:0,0,13,11 chr1 6308695 . A G 2045.73 PASS AC=2;AF=0.731;AN=2;DP=2479;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-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2338,204,0:0,0,33,35 chr1 6309319 . C G 1832.33 PASS AC=2;AF=0.736;AN=2;DP=2317;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,58:59:99:1809,131,0:0,1,29,29 chr1 6313938 . C T 3373.14 PASS AC=2;AF=0.75;AN=2;DP=4354;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3473,319,0:0,0,56,51 chr1 6314349 . A G 483.91 PASS AC=2;AF=0.797;AN=2;DP=783;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:693,51,0:0,0,5,12 chr1 6314479 . C T 1344.56 PASS AC=2;AF=0.736;AN=2;DP=2602;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2516,222,0:0,0,55,19 chr1 6314822 . T C 3944.02 PASS AC=2;AF=0.75;AN=2;DP=5555;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,171:171:99:5108,513,0:0,0,75,96 chr1 6410031 . C T 563.03 PASS AC=1;AF=0.5;AN=2;DP=142;FS=0;FractionInformativeReads=1;MQ=60;set=variant18-variant23-variant38 GT:AD:DP:GQ:PL:SB 0/1:24,15:39:99:307,0,621:9,15,5,10 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 1/1:0,23:23:69:920,69,0:0,0,9,14 chr1 6453623 . C T 407.97 PASS AC=1;AF=0.536;AN=2;DP=295;MQ=60;set=variant6-variant8-variant10-variant15-variant17-variant18-variant22-variant23-variant26-variant31-variant36-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,14:30:99:334,0,432:9,7,9,5 chr1 6453710 . T G 142.64 PASS AC=1;AF=0.543;AN=2;DP=902;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant13-variant15-variant17-variant18-variant21-variant22-variant23-variant25-variant26-variant31-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,29:51:99:683,0,485:10,12,15,14 chr1 6453744 . C A 521.09 PASS AC=1;AF=0.536;AN=2;DP=596;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant10-variant15-variant17-variant18-variant22-variant23-variant26-variant31-variant36-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,29:45:99:752,0,336:8,8,14,15 chr1 6476116 . A G 221.14 PASS AC=1;AF=0.545;AN=2;DP=850;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant8-variant9-variant10-variant13-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant36-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,10:32:99:192,0,605:16,6,6,4 chr1 6476286 . T C 1164.99 PASS AC=1;AF=0.55;AN=2;DP=843;MQ=60;set=variant6-variant8-variant15-variant18-variant22-variant23-variant31-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,29:68:99:669,0,1202:23,16,18,11 chr1 6476492 . C G 1510.39 PASS AC=1;AF=0.55;AN=2;DP=1508;MQ=60;set=variant6-variant8-variant15-variant18-variant22-variant23-variant31-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:84,63:147:99:1549,0,2239:36,48,30,33 chr1 6477662 . A T 110.19 PASS AC=1;AF=0.563;AN=2;DP=131;MQ=60;set=variant6-variant15-variant18-variant22-variant23-variant31-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:142,0,241:2,7,1,6 chr1 6479925 . A T 4136.56 PASS AC=1;AF=0.55;AN=2;DP=2799;MQ=60;set=variant6-variant8-variant15-variant18-variant22-variant23-variant31-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:131,152:283:99:5748,0,6451:60,71,81,71 chr1 6479938 . A G 3295.15 PASS AC=1;AF=0.536;AN=2;DP=3861;MQ=60;set=variant4-variant6-variant8-variant15-variant18-variant22-variant23-variant24-variant25-variant31-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:129,150:279:99:5745,0,6326:59,70,76,74 chr1 6484675 . C A 476.78 PASS AC=1;AF=0.55;AN=2;DP=288;FractionInformativeReads=1;set=variant6-variant8-variant15-variant18-variant22-variant23-variant31-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,11:25:99:417,0,551:6,8,5,6 chr1 6484685 . G A 498.51 PASS AC=1;AF=0.55;AN=2;DP=275;FractionInformativeReads=1;set=variant6-variant8-variant15-variant18-variant22-variant23-variant31-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,10:21:99:384,0,525:5,6,5,5 chr1 6484880 . A G 88.7 PASS AC=2;AF=0.595;AN=2;DP=242;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant13-variant15-variant17-variant21-variant22-variant23-variant25-variant28-variant31-variant36-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:99,12,0:0,0,2,2 chr1 6489866 . C T 1023.39 PASS AC=1;AF=0.556;AN=2;DP=513;FractionInformativeReads=1;set=variant6-variant8-variant15-variant22-variant23-variant31-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,33:53:99:937,0,506:15,5,21,12 chr1 6500547 . G A 240.61 PASS AC=1;AF=0.563;AN=2;DP=201;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant15-variant23-variant31-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,16:27:99:494,0,330:2,9,3,13 chr1 6500919 . T C 2027.54 PASS AC=1;AF=0.523;AN=2;DP=3133;set=variant4-variant6-variant7-variant8-variant9-variant10-variant13-variant15-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant31-variant33-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,71:134:99:1798,0,1358:29,34,39,32 chr1 6508122 . G C 1212.45 PASS AC=1;AF=0.5;AN=2;DP=1410;MQ=60;set=variant6-variant8-variant10-variant13-variant15-variant17-variant18-variant23-variant24-variant26-variant31-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,62:119:99:1405,0,1212:26,31,28,34 chr1 6508267 . C G 248.87 PASS AC=1;AF=0.536;AN=2;DP=236;set=variant6-variant8-variant10-variant13-variant15-variant17-variant18-variant23-variant24-variant26-variant31-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,5:18:99:130,0,283:6,7,1,4 chr1 6508625 . A G 2972.62 PASS AC=1;AF=0.5;AN=2;DP=2037;FractionInformativeReads=1;set=variant6-variant8-variant10-variant13-variant15-variant17-variant18-variant23-variant24-variant26-variant31-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,80:150:99:3090,0,3077:40,30,47,33 chr1 6508633 . G T 2994.37 PASS AC=1;AF=0.5;AN=2;DP=2161;FractionInformativeReads=1;set=variant6-variant8-variant10-variant13-variant15-variant17-variant18-variant23-variant24-variant26-variant31-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,83:159:99:3148,0,3191:42,34,47,36 chr1 6508712 . T C 2099.15 PASS AC=1;AF=0.5;AN=2;DP=2826;set=variant6-variant8-variant10-variant13-variant15-variant17-variant18-variant23-variant24-variant26-variant31-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,113:204:99:2634,0,2016:47,44,50,63 chr1 6508872 . C T 417.58 PASS AC=1;AF=0.5;AN=2;DP=672;FractionInformativeReads=1;set=variant6-variant8-variant10-variant13-variant15-variant17-variant18-variant23-variant24-variant26-variant31-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,18:52:99:405,0,933:14,20,7,11 chr1 6511582 . A G 1267.14 PASS AC=1;AF=0.5;AN=2;DP=2133;set=variant-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant34-variant36-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,56:110:99:1600,0,1476:42,12,43,13 chr1 6520024 . C A 517.45 PASS AC=1;AF=0.5;AN=2;DP=457;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant15-variant23-variant24-variant31-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,28:58:99:676,0,708:19,11,19,9 chr1 6521150 . A C 368.56 PASS AC=1;AF=0.5;AN=2;DP=1838;MQ=60;set=variant-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant34-variant36-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,30:57:99:722,0,632:16,11,13,17 chr1 6525347 . A C 112.85 PASS AC=1;AF=0.5;AN=2;DP=273;set=variant6-filterInvariant10-variant12-variant13-variant15-variant19-variant22-variant23-variant25-variant27-variant32-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:311,0,1313:2,10,11,0 chr1 6525356 . T C 184.57 PASS AC=1;AF=0.5;AN=2;DP=148;FractionInformativeReads=1;set=variant12-variant13-variant19-variant23-variant25-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,8:27:99:215,0,1605:9,10,8,0 chr1 6525360 . T C 181.56 PASS AC=1;AF=0.5;AN=2;DP=152;FractionInformativeReads=1;set=variant12-variant13-variant19-variant23-variant25-variant41-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:19,7:26:99:208,0,1607:9,10,7,0 chr1 6525915 . T C 158.4 PASS AC=1;AF=0.5;AN=2;DP=208;MQ=60;set=variant6-variant8-variant15-variant23-variant24-variant31-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,6:25:99:114,0,534:12,7,4,2 chr1 6525953 . G C 787.76 PASS AC=1;AF=0.5;AN=2;DP=49;FS=2.656;FractionInformativeReads=1;MQ=60;MQRankSum=-0.228;QD=16.08;ReadPosRankSum=1.312;SOR=0.382;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:15,34:49:99:816,0,315:10,5,19,15 chr1 6526008 . A G 687.49 PASS AC=1;AF=0.5;AN=2;DP=707;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant10-variant15-variant18-variant23-variant26-variant31-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,39:93:99:755,0,1224:27,27,22,17 chr1 6526183 . G A 924.2 PASS AC=1;AF=0.5;AN=2;DP=500;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant10-variant15-variant18-variant23-variant26-variant31-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,21:32:99:806,0,370:5,6,8,13 chr1 6526202 . CCGTGCTCT C 962.92 PASS AC=1;AF=0.5;AN=2;DP=444;MQ=60;set=variant6-variant8-variant10-variant15-variant18-variant23-variant26-variant31-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,16:28:99:636,0,452:6,6,7,9 chr1 6526240 . GCGCC G 931.33 PASS AC=1;AF=0.5;AN=2;DP=373;MQ=60;set=variant6-variant8-variant10-variant15-variant18-variant23-variant26-variant31-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,13:21:99:522,0,316:4,4,7,6 chr1 6526319 . C T 442.08 PASS AC=1;AF=0.5;AN=2;DP=437;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant15-variant23-variant31-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,19:35:99:495,0,339:10,6,11,8 chr1 6526465 . C G 969.1 PASS AC=1;AF=0.5;AN=2;DP=1136;MQ=60;set=variant6-variant8-variant10-variant15-variant18-variant23-variant26-variant31-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,32:94:99:659,0,1429:30,32,14,18 chr1 6526633 . G A 76.4 PASS AC=1;AF=0.5;AN=2;DP=130;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant10-variant15-variant18-variant23-variant26-variant31-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:70:70,0,205:0,5,1,2 chr1 6527333 . A G 1638.56 PASS AC=1;AF=0.5;AN=2;DP=3184;FractionInformativeReads=1;set=variant-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant18-variant21-variant22-variant23-variant26-variant28-variant31-variant34-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,77:148:99:1881,0,1657:42,29,46,31 chr1 6527745 . C T 1372.37 PASS AC=1;AF=0.5;AN=2;DP=1196;MQ=60;set=variant6-variant8-variant10-variant13-variant15-variant18-variant23-variant26-variant31-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,58:111:99:1379,0,1332:26,27,22,36 chr1 6528589 . C T 1508.09 PASS AC=1;AF=0.5;AN=2;DP=1165;MQ=60;set=variant6-variant8-variant15-variant23-variant31-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,72:154:99:1766,0,2153:36,46,34,38 chr1 6529182 . TTCCTCC TTCC,T 1392.23 PASS AC=1,0;AF=0.438,0.063;AN=2;DP=847;MQ=60;set=variant6-variant8-variant15-variant23-variant24-variant31-variant38-variant44 GT:DP:GQ:SB 0/1:70:99:13,20,16,21 chr1 6529443 . A G 929.12 PASS AC=1;AF=0.5;AN=2;DP=3517;MQ=60;set=variant-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant18-variant21-variant22-variant23-variant26-variant28-variant31-variant34-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,56:143:99:1269,0,2137:41,46,28,28 chr1 6529807 . C T 133.71 PASS AC=1;AF=0.583;AN=2;DP=59;MQ=60;set=variant6-variant8-variant15-variant23-variant31-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:199,0,206:1,3,2,4 chr1 6530435 . A G 1418.24 PASS AC=1;AF=0.5;AN=2;DP=1963;set=variant-variant6-variant7-variant8-variant9-variant11-variant13-variant15-variant21-variant22-variant23-variant28-variant31-variant34-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,55:99:99:1549,0,1205:23,21,25,30 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 1/1:0,111:111:99:3809,343,0:0,0,50,61 chr1 6531589 . C T 2158.61 PASS AC=1;AF=0.5;AN=2;DP=1107;MQ=60;set=variant6-variant8-variant15-variant23-variant31-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,69:137:99:1575,0,1655:32,36,34,35 chr1 6533393 . G C 2077.81 PASS AC=1;AF=0.5;AN=2;DP=1976;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant8-variant9-variant10-variant13-variant15-variant17-variant18-variant21-variant22-variant23-variant26-variant28-variant31-variant34-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,45:92:99:1112,0,1178:22,25,24,21 chr1 6546049 . C T 941.24 PASS AC=1;AF=0.5;AN=2;DP=105;FS=3.857;FractionInformativeReads=1;MQ=60;MQRankSum=-1.789;QD=8.96;ReadPosRankSum=2.888;SOR=1.112;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:63,42:105:99:969,0,1427:25,38,13,29 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 0/1:48,42:90:99:1112,0,1137:22,26,19,23 chr1 6579653 . G C 1041.69 PASS AC=1;AF=0.542;AN=2;DP=1048;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant8-variant14-variant15-variant22-variant23-variant30-variant31-variant32-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:43,44:87:99:1082,0,1147:21,22,20,24 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 0/1:26,35:61:99:867,0,689:14,12,19,16 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 1/1:0,9:9:27:280,27,0:0,0,3,6 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 0/1:3,2:5:64:64,0,79:1,2,0,2 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 0/1:19,21:40:99:535,0,446:10,9,14,7 chr1 6583183 . C T 507.97 PASS AC=1;AF=0.542;AN=2;DP=450;FractionInformativeReads=1;set=variant-variant2-variant8-variant14-variant15-variant22-variant23-variant30-variant31-variant32-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,12:32:99:351,0,713:17,3,10,2 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 0/1:64,38:102:99:1171,0,2190:38,26,24,14 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 0/1:66,28:94:99:496,0,2271:39,27,19,9 chr1 6583270 . C G 2244.38 PASS AC=1;AF=0.542;AN=2;DP=2183;MQ=60;set=variant-variant2-variant8-variant14-variant15-variant22-variant23-variant30-variant31-variant32-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:92,77:169:99:1757,0,2256:51,41,49,28 chr1 6583701 . T C 124.46 PASS AC=1;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 0/1:5,8:13:99:277,0,186:4,1,5,3 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 1/1:0,92:92:99:3239,275,0:0,0,65,27 chr1 6584045 . C G 1773.18 PASS AC=1;AF=0.545;AN=2;DP=972;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant8-variant14-variant15-variant22-variant23-variant30-variant31-variant32-variant41 GT:AD:DP:GQ:PL:SB 0/1:55,54:109:99:1355,0,1657:39,16,33,21 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 0/1:83,110:193:99:2617,0,1964:44,39,63,47 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 1/1:0,133:133:99:5753,400,0:0,0,61,72 chr1 6584420 . C A 1026.38 PASS AC=1;AF=0.542;AN=2;DP=783;MQ=60;set=variant-variant2-variant8-variant14-variant15-variant22-variant23-variant30-variant31-variant32-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,35:71:99:996,0,1030:14,22,16,19 chr1 6584657 . T C 400.2 PASS AC=1;AF=0.542;AN=2;DP=630;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant8-variant14-variant15-variant22-variant23-variant30-variant31-variant32-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:33,29:62:99:759,0,835:15,18,10,19 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 0/1:12,6:18:80:80,0,307:4,8,2,4 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 1/1:0,24:24:72:885,72,0:0,0,19,5 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 0/1:28,28:56:99:712,0,773:14,14,17,11 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 0/1:101,90:191:99:1850,0,2335:56,45,48,42 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 1/1:0,120:120:99:3670,359,0:0,0,50,70 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 0/1:12,8:20:99:208,0,257:8,4,6,2 chr1 6592377 . A G 797.25 PASS AC=1;AF=0.542;AN=2;DP=768;MQ=60;set=variant-variant2-variant8-variant14-variant15-variant22-variant23-variant30-variant31-variant32-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,27:47:99:705,0,463:13,7,14,13 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 0/1:47,35:82:99:822,0,1136:23,24,13,22 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 1/1:8:27:0,0,1,7 chr1 6602241 . C A 74.01 PASS AC=1;AF=0.859;AN=2;DP=321;FS=0;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:159,0,155:1,4,0,5 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 0/1:9,15:24:99:478,0,333:8,1,12,3 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 0/1:16,9:25:99:311,0,645:13,3,8,1 chr1 6609792 . G GT 2295.51 PASS AC=1;AF=0.536;AN=2;DP=1983;MQ=60;set=variant-variant2-variant8-variant11-variant13-variant14-variant15-variant22-variant23-variant30-variant31-variant32-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:79,65:144:99:1981,0,2488:37,42,29,36 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 1/1:1,90:91:99:2780,233,0:1,0,32,58 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 0/1:20,18:38:99:539,0,638:3,17,3,15 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 0/1:13,9:22:99:324,0,319:8,5,9,0 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 0/1:15,15:30:99:429,0,335:9,6,12,3 chr1 6610743 . CT CTT,C,CTTT 41.4 PASS AC=1,0,0;AF=0.477,0.045,0.068;AN=2;DP=346;set=variant4-variant5-variant6-variant9-variant14-variant15-variant16-variant18-variant19-variant20-variant21-filterInvariant23-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant36-variant38-variant43 GT:DP:GQ:SB 0/1:13:70:1,6,1,5 chr1 6614230 . G A 1428.89 PASS AC=1;AF=0.536;AN=2;DP=1135;MQ=60;set=variant-variant2-variant8-variant11-variant13-variant14-variant15-variant22-variant23-variant30-variant31-variant32-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:33,41:74:99:994,0,789:18,15,22,19 chr1 6614391 . A C 3608.65 PASS AC=2;AF=0.977;AN=2;DP=2981;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:2499,172,0:0,0,23,32 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 1/1:0,62:62:99:2672,187,0:0,0,31,31 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 0/1:53,37:90:99:844,0,1164:24,29,17,20 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 0/1:8,11:19:99:244,0,180:2,6,4,7 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 0/1:15,21:36:99:788,0,813:5,10,6,15 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 0/1:15,18:33:99:722,0,819:5,10,5,13 chr1 6631106 . C T 1610.98 PASS AC=1;AF=0.5;AN=2;DP=279;MQ=60;set=variant-variant23 GT:AD:DP:GQ:PL:SB 0/1:86,65:151:99:1661,0,2264:34,52,33,32 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 1/1:0,18:18:53:603,53,0:0,0,3,15 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 1/1:0,174:174:99:5777,522,0:0,0,102,72 chr1 6636461 . C T 1707.18 PASS AC=1;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 0/1:75,75:150:99:1651,0,1977:45,30,41,34 chr1 6637171 . G A 675.39 PASS AC=1;AF=0.536;AN=2;DP=609;MQ=60;set=variant-variant2-variant8-variant14-variant15-variant18-variant22-variant23-variant27-variant30-variant31-variant32-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:28,16:44:99:457,0,719:9,19,4,12 chr1 6639847 . G T 320.52 PASS AC=1;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 0/1:28,21:49:99:536,0,727:13,15,9,12 chr1 6645857 . T G 136.46 PASS AC=1;AF=0.5;AN=2;DP=14;FS=5.88;FractionInformativeReads=1;MQ=60;MQRankSum=-0.8;QD=9.75;ReadPosRankSum=1.467;SOR=2.546;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:9,5:14:99:165,0,244:6,3,5,0 chr1 6646959 . GCCTGCCTTC G 4676.85 PASS AC=1;AF=0.833;AN=2;DP=6782;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-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,69:134:99:2666,0,3406:24,41,25,44 chr1 6649228 . T G 1405.83 PASS AC=1;AF=0.6;AN=2;DP=544;MQ=60;set=variant-variant2-variant23-variant30-variant31 GT:AD:DP:GQ:PL:SB 0/1:52,55:107:99:1697,0,1432:21,31,20,35 chr1 6651450 . CA C 92.32 PASS AC=1;AF=0.63;AN=2;DP=1035;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant10-variant14-variant15-variant16-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,19:35:99:500,0,403:6,10,7,12 chr1 6651728 . C T 583.89 PASS AC=1;AF=0.66;AN=2;DP=1098;MQ=60;set=variant-variant4-variant7-variant9-variant10-variant14-variant15-variant16-variant18-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-filterInvariant34-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,20:36:99:538,0,452:10,6,10,10 chr1 6652718 . G A 556.05 PASS AC=1;AF=0.615;AN=2;DP=1807;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant14-variant15-variant16-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,45:80:99:1174,0,838:14,21,23,22 chr1 6652745 . G A 644.1 PASS AC=1;AF=0.63;AN=2;DP=1819;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant10-variant14-variant15-variant16-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,48:83:99:1287,0,832:15,20,22,26 chr1 6673780 . C G 250.21 PASS AC=1;AF=0.62;AN=2;DP=1037;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant14-variant15-variant16-variant18-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,21:35:99:492,0,364:7,7,8,13 chr1 6679848 . C T 884.41 PASS AC=1;AF=0.62;AN=2;DP=1553;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant14-variant15-variant16-variant18-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,28:62:99:662,0,843:16,18,16,12 chr1 6681375 . C T 1378.1 PASS AC=1;AF=0.62;AN=2;DP=2331;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant14-variant15-variant16-variant18-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,29:72:99:705,0,1141:28,15,20,9 chr1 6681744 . C T 1502.47 PASS AC=1;AF=0.838;AN=2;DP=2635;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,18:40:99:574,0,637:6,16,5,13 chr1 6683565 . GA G 962.27 PASS AC=1;AF=0.838;AN=2;DP=1437;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,16:23:99:382,0,128:2,5,8,8 chr1 6684906 . C G 636.43 PASS AC=1;AF=0.635;AN=2;DP=1506;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant14-variant15-variant16-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,15:40:99:339,0,656:14,11,10,5 chr1 6685442 . A G 679.65 PASS AC=1;AF=0.833;AN=2;DP=741;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:180,0,361:3,8,2,5 chr1 6690140 . A G 923.42 PASS AC=1;AF=0.833;AN=2;DP=796;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-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,17:30:99:485,0,378:11,2,14,3 chr1 6692273 . C CA,CAA 252.53 PASS AC=1,0;AF=0.671,0.013;AN=2;DP=642;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:14:99:7,0,6,1 chr1 6693102 . C T 828.32 PASS AC=1;AF=0.5;AN=2;DP=57;FS=3.908;FractionInformativeReads=1;MQ=60;MQRankSum=0.152;QD=14.53;ReadPosRankSum=3.709;SOR=0.321;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:26,31:57:99:857,0,697:7,19,12,19 chr1 6694327 . C T 1602.07 PASS AC=1;AF=0.5;AN=2;DP=337;FractionInformativeReads=1;MQ=60;set=variant-variant23-variant31 GT:AD:DP:GQ:PL:SB 0/1:59,42:101:99:958,0,1494:31,28,19,23 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 0/1:48,41:89:99:1528,0,2670:24,24,23,18 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 0/1:48,40:88:99:1528,0,2670:24,24,22,18 chr1 6694927 . C T 999 PASS AC=1;AF=0.635;AN=2;DP=2347;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant10-variant14-variant15-variant16-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,41:70:99:1064,0,815:11,18,16,25 chr1 6694980 . G A 2050.71 PASS AC=1;AF=0.813;AN=2;DP=3052;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,35:59:99:827,0,571:11,13,16,19 chr1 6695123 . C T 933.68 PASS AC=1;AF=0.825;AN=2;DP=1672;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,24:40:99:601,0,380:10,6,12,12 chr1 6695244 . A G 775.01 PASS AC=1;AF=0.825;AN=2;DP=1676;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,22:37:99:658,0,433:6,9,12,10 chr1 6695802 . A G 3501.87 PASS AC=1;AF=0.825;AN=2;DP=4032;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,39:80:99:894,0,1041:15,26,16,23 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 1/1:0,146:146:99:4197,438,0:0,0,67,79 chr1 6705874 . G C 2062.55 PASS AC=1;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 0/1:53,66:119:99:1677,0,1251:29,24,41,25 chr1 6713114 . C T 272.91 PASS AC=1;AF=0.635;AN=2;DP=712;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant10-variant14-variant15-variant16-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,13:28:99:326,0,434:4,11,4,9 chr1 6866978 . G A 366.29 PASS AC=1;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 0/1:10,11:21:99:313,0,306:8,2,9,2 chr1 6947717 . C T 929.22 PASS AC=1;AF=0.55;AN=2;DP=810;MQ=60;set=variant5-variant8-variant12-variant15-variant18-variant20-variant23-variant28-variant34-variant36 GT:AD:DP:GQ:PL:SB 0/1:43,35:78:99:865,0,955:23,20,20,15 chr1 6947973 . C T 289.03 PASS AC=1;AF=0.55;AN=2;DP=423;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant12-variant15-variant18-variant20-variant23-variant28-variant34-variant36 GT:AD:DP:GQ:PL:SB 0/1:21,35:56:99:848,0,495:8,13,16,19 chr1 7151479 . T C 1381.15 PASS AC=1;AF=0.571;AN=2;DP=1659;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant10-variant11-variant15-variant16-variant17-variant18-variant23-variant27-variant29-variant31-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:52,53:105:99:1161,0,1279:25,27,26,27 chr1 7166332 . G A 463.72 PASS AC=1;AF=0.531;AN=2;DP=495;MQ=60;set=variant2-variant4-variant6-variant9-variant12-variant17-variant19-variant22-variant23-variant24-variant31-variant34-variant36-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:13,12:25:99:336,0,341:9,4,10,2 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 0/1:48,45:93:99:1089,0,1316:25,23,21,24 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 1/1:5:18:0,0,4,1 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 1/1:0,5:5:15:225,15,0:0,0,5,0 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 1/1:0,6:6:18:260,18,0:0,0,6,0 chr1 7289777 . G A 887.36 PASS AC=1;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 0/1:43,23:66:99:424,0,996:21,22,11,12 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 0/1:58,47:105:99:1125,0,1449:20,38,15,32 chr1 7624855 . G T 472.44 PASS AC=1;AF=0.553;AN=2;DP=587;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant9-variant10-variant12-variant16-variant18-variant21-variant22-variant23-variant25-variant26-variant29-variant30-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,13:34:99:379,0,564:13,8,11,2 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 0/1:100,109:209:99:2756,0,2615:48,52,52,57 chr1 7725284 . C A 667.23 PASS AC=1;AF=0.586;AN=2;DP=1402;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant12-variant13-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant34-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,21:40:99:503,0,531:5,14,8,13 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 0/1:53,51:104:99:1353,0,1358:18,35,15,36 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 0/1:41,55:96:99:1380,0,909:19,22,24,31 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 0/1:15,15:30:99:307,0,318:3,12,4,11 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 0/1:14,16:30:99:327,0,280:10,4,14,2 chr1 7810059 . A AT 74.66 PASS AC=1;AF=0.5;AN=2;DP=16;FS=0;FractionInformativeReads=0.812;MQ=60;MQRankSum=0.696;QD=4.67;ReadPosRankSum=-0.437;SOR=0.765;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:112,0,203:2,6,1,4 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 0/1:34,27:61:99:660,0,855:20,14,16,11 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 0/1:51,45:96:99:1074,0,1273:25,26,21,24 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 0/1:1,2:3:37:81,0,37:1,0,2,0 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 0/1:23,11:34:99:285,0,675:16,7,8,3 chr1 7827743 . CAG C 1814.16 PASS AC=1;AF=0.5;AN=2;DP=488;MQ=60;set=variant10-variant23-variant27-variant30-variant34-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,48:80:99:1826,0,1122:15,17,23,25 chr1 7827963 . T TA,TAA 404.77 PASS AC=1,0;AF=0.526,0.026;AN=2;DP=756;MQ=60;set=variant2-variant5-variant9-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant25-variant27-variant28-variant29-variant32-variant33-variant36-variant42 GT:DP:GQ:SB 0/1:48:99:14,8,16,10 chr1 7828173 . TAAAAA TAAA,TAAAA,T,TAA,TA 988.58 PASS AC=0,1,1,0,0;AF=0.227,0.295,0.193,0.216,0.011;AN=2;DP=3661;set=Intersection GT:DP:GQ:SB 3/2:51:99:3,3,16,29 chr1 7828278 . CA C 1013.14 PASS AC=2;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 1/1:0,43:43:99:1166,128,0:0,0,27,16 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 1/1:0,59:59:99:2104,176,0:0,0,22,37 chr1 7840926 . G C 764.8 PASS AC=1;AF=0.795;AN=2;DP=2170;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:32,21:53:99:637,0,1069:12,20,3,18 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 0/1:9,7:16:99:246,0,318:1,8,2,5 chr1 7844443 . G T 488.23 PASS AC=1;AF=0.526;AN=2;DP=420;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant25-variant27-variant29-variant33-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,7:22:99:223,0,609:8,7,4,3 chr1 7844444 . C A 488.23 PASS AC=1;AF=0.526;AN=2;DP=418;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant25-variant27-variant29-variant33-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,7:22:99:223,0,609:8,7,4,3 chr1 7844469 . G A 304.31 PASS AC=1;AF=0.5;AN=2;DP=144;FractionInformativeReads=1;MQ=60;set=variant10-variant23-variant27-variant30-variant32-variant34 GT:AD:DP:GQ:PL:SB 0/1:7,19:26:99:392,0,259:4,3,9,10 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 0/1:17,12:29:99:310,0,464:12,5,9,3 chr1 7845695 . T C 348.01 PASS AC=2;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 1/1:0,20:20:60:707,60,0:0,0,5,15 chr1 7847362 . C CT 1013.52 PASS AC=2;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 1/1:0,19:19:57:590,57,0:0,0,16,3 chr1 7847529 . A G 882.98 PASS AC=1;AF=0.524;AN=2;DP=2214;set=variant2-variant5-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant25-variant27-variant28-variant29-variant32-variant33-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:62,52:114:99:1091,0,1561:25,37,23,29 chr1 7847614 . G A 442.55 PASS AC=1;AF=0.569;AN=2;DP=1051;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,17:31:99:443,0,474:3,11,5,12 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 0/1:23,25:48:99:981,0,1247:14,9,14,11 chr1 7861158 . T G 844.74 PASS AC=1;AF=0.5;AN=2;DP=252;MQ=60;set=variant10-variant23-variant27-variant30-variant34 GT:AD:DP:GQ:PL:SB 0/1:23,25:48:99:981,0,1247:14,9,14,11 chr1 7861304 . T C 558.95 PASS AC=1;AF=0.597;AN=2;DP=955;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant36-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,15:26:99:420,0,252:4,7,4,11 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 0/1:5,5:10:99:154,0,195:0,5,1,4 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 0/1:17,10:27:99:250,0,477:5,12,3,7 chr1 7869915 . G C 2617.21 PASS AC=2;AF=0.989;AN=2;DP=3567;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2519,246,0:0,0,49,33 chr1 7870048 . T C 4008.62 PASS AC=2;AF=0.966;AN=2;DP=4639;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:2909,290,0:0,0,42,55 chr1 7870144 . A C 2322.83 PASS AC=2;AF=0.989;AN=2;DP=3008;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,60:61:99:1847,173,0:0,1,24,36 chr1 7870418 . C T 191.61 PASS AC=1;AF=0.5;AN=2;DP=67;FractionInformativeReads=1;MQ=60;set=variant10-variant23-variant27-variant30-variant34 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:128,0,160:4,1,4,0 chr1 7879322 . C T 413.57 PASS AC=1;AF=0.5;AN=2;DP=140;FractionInformativeReads=1;MQ=60;set=variant23-variant27-variant34 GT:AD:DP:GQ:PL:SB 0/1:21,17:38:99:442,0,510:11,10,12,5 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 0/1:13,7:20:99:205,0,442:8,5,5,2 chr1 7880712 . G A 957.35 PASS AC=1;AF=0.5;AN=2;DP=187;FractionInformativeReads=1;MQ=60;set=variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:53,42:95:99:986,0,1414:26,27,20,22 chr1 7886424 . G A 124.7 PASS AC=1;AF=0.526;AN=2;DP=315;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant27-variant28-variant29-variant32-variant33-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:197,0,134:4,2,5,3 chr1 7887248 . G A 792 PASS AC=1;AF=0.583;AN=2;DP=3162;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:58,42:100:99:990,0,1368:30,28,23,19 chr1 7887493 . T C 6582.06 PASS AC=2;AF=0.989;AN=2;DP=12069;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,233:233:99:7092,697,0:0,0,123,110 chr1 7887579 . C G 4347.19 PASS AC=1;AF=0.5;AN=2;DP=1537;MQ=60;set=variant10-variant23-variant27-variant30-variant34 GT:AD:DP:GQ:PL:SB 0/1:165,136:301:99:3292,0,3902:83,82,73,63 chr1 7889804 . C G 1071.49 PASS AC=2;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 1/1:0,68:68:99:2331,204,0:0,0,48,20 chr1 7889941 . C T 1946.52 PASS AC=1;AF=0.524;AN=2;DP=5168;set=variant2-variant5-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant25-variant27-variant28-variant29-variant32-variant33-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:131,100:231:99:2377,0,3331:65,66,53,47 chr1 7889972 . GAGAATCCATCCCATCCTACTGCCAGCGCTCTGTCCACAGGATCGCCTCCCATGA G 3477.95 PASS AC=2;AF=0.773;AN=2;DP=5916;set=variant2-variant5-variant6-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant20-variant23-variant25-variant27-variant28-variant29-variant32-variant33-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:4278,350,0:0,0,44,53 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 0/1:126,112:238:99:3286,0,3087:60,66,58,54 chr1 7890264 . A G 766.51 PASS AC=2;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 1/1:0,102:102:99:3415,306,0:0,0,29,73 chr1 7897228 . G A 557.39 PASS AC=1;AF=0.5;AN=2;DP=214;FractionInformativeReads=1;MQ=60;set=variant10-variant23-variant27-variant30-variant34 GT:AD:DP:GQ:PL:SB 0/1:22,21:43:99:524,0,621:6,16,7,14 chr1 7902559 . C CAA,CA 59.28 PASS AC=1,0;AF=0.25,0.25;AN=2;DP=18;MQ=60;set=variant23-variant41 GT:DP:GQ:SB 0/1:5:23:1,0,4,0 chr1 7904247 . C T 11453.9 PASS AC=2;AF=0.989;AN=2;DP=14073;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,276:276:99:8708,827,0:0,0,152,124 chr1 7904475 . G A 20838 PASS AC=2;AF=0.989;AN=2;DP=23485;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,507:508:99:15909,1512,0:1,0,227,280 chr1 7906476 . G T 4185.69 PASS AC=2;AF=0.989;AN=2;DP=6794;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3313,353,0:0,0,62,56 chr1 7906702 . A G 562.84 PASS AC=1;AF=0.5;AN=2;DP=88;FractionInformativeReads=1;MQ=60;set=variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:25,17:42:99:591,0,808:13,12,10,7 chr1 7907007 . G A 479.05 PASS AC=1;AF=0.569;AN=2;DP=1085;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,16:22:99:395,0,121:2,4,4,12 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 0/1:94,64:158:99:2536,0,5204:64,30,41,23 chr1 7907971 . C A 398.18 PASS AC=1;AF=0.5;AN=2;DP=889;set=variant2-variant5-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant25-variant27-variant28-variant29-variant32-variant33-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,19:42:99:356,0,674:7,16,6,13 chr1 7911099 . C T 1083.31 PASS AC=1;AF=0.571;AN=2;DP=393;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant8-variant10-variant13-variant20-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:99:106,0,269:1,6,1,3 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 0/1:137:99:25,30,35,47 chr1 7913430 . G A 1932.03 PASS AC=1;AF=0.721;AN=2;DP=5519;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant10-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,70:153:99:1923,0,2247:52,31,40,30 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 1/1:0,75:75:99:2338,225,0:0,0,29,46 chr1 8021778 . T C 2307.24 PASS AC=2;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 1/1:0,140:140:99:4211,420,0:0,0,74,66 chr1 8022171 . C T 451.53 PASS AC=2;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 1/1:1,39:40:77:1203,77,0:1,0,12,27 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 0/1:30:99:9,3,13,5 chr1 8037496 . G A 1506.34 PASS AC=2;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 1/1:0,114:114:99:3333,341,0:0,0,51,63 chr1 8064578 . A G 1351.65 PASS AC=2;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 1/1:0,98:98:99:3076,294,0:0,0,58,40 chr1 8072466 . C T 1422.24 PASS AC=2;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 1/1:0,129:129:99:3982,387,0:0,0,51,78 chr1 8377828 . G A 314.62 PASS AC=1;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 0/1:15,13:28:99:373,0,493:12,3,9,4 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 1/1:0,58:58:99:1743,174,0:0,0,38,20 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 0/1:82,32:114:75:75,0,3370:11,71,32,0 chr1 8384582 . A C 665.11 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1577;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:80,29:109:99:364,0,1710:11,69,29,0 chr1 8385485 . GA G 59.98 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=106;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:28,6:34:70:70,0,678:16,12,2,4 chr1 8390384 . G C 1020.96 PASS AC=1;AF=0.571;AN=2;DP=1508;FractionInformativeReads=1;MQ=60;set=variant2-variant14-variant16-variant18-variant19-variant21-variant23-variant24-variant26-variant27-variant30-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:70,51:121:99:1157,0,1573:34,36,23,28 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 1/1:0,59:59:99:1937,176,0:0,0,34,25 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 0/1:102,105:207:99:2444,0,2451:65,37,62,43 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 0/1:179,145:324:99:3137,0,4307:78,101,65,80 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 0/1:24,31:55:99:790,0,515:10,14,14,17 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 1/1:0,44:44:99:1267,131,0:0,0,17,27 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 0/1:16,19:35:99:463,0,333:8,8,10,9 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 0/1:37,37:74:99:983,0,876:21,16,18,19 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 0/1:29,27:56:99:725,0,748:13,16,8,19 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 0/1:8,10:18:99:212,0,170:3,5,5,5 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 0/1:18,13:31:99:321,0,448:12,6,7,6 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 0/1:76,76:152:99:2868,0,4176:41,35,42,34 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 0/1:81,84:165:99:3089,0,4240:46,35,46,38 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 0/1:68,60:128:99:1427,0,1659:34,34,27,33 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 0/1:99,69:168:99:1506,0,2265:56,43,41,28 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 0/1:5,4:9:99:121,0,202:5,0,3,1 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 0/1:6,7:13:99:217,0,151:3,3,6,1 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 0/1:30,34:64:99:881,0,765:17,13,19,15 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 0/1:55,48:103:99:1143,0,1428:22,33,22,26 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 0/1:2,4:6:64:145,0,64:2,0,4,0 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 0/1:21,6:27:99:129,0,574:5,16,2,4 chr1 8877520 . AT ATTT,ATT,A 833 PASS AC=1,0,0;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 0/1:40:99:13,11,9,7 chr1 8925112 . T C 192.99 PASS AC=1;AF=0.833;AN=2;DP=76;FS=0;FractionInformativeReads=1;set=variant2-variant3-variant4-variant8-variant11-variant12-variant13-variant16-variant19-variant20-variant22-variant23-variant24-variant26-variant28-variant29-variant33-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:30:111,0,30:1,0,3,0 chr1 8926285 . A AG 908.96 PASS AC=1;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 0/1:38,29:67:99:736,0,1101:23,15,24,5 chr1 8930369 . T C 1482.85 PASS AC=1;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 0/1:16,22:38:99:527,0,470:12,4,12,10 chr1 8930385 . G A 1853.1 PASS AC=1;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 0/1:22,30:52:99:700,0,580:15,7,17,13 chr1 8935149 . A G 582.26 PASS AC=1;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 0/1:5,6:11:99:196,0,166:0,5,1,5 chr1 9009444 . A C 2520.64 PASS AC=1;AF=0.676;AN=2;DP=4318;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,48:98:99:1845,0,2029:24,26,24,24 chr1 9009451 . G C 2305.59 PASS AC=1;AF=0.5;AN=2;DP=805;FractionInformativeReads=1;MQ=60;set=variant6-variant23-variant32-variant33-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,50:96:99:1952,0,1990:22,24,24,26 chr1 9009470 . G C 1956.67 PASS AC=1;AF=0.5;AN=2;DP=1239;MQ=60;set=variant6-variant18-variant21-variant23-variant30-variant32-variant33-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,45:91:99:1770,0,1857:22,24,22,23 chr1 9009547 . C A 743.79 PASS AC=1;AF=0.5;AN=2;DP=497;MQ=60;set=variant6-variant21-variant23-variant30-variant32-variant33-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,25:56:99:556,0,773:11,20,8,17 chr1 9011586 . T G 1417.19 PASS AC=2;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 1/1:0,102:102:99:3251,306,0:0,0,40,62 chr1 9011627 . G A 1604.68 PASS AC=1;AF=0.5;AN=2;DP=780;MQ=60;set=variant6-variant23-variant32-variant33-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,41:72:99:1089,0,761:11,20,17,24 chr1 9011722 . G T 441.05 PASS AC=2;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 1/1:0,25:25:75:791,75,0:0,0,8,17 chr1 9017091 . C T 147.24 PASS AC=2;AF=0.643;AN=2;DP=200;MQ=60;set=variant2-variant12-variant16-variant18-variant21-variant23-variant24-variant28-variant31-variant33-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:444,39,0:0,0,9,4 chr1 9034421 . G A 607 PASS AC=2;AF=0.607;AN=2;DP=2232;MQ=60;set=variant-variant2-variant6-variant9-variant10-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2853,269,0:0,0,41,49 chr1 9034598 . A G 1285.85 PASS AC=2;AF=0.597;AN=2;DP=2637;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2420,240,0:0,0,38,42 chr1 9034815 . C CAGA 1845.29 PASS AC=2;AF=0.691;AN=2;DP=3428;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:3375,226,0:0,0,40,35 chr1 9063602 . G C 848.38 PASS AC=2;AF=0.667;AN=2;DP=1883;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1395,141,0:0,0,16,31 chr1 9063646 . T C 413.05 PASS AC=2;AF=0.654;AN=2;DP=607;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant19-variant22-variant23-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:994,81,0:0,0,6,21 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 0/1:3,4:7:59:111,0,59:1,2,1,3 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 0/1:28,41:69:99:1135,0,691:9,19,13,28 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 0/1:24,21:45:99:637,0,744:5,19,6,15 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 0/1:7,9:16:99:223,0,223:6,1,7,2 chr1 9084924 . T C 552.78 PASS AC=1;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 0/1:40,43:83:99:1133,0,1062:28,12,31,12 chr1 9095202 . C T 1848.88 PASS AC=2;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 1/1:0,69:69:99:2004,206,0:0,0,40,29 chr1 9095229 . G A 2072.77 PASS AC=1;AF=0.571;AN=2;DP=3494;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant34-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:56,33:89:99:590,0,1328:28,28,18,15 chr1 9095444 . C T 408.5 PASS AC=1;AF=0.571;AN=2;DP=1882;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant34-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,29:69:99:721,0,1201:24,16,17,12 chr1 9095494 . G A 862.44 PASS AC=1;AF=0.571;AN=2;DP=2033;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant34-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,34:79:99:946,0,1272:28,17,22,12 chr1 9095610 . T C 3076.79 PASS AC=1;AF=0.571;AN=2;DP=6254;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant34-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:96,113:209:99:2717,0,2652:59,37,66,47 chr1 9095847 . C T 1427.54 PASS AC=1;AF=0.571;AN=2;DP=2282;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant34-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:47,38:85:99:1183,0,1595:5,42,6,32 chr1 9096050 . C A 202.22 PASS AC=1;AF=0.571;AN=2;DP=563;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant34-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:269,0,212:6,1,7,2 chr1 9096695 . T C 130.63 PASS AC=1;AF=0.574;AN=2;DP=447;FractionInformativeReads=1;set=variant-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant34-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,3:14:84:84,0,391:2,9,0,3 chr1 9097241 . C T 808.01 PASS AC=1;AF=0.569;AN=2;DP=1615;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant34-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,19:38:99:720,0,865:10,9,9,10 chr1 9097251 . A G 792.44 PASS AC=1;AF=0.569;AN=2;DP=1723;MQ=60;set=variant-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant34-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,22:42:99:803,0,856:10,10,12,10 chr1 9118423 . C T 1235.38 PASS AC=1;AF=0.5;AN=2;DP=268;FractionInformativeReads=1;MQ=60;set=variant17-variant23-variant28 GT:AD:DP:GQ:PL:SB 0/1:43,50:93:99:1296,0,1151:20,23,20,30 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 0/1:15,11:26:99:396,0,2160:4,11,3,8 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 0/1:55,58:113:99:1357,0,1327:27,28,25,33 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 0/1:35,26:61:99:659,0,1009:11,24,9,17 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 0/1:24,16:40:99:414,0,687:9,15,5,11 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 0/1:20,19:39:99:482,0,496:8,12,6,13 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 0/1:4,7:11:99:201,0,129:0,4,3,4 chr1 9162470 . A AC 309.77 PASS AC=1;AF=0.5;AN=2;DP=1629;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-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,17:42:99:366,0,546:17,8,14,3 chr1 9162471 . A C 31.61 PASS AC=1;AF=0.5;AN=2;DP=601;set=filterInvariant2-variant6-variant7-variant12-filterInvariant14-filterInvariant23-filterInvariant27-filterInvariant28-filterInvariant32-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:32,14:46:99:122,0,924:20,12,11,3 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 0/1:95:99:22,11,44,18 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 0/1:26,26:52:99:739,0,690:15,11,13,13 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 0/1:25,38:63:99:1089,0,749:16,9,17,21 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 0/1:110:99:29,25,29,27 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 1/1:0,12:12:36:484,36,0:0,0,1,11 chr1 9188677 . T C 5586.53 PASS AC=1;AF=0.5;AN=2;DP=1175;MQ=60;set=variant17-variant23-variant28 GT:AD:DP:GQ:PL:SB 0/1:182,180:362:99:4672,0,4700:107,75,99,81 chr1 9188989 . A G 1253.47 PASS AC=1;AF=0.5;AN=2;DP=327;FractionInformativeReads=1;MQ=60;set=variant13-variant17-variant23-variant28 GT:AD:DP:GQ:PL:SB 0/1:51,37:88:99:1049,0,1426:18,33,12,25 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 0/1:70,72:142:99:1796,0,1726:30,40,35,37 chr1 9323910 . G A 2220.22 PASS AC=1;AF=0.545;AN=2;DP=3814;MQ=60;set=variant-variant2-variant3-variant5-variant8-variant13-variant15-variant17-variant19-variant21-variant22-variant23-variant24-variant27-variant30-variant31-variant34-variant36-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:77,72:149:99:1699,0,1921:35,42,33,39 chr1 9325676 . C T 307.78 PASS AC=1;AF=0.6;AN=2;DP=704;MQ=60;set=variant-variant2-variant3-variant5-variant8-variant15-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant31-variant34-variant36-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:19,12:31:99:393,0,627:5,14,1,11 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 0/1:10,4:14:82:82,0,269:4,6,1,3 chr1 9326887 . CTT C,CT 218.26 PASS AC=2,0;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 1/1:6:18:0,0,1,5 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 0/1:29,24:53:99:690,0,834:15,14,11,13 chr1 9329112 . A AG 258.8 PASS AC=1;AF=0.605;AN=2;DP=692;MQ=60;set=variant-variant2-variant3-variant5-variant8-variant15-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant31-variant34-variant36-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:7,17:24:99:596,0,185:4,3,11,6 chr1 9329289 . C T 3932.27 PASS AC=1;AF=0.553;AN=2;DP=2289;MQ=60;set=variant2-variant3-variant5-variant8-variant13-variant15-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant31-variant34-variant36-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:40,50:90:99:1201,0,1023:20,20,26,24 chr1 9330479 . C T 618.6 PASS AC=1;AF=0.5;AN=2;DP=709;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant15-variant17-variant19-variant22-variant23-variant24-variant25-variant40 GT:AD:DP:GQ:PL:SB 0/1:18,26:44:99:670,0,438:10,8,11,15 chr1 9330740 . G C 586.33 PASS AC=1;AF=0.605;AN=2;DP=1326;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant8-variant15-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant31-variant34-variant36-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:28,38:66:99:922,0,598:12,16,19,19 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 1/1:0,21:21:63:871,63,0:0,0,10,11 chr1 9353122 . C G 79.46 PASS AC=1;AF=0.542;AN=2;DP=176;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant7-variant10-variant18-variant20-variant21-variant22-variant23-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:75:75,0,113:1,3,2,2 chr1 9411469 . G C 416 PASS AC=1;AF=0.643;AN=2;DP=744;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant16-variant20-variant21-variant23-variant24-variant25-variant28-variant30-variant34-variant36-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,22:29:99:523,0,132:4,3,13,9 chr1 9411667 . A G 599.75 PASS AC=1;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 0/1:11,7:18:99:174,0,299:4,7,2,5 chr1 9415727 . G A 669.39 PASS AC=1;AF=0.5;AN=2;DP=772;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant9-variant10-variant11-variant13-variant16-variant19-variant20-variant22-variant23-variant28-variant29-variant31-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,22:42:99:550,0,506:14,6,14,8 chr1 9416151 . G A 3188.31 PASS AC=1;AF=0.5;AN=2;DP=4443;MQ=60;set=variant2-variant7-variant9-variant10-variant11-variant13-variant16-variant19-variant20-variant22-variant23-variant28-variant29-variant31-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:98,131:229:99:3205,0,2438:52,46,73,58 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 0/1:103,100:203:99:2703,0,2589:57,46,51,49 chr1 9416747 . A T 1083.15 PASS AC=1;AF=0.542;AN=2;DP=1136;MQ=60;set=variant2-variant7-variant10-variant13-variant19-variant22-variant23-variant28-variant29-variant31-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:40,40:80:99:1157,0,1057:14,26,16,24 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 1/1:0,122:122:99:3803,365,0:0,0,54,68 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 0/1:68,47:115:99:1102,0,1686:30,38,22,25 chr1 9428563 . A G 955.59 PASS AC=1;AF=0.5;AN=2;DP=110;FS=1.559;FractionInformativeReads=0.991;MQ=60;MQRankSum=4.814;QD=8.69;ReadPosRankSum=0.269;SOR=0.548;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:65,44:109:99:984,0,1606:27,38,20,24 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 1/1:0,34:34:99:1183,102,0:0,0,12,22 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 1/1:1,27:28:73:936,73,0:0,1,14,13 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 1/1:0,75:75:99:2562,225,0:0,0,53,22 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 1/1:0,46:46:99:1541,138,0:0,0,13,33 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 1/1:0,36:36:99:1358,108,0:0,0,30,6 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 1/1:0,99:99:99:3116,296,0:0,0,66,33 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 1/1:0,80:80:99:2346,238,0:0,0,33,47 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 1/1:23:7:1,2,4,16 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 1/1:3,102:105:99:2904,277,0:3,0,49,53 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 0/1:55,46:101:99:1226,0,1650:19,36,20,26 chr1 9782386 . C T 870.47 PASS AC=1;AF=0.5;AN=2;DP=145;FractionInformativeReads=1;MQ=60;set=variant12-variant23 GT:AD:DP:GQ:PL:SB 0/1:39,32:71:99:826,0,1158:17,22,13,19 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 0/1:35,37:72:99:1037,0,885:22,13,17,20 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 1/1:0,123:123:99:3839,369,0:0,0,58,65 chr1 9787840 . G T 119.97 PASS AC=2;AF=0.756;AN=2;DP=943;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-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:795,72,0:0,0,7,17 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 1/1:0,15:15:45:428,45,0:0,0,3,12 chr1 9804315 . C T 393.96 PASS AC=1;AF=0.5;AN=2;DP=53;FractionInformativeReads=1;MQ=60;set=variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:422,0,457:8,5,7,8 chr1 9811653 . C T 1303.3 PASS AC=1;AF=0.5;AN=2;DP=193;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:45,53:98:99:1332,0,980:21,24,25,28 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 1/1:0,75:75:99:2259,225,0:0,0,41,34 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 1/1:0,16:16:48:462,48,0:0,0,8,8 chr1 9908269 . C T 2203.24 PASS AC=2;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 1/1:0,119:119:99:3378,355,0:0,0,64,55 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 1/1:0,48:48:99:1672,144,0:0,0,18,30 chr1 9908674 . CCT C 733.45 PASS AC=1;AF=0.5;AN=2;DP=65;MQ=60;set=variant13-variant23 GT:AD:DP:GQ:PL:SB 0/1:11,25:36:99:1006,0,387:4,7,11,14 chr1 9908680 . C T 903.43 PASS AC=2;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 1/1:0,36:36:99:1514,111,0:0,0,15,21 chr1 9909506 . G A 619.13 PASS AC=2;AF=0.567;AN=2;DP=585;MQ=60;set=variant4-variant9-filterInvariant10-variant12-variant13-variant18-variant23-variant24-variant25-variant28-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,39:40:99:1211,109,0:0,1,18,21 chr1 9910357 . A T 2297.48 PASS AC=2;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 1/1:0,37:37:99:1639,111,0:0,0,19,18 chr1 9910358 . T C 2297.48 PASS AC=2;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 1/1:0,37:37:99:1639,111,0:0,0,19,18 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 0/1:7,7:14:99:174,0,173:3,4,5,2 chr1 10001235 . TTTCG T 3170.84 PASS AC=2;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 1/1:1,57:58:99:2339,116,0:0,1,19,38 chr1 10003320 . G A 1446.75 PASS AC=2;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 1/1:0,44:44:99:1405,131,0:0,0,28,16 chr1 10027540 . G A 611.73 PASS AC=2;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 1/1:0,20:20:60:697,60,0:0,0,5,15 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 0/1:26,7:33:99:102,0,417:10,16,5,2 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 0/1:171:99:64,77,13,17 chr1 10335315 . G A 1209.71 PASS AC=2;AF=0.977;AN=2;DP=1349;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:888,69,0:0,0,18,5 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 0/1:27:99:6,12,4,5 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 0/1:26:95:16,2,8,0 chr1 10479849 . C T 617.44 PASS AC=1;AF=0.5;AN=2;DP=54;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.779;QD=11.43;ReadPosRankSum=-0.616;SOR=0.801;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:35,19:54:99:646,0,1119:14,21,7,12 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 1/1:0,14:14:42:403,42,0:0,0,10,4 chr1 10502710 . A G 5629.8 PASS AC=2;AF=0.966;AN=2;DP=6909;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,138:138:99:3935,413,0:0,0,68,70 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 1/1:1,27:28:38:997,38,0:1,0,24,3 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 1/1:21:63:0,0,16,5 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 1/1:0,109:109:99:3229,324,0:0,0,59,50 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 1/1:0,117:117:99:3860,350,0:0,0,63,54 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 1/1:0,187:187:99:5880,560,0:0,0,117,70 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 1/1:0,28:28:84:1189,84,0:0,0,15,13 chr1 10518596 . C T 275.94 PASS AC=2;AF=1;AN=2;DP=122;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.747;ReadPosRankSum=-0.747;set=variant2-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant31-variant33-variant34-variant36-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:96,9,0:0,0,0,3 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 0/1:15,49:64:99:918,0,150:3,12,8,41 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 1/1:0,64:64:99:2001,192,0:0,0,42,22 chr1 10529326 . A G 2126.48 PASS AC=1;AF=0.5;AN=2;DP=505;FractionInformativeReads=1;MQ=60;set=variant10-variant23-variant32 GT:AD:DP:GQ:PL:SB 0/1:77,65:142:99:1532,0,1874:38,39,31,34 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 1/1:0,55:55:99:1736,164,0:0,0,37,18 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 1/1:0,51:51:99:1688,153,0:0,0,15,36 chr1 10697179 . T TC 2776.39 PASS AC=1;AF=0.5;AN=2;DP=229;FS=0.495;FractionInformativeReads=0.991;MQ=60;MQRankSum=-0.658;QD=12.12;ReadPosRankSum=-1.799;SOR=0.637;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:101,126:227:99:2814,0,2901:41,60,53,73 chr1 10697392 . C T 1003.53 PASS AC=1;AF=0.5;AN=2;DP=626;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant10-variant18-variant20-variant23-variant27-variant28-variant32-variant34-variant39 GT:AD:DP:GQ:PL:SB 0/1:26,31:57:99:768,0,660:15,11,15,16 chr1 10720339 . A C 1670.13 PASS AC=1;AF=0.5;AN=2;DP=153;FS=0;FractionInformativeReads=0.987;MQ=60;MQRankSum=1.511;QD=10.92;ReadPosRankSum=0.885;SOR=0.648;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:88,63:151:99:1698,0,2195:54,34,38,25 chr1 10856513 . TG T 545.81 PASS AC=2;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 1/1:0,46:46:99:2092,142,0:0,0,29,17 chr1 10856517 . G A 619.42 PASS AC=2;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 1/1:0,47:47:99:2023,141,0:0,0,30,17 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 0/1:20,30:50:99:907,0,455:6,14,7,23 chr1 11036050 . T C 400.7 PASS AC=1;AF=0.533;AN=2;DP=397;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant10-variant11-variant18-variant19-variant22-variant23-variant24-variant26-variant29-variant30-variant31-variant33-variant41 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:390,0,369:10,0,8,4 chr1 11036394 . CT C,CTT 117.5 PASS AC=0,1;AF=0.375,0.125;AN=2;DP=61;MQ=60;set=variant12-variant17-variant23-variant30 GT:DP:GQ:SB 0/2:9:71:0,5,2,2 chr1 11042201 . C CAG,CG 504.4 PASS AC=1,0;AF=0.5,0.028;AN=2;DP=647;MQ=60;set=variant-variant2-variant5-variant8-variant10-variant11-variant18-variant19-variant22-variant23-variant24-variant26-variant29-variant30-variant31-variant33-variant39-variant41 GT:DP:GQ:SB 0/1:31:99:6,12,3,10 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 1/1:0,19:19:57:633,57,0:0,0,13,6 chr1 11072885 . C T 381.29 PASS AC=2;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 1/1:0,15:15:45:577,45,0:0,0,3,12 chr1 11079077 . A G 267.07 PASS AC=2;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 1/1:0,17:17:51:600,51,0:0,0,4,13 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 1/1:0,7:7:21:248,21,0:0,0,2,5 chr1 11082054 . AG A 103.61 PASS AC=2;AF=0.872;AN=2;DP=346;MQ=60;set=variant-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-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:162,12,0:0,0,4,0 chr1 11086097 . A AT 1336.83 PASS AC=2;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 1/1:0,69:69:99:2527,208,0:0,0,29,40 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 1/1:0,29:29:87:929,87,0:0,0,16,13 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 1/1:0,128:128:99:3928,384,0:0,0,57,71 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 1/1:0,7:7:21:265,21,0:0,0,1,6 chr1 11090916 . C A 846.21 PASS AC=2;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 1/1:1,55:56:99:1782,125,0:1,0,16,39 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 1/1:0,6:6:18:267,18,0:0,0,4,2 chr1 11094757 . G GA,GAA 377.46 PASS AC=1,0;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 0/1:18:92:4,2,8,4 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 1/1:0,20:20:59:534,59,0:0,0,8,12 chr1 11104676 . G A 331.62 PASS AC=2;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 1/1:0,12:12:36:406,36,0:0,0,8,4 chr1 11104712 . G A 576.02 PASS AC=2;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 1/1:0,19:19:57:712,57,0:0,0,14,5 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 1/1:0,103:103:99:3132,308,0:0,0,60,43 chr1 11105106 . C T 597.83 PASS AC=2;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 1/1:0,51:51:99:2126,153,0:0,0,19,32 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 1/1:0,45:45:99:2040,141,0:0,0,19,26 chr1 11107439 . G T 72.1 PASS AC=2;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 1/1:0,17:17:50:627,50,0:0,0,3,14 chr1 11115177 . CTT CTTT,CT,C 50.09 PASS AC=1,0,0;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 0/1:28:99:3,10,7,8 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 1/1:0,206:206:99:5748,615,0:0,0,89,117 chr1 11126517 . C T 104.96 PASS AC=1;AF=0.803;AN=2;DP=378;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-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:99:244,0,107:3,0,6,1 chr1 11126569 . C A 215.23 PASS AC=1;AF=0.774;AN=2;DP=845;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,14:26:99:389,0,332:9,3,10,4 chr1 11126941 . C T 323.54 PASS AC=1;AF=0.774;AN=2;DP=1294;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,12:20:99:311,0,241:1,7,4,8 chr1 11128001 . A G 412.34 PASS AC=1;AF=0.774;AN=2;DP=911;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,13:22:99:308,0,291:8,1,9,4 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 0/1:4,4:8:99:153,0,117:1,3,0,4 chr1 11128654 . G A 1127.29 PASS AC=1;AF=0.762;AN=2;DP=2227;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,22:47:99:544,0,650:16,9,15,7 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 0/1:17,7:24:99:220,0,487:3,14,2,5 chr1 11132217 . G A 629.98 PASS AC=1;AF=0.774;AN=2;DP=2364;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,33:54:99:739,0,564:8,13,15,18 chr1 11133934 . CAAAA C,CAAAAAA 58.54 PASS AC=1,0;AF=0.167,0.333;AN=2;DP=59;set=variant23-variant29-variant35 GT:DP:GQ:SB 0/1:23:96:14,5,2,2 chr1 11133956 . A AAAG,AAG,AG,AAAAG,AAAAAG 822.77 PASS AC=1,0,0,0,0;AF=0.448,0.207,0.034,0.052,0.069;AN=2;DP=1046;set=variant2-variant4-variant5-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant34-variant36-variant37-variant38-variant40-variant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/1:50:99:16,10,15,9 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 0/1:16,29:45:99:900,0,476:11,5,14,15 chr1 11134470 . A AT,ATT 30.14 PASS AC=1,0;AF=0.2,0.3;AN=2;DP=239;set=filterInvariant14-filterInvariant23-variant29-variant35-variant44 GT:DP:GQ:SB 0/1:30:99:4,18,1,7 chr1 11137778 . C T 493.49 PASS AC=1;AF=0.774;AN=2;DP=1450;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,12:28:99:357,0,404:4,12,2,10 chr1 11140620 . AACAC AACACAC,AACACACAC,A 55.13 PASS AC=1,0,0;AF=0.3,0.2,0.1;AN=2;DP=60;MQ=60;set=variant3-variant12-variant16-variant23-variant28 GT:DP:GQ:SB 0/1:8:2:1,0,2,5 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 0/1:55,53:108:99:1263,0,1321:31,24,27,26 chr1 11150945 . CTGGGCTCCCTTTGAACAAAGGAGGG C 482.91 PASS AC=1;AF=0.5;AN=2;DP=109;MQ=60;set=variant20-variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:21,11:32:99:401,0,4435:14,7,9,2 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 0/1:4,5:9:99:158,0,101:0,4,1,4 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 0/1:53,45:98:99:992,0,1268:32,21,28,17 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 1/1:0,44:44:99:1539,132,0:0,0,13,31 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 0/1:79,79:158:99:1798,0,2000:43,36,42,37 chr1 11205058 . C T 1414.83 PASS AC=1;AF=0.762;AN=2;DP=5052;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,53:108:99:1207,0,1249:28,27,29,24 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 0/1:17,21:38:99:463,0,366:10,7,12,9 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 0/1:20,20:40:99:497,0,398:11,9,11,9 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 0/1:40,37:77:99:1040,0,1120:26,14,24,13 chr1 11292666 . T A 152.9 PASS AC=1;AF=0.776;AN=2;DP=367;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:190,0,235:1,6,2,4 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 0/1:11,12:23:99:445,0,398:2,9,0,12 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 0/1:25,30:55:99:703,0,634:15,10,16,14 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 0/1:3,6:9:99:196,0,110:0,3,1,5 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 0/1:70,56:126:99:1238,0,1581:37,33,31,25 chr1 11317320 . C T 278.98 PASS AC=1;AF=0.762;AN=2;DP=1358;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,16:33:99:405,0,534:3,14,5,11 chr1 11318763 . C G 201.16 PASS AC=1;AF=0.775;AN=2;DP=429;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-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:99:144,0,237:1,6,0,4 chr1 11319587 . A G 416.97 PASS AC=1;AF=0.762;AN=2;DP=2096;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,11:32:99:274,0,595:9,12,3,8 chr1 11322565 . C G 740.98 PASS AC=1;AF=0.774;AN=2;DP=2155;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,22:52:99:549,0,710:14,16,12,10 chr1 11322628 . G T 562.23 PASS AC=1;AF=0.774;AN=2;DP=2173;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,25:56:99:615,0,790:13,18,13,12 chr1 11347155 . C CTGTT 589.02 PASS AC=1;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 0/1:8,27:35:99:1089,0,363:5,3,14,13 chr1 11561593 . G A 5270.66 PASS AC=2;AF=0.611;AN=2;DP=5850;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,146:146:99:4674,436,0:0,0,83,63 chr1 11575375 . T A 1535.61 PASS AC=2;AF=0.611;AN=2;DP=2490;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:98:1170,98,0:0,0,27,6 chr1 11579470 . G A 3818.46 PASS AC=2;AF=0.618;AN=2;DP=5083;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,108:109:99:3267,312,0:0,1,63,45 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 1/1:0,53:53:99:1613,159,0:0,0,35,18 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 1/1:0,68:68:99:2413,227,0:0,0,37,31 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 1/1:0,158:158:99:4530,473,0:0,0,81,77 chr1 11709051 . A AG 651.78 PASS AC=2;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 1/1:0,29:29:90:1234,90,0:0,0,14,15 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 2/2:29:90:0,0,14,15 chr1 11714368 . T G 1148.72 PASS AC=1;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 0/1:23,21:44:99:442,0,675:8,15,10,11 chr1 11714793 . A G 422.99 PASS AC=1;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 0/1:5,13:18:99:406,0,133:1,4,3,10 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 1/1:0,5:5:15:144,15,0:0,0,3,2 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 1/1:0,5:5:15:144,15,0:0,0,3,2 chr1 11718390 . G A 1432.47 PASS AC=1;AF=0.5;AN=2;DP=139;FS=0.625;FractionInformativeReads=1;MQ=59.88;MQRankSum=-0.845;QD=10.31;ReadPosRankSum=-0.689;SOR=0.617;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:72,67:139:99:1461,0,1648:34,38,33,34 chr1 11721693 . G A 1412.88 PASS AC=1;AF=0.5;AN=2;DP=1164;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant14-variant20-variant23-variant26-variant28-variant31-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:41,52:93:99:1333,0,1061:18,23,23,29 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 0/1:49,44:93:99:1060,0,1220:28,21,21,23 chr1 11721949 . C T 717.05 PASS AC=1;AF=0.5;AN=2;DP=1037;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant14-variant20-variant23-variant26-variant28-variant31-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:38,35:73:99:842,0,1001:14,24,13,22 chr1 11724092 . G C 386.78 PASS AC=2;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 1/1:0,49:49:99:1515,146,0:0,0,30,19 chr1 11731927 . AG A 212.44 PASS AC=1;AF=0.587;AN=2;DP=639;MQ=60;set=variant3-variant5-variant10-variant11-variant13-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant31-variant32-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,16:26:99:402,0,210:7,3,11,5 chr1 11733846 . C A 1519.44 PASS AC=1;AF=0.5;AN=2;DP=785;MQ=60;set=variant8-variant23-variant28-variant31 GT:AD:DP:GQ:PL:SB 0/1:91,99:190:99:2459,0,2294:44,47,45,54 chr1 11734293 . A G 70.68 PASS AC=2;AF=0.875;AN=2;DP=18;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.406;ReadPosRankSum=1.537;SOR=0.693;set=variant23-variant32-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:99,12,0:0,0,2,2 chr1 11735262 . C T 933.82 PASS AC=1;AF=0.526;AN=2;DP=1363;MQ=60;set=variant3-variant5-variant8-variant11-variant15-variant22-variant23-variant26-variant28-variant31-variant32-variant33-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,32:59:99:785,0,723:9,18,13,19 chr1 11735841 . C A 2751.05 PASS AC=1;AF=0.526;AN=2;DP=3458;MQ=60;set=variant3-variant5-variant8-variant11-variant15-variant22-variant23-variant26-variant28-variant31-variant32-variant33-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,90:163:99:2197,0,1864:32,41,40,50 chr1 11737051 . G C 1069.23 PASS AC=2;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 1/1:0,85:85:99:2717,255,0:0,0,35,50 chr1 11740358 . A G 1506.26 PASS AC=2;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 1/1:0,91:91:99:2790,273,0:0,0,57,34 chr1 11740812 . A C 764.93 PASS AC=1;AF=0.526;AN=2;DP=814;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant8-variant11-variant15-variant18-variant22-variant23-variant26-variant28-variant31-variant32-variant33-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,20:37:99:472,0,474:8,9,7,13 chr1 11741304 . A C 727.8 PASS AC=1;AF=0.526;AN=2;DP=1018;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant8-variant11-variant15-variant18-variant22-variant23-variant26-variant28-variant31-variant32-variant33-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,27:58:99:655,0,743:19,12,17,10 chr1 11741506 . A C 1259.52 PASS AC=1;AF=0.526;AN=2;DP=1655;MQ=60;set=variant3-variant5-variant8-variant11-variant15-variant18-variant22-variant23-variant26-variant28-variant31-variant32-variant33-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,30:68:99:749,0,861:14,24,12,18 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 1/1:0,5:5:15:184,15,0:0,0,1,4 chr1 11751379 . C T 248.24 PASS AC=2;AF=0.55;AN=2;DP=205;FractionInformativeReads=1;MQ=60;set=variant8-variant13-variant17-variant21-variant23-variant24-variant28-variant31-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:760,60,0:0,0,17,3 chr1 11751642 . C G 782.9 PASS AC=2;AF=0.6;AN=2;DP=475;MQ=60;set=variant8-variant13-variant17-variant21-variant23-variant24-variant28-variant31-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1450,141,0:0,0,17,30 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 1/1:0,11:11:33:428,33,0:0,0,3,8 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 0/1:57,73:130:99:1791,0,1252:28,29,40,33 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 1/1:0,94:94:99:3040,281,0:0,0,56,38 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 0/1:65,58:123:99:1392,0,1668:33,32,29,29 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 0/1:20,16:36:99:460,0,612:6,14,3,13 chr1 11779499 . T C 663.31 PASS AC=2;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 1/1:0,20:20:60:678,60,0:0,0,13,7 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 0/1:75,55:130:99:1257,0,1860:35,40,26,29 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 1/1:0,80:80:99:2672,240,0:0,0,29,51 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 1/1:0,24:24:72:776,72,0:0,0,9,15 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 1/1:0,104:104:99:3292,311,0:0,0,44,60 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 1/1:0,39:39:99:1316,117,0:0,0,12,27 chr1 11782886 . C T 282.21 PASS AC=2;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 1/1:0,11:11:33:317,33,0:0,0,3,8 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 1/1:0,39:39:99:1215,117,0:0,0,26,13 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 1/1:0,81:81:99:2325,242,0:0,0,38,43 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 1/1:0,130:130:99:5812,392,0:0,0,80,50 chr1 11807426 . C T 2030.6 PASS AC=1;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 0/1:89,68:157:99:1731,0,2324:47,42,39,29 chr1 11810505 . C T 438.91 PASS AC=1;AF=0.575;AN=2;DP=1320;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant17-variant18-variant23-variant30-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,15:61:99:287,0,1070:21,25,5,10 chr1 11810674 . G A 210.78 PASS AC=1;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 0/1:22,20:42:99:432,0,577:14,8,11,9 chr1 11810691 . C T 146.82 PASS AC=1;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 0/1:23,21:44:99:489,0,609:14,9,10,11 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 1/1:0,42:42:99:1313,126,0:0,0,21,21 chr1 11810844 . A G 698.58 PASS AC=1;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 0/1:21,8:29:99:153,0,461:9,12,3,5 chr1 11824242 . A C 411.86 PASS AC=1;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 0/1:5,9:14:99:265,0,145:5,0,6,3 chr1 11824303 . T C 993.62 PASS AC=1;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 0/1:13,16:29:99:511,0,323:8,5,9,7 chr1 11824346 . G A 1231.62 PASS AC=1;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 0/1:20,20:40:99:603,0,528:12,8,11,9 chr1 11824556 . A G 1282.88 PASS AC=1;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 0/1:19,24:43:99:486,0,552:7,12,10,14 chr1 11824575 . T C 1536.01 PASS AC=1;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 0/1:11,20:31:99:773,0,748:3,8,8,12 chr1 11824578 . C T 1536.01 PASS AC=1;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 0/1:11,20:31:99:773,0,748:3,8,8,12 chr1 11825851 . G C 2300.83 PASS AC=1;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 0/1:24,19:43:99:422,0,549:13,11,11,8 chr1 11826630 . C T 3950.11 PASS AC=1;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 0/1:86,69:155:99:1540,0,2180:44,42,35,34 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 1/1:0,71:71:99:2207,212,0:0,0,53,18 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 1/1:0,83:83:99:2555,249,0:0,0,39,44 chr1 11827355 . A G 1169.09 PASS AC=1;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 0/1:29,19:48:99:453,0,699:12,17,8,11 chr1 11828238 . G A 4150.89 PASS AC=1;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 0/1:71,68:139:99:1766,0,1613:38,33,39,29 chr1 11828319 . G A 3768.55 PASS AC=1;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 0/1:56,73:129:99:1899,0,1302:27,29,35,38 chr1 11831615 . C T 5209.33 PASS AC=1;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 0/1:38,37:75:99:987,0,975:16,22,21,16 chr1 11831756 . A G 1206.15 PASS AC=1;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 0/1:15,23:38:99:653,0,379:4,11,6,17 chr1 11832100 . T A 2778.98 PASS AC=1;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 0/1:44,36:80:99:874,0,1067:28,16,22,14 chr1 11832311 . G C 1113.31 PASS AC=1;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 0/1:27,21:48:99:578,0,774:8,19,5,16 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 1/1:0,194:194:99:7283,586,0:0,0,116,78 chr1 11836442 . G A 7432.29 PASS AC=1;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 0/1:102,94:196:99:2125,0,2589:61,41,55,39 chr1 11836628 . T C 5274.21 PASS AC=1;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 0/1:78,68:146:99:1729,0,2067:31,47,27,41 chr1 11836682 . C T 3739.16 PASS AC=1;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 0/1:46,55:101:99:1352,0,1159:18,28,25,30 chr1 11836868 . A G 370.91 PASS AC=1;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 0/1:4,12:16:89:404,0,89:1,3,3,9 chr1 11838848 . G T 4221.75 PASS AC=1;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 0/1:58,70:128:99:2042,0,1764:33,25,39,31 chr1 11839208 . C T 571.76 PASS AC=1;AF=0.5;AN=2;DP=529;MQ=60;set=variant12-variant15-variant17-variant21-variant22-variant23-variant31-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:29,32:61:99:831,0,752:11,18,13,19 chr1 11839966 . G A 2011.5 PASS AC=1;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 0/1:25,35:60:99:877,0,912:9,16,15,20 chr1 11839971 . C T 858.84 PASS AC=1;AF=0.5;AN=2;DP=751;MQ=60;set=variant12-variant15-variant17-variant21-variant22-variant23-variant31-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:32,24:56:99:594,0,1270:13,19,9,15 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 1/1:0,48:48:99:1451,143,0:0,0,19,29 chr1 11842144 . C G 941.67 PASS AC=1;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 0/1:28,24:52:99:627,0,746:18,10,15,9 chr1 11844330 . C T 5522.19 PASS AC=1;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 0/1:95,69:164:99:1448,0,2360:49,46,33,36 chr1 11844454 . A C 1460.86 PASS AC=1;AF=0.5;AN=2;DP=1190;MQ=60;set=variant12-variant15-variant17-variant21-variant22-variant23-variant31-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:43,74:117:99:1979,0,996:24,19,32,42 chr1 11844827 . A G 102.92 PASS AC=1;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 0/1:1,6:7:21:130,0,21:1,0,2,4 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 1/1:0,30:30:90:945,90,0:0,0,17,13 chr1 11845169 . T G 2244.83 PASS AC=1;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 0/1:41,24:65:99:523,0,932:24,17,14,10 chr1 11846092 . G GT 700.62 PASS AC=1;AF=0.977;AN=2;DP=1286;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:4,26:30:21:605,0,21:2,2,19,7 chr1 11846252 . G A 2679.15 PASS AC=1;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 0/1:47,61:108:99:1521,0,1070:20,27,32,29 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 1/1:0,16:16:48:545,48,0:0,0,5,11 chr1 11846659 . ATTTTTTTT ATTTT,A,ATTTTTTTTT,ATTT 363.12 PASS AC=0,2,0,0;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 2/2:8:3:1,0,6,1 chr1 11847334 . G GGAA 2354.32 PASS AC=1;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 0/1:37,26:63:99:1022,0,1730:23,14,15,11 chr1 11847436 . T C 1380.16 PASS AC=1;AF=0.5;AN=2;DP=1276;FractionInformativeReads=1;MQ=60;set=variant12-variant15-variant17-variant21-variant22-variant23-variant31-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:53,68:121:99:1746,0,1268:29,24,37,31 chr1 11847759 . C T 3767.72 PASS AC=1;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 0/1:73,84:157:99:2093,0,1816:34,39,46,38 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 1/1:0,98:98:99:3172,294,0:0,0,38,60 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 1/1:0,96:96:99:2899,288,0:0,0,47,49 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 1/1:0,100:100:99:2974,301,0:0,0,46,54 chr1 11851185 . C T 135.91 PASS AC=1;AF=0.5;AN=2;DP=120;FractionInformativeReads=1;MQ=60;set=variant12-variant15-variant17-variant23-variant31 GT:AD:DP:GQ:PL:SB 0/1:10,7:17:99:159,0,271:6,4,5,2 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 1/1:0,197:197:99:5961,589,0:0,0,110,87 chr1 11854755 . G A 3171.03 PASS AC=1;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 0/1:48,35:83:99:838,0,1285:24,24,20,15 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 0/1:73,78:151:99:1725,0,1737:35,38,37,41 chr1 11860683 . T C 136.72 PASS AC=1;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 0/1:2,5:7:70:201,0,70:0,2,1,4 chr1 11867044 . T C 237.06 PASS AC=1;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 0/1:15,18:33:99:508,0,337:10,5,12,6 chr1 11876417 . C T 489.01 PASS AC=1;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 0/1:8,5:13:99:175,0,260:8,0,5,0 chr1 11879685 . C T 1324.55 PASS AC=1;AF=0.6;AN=2;DP=1723;MQ=60;set=variant-variant3-variant4-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:30,20:50:99:526,0,866:10,20,6,14 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 1/1:0,72:72:99:2142,215,0:0,0,34,38 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 0/1:14,14:28:99:350,0,352:4,10,4,10 chr1 11888384 . A G 1001.56 PASS AC=1;AF=0.613;AN=2;DP=1673;MQ=60;set=variant-variant3-variant4-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:20,34:54:99:879,0,592:9,11,17,17 chr1 11889468 . A G 1530.75 PASS AC=1;AF=0.617;AN=2;DP=3526;MQ=60;set=variant-variant3-variant4-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:52,47:99:99:1278,0,1266:23,29,18,29 chr1 11896345 . T C 467.96 PASS AC=1;AF=0.536;AN=2;DP=293;FractionInformativeReads=1;MQ=60;set=variant9-variant12-variant13-variant15-variant16-variant17-variant21-variant22-variant23-variant25-variant33-variant34-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:13,16:29:99:594,0,396:2,11,0,16 chr1 11897271 . T C 707.28 PASS AC=1;AF=0.536;AN=2;DP=786;MQ=60;set=variant9-variant12-variant13-variant15-variant16-variant17-variant21-variant22-variant23-variant25-variant33-variant34-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:32,18:50:99:481,0,950:19,13,11,7 chr1 11897592 . A G 174.97 PASS AC=1;AF=0.6;AN=2;DP=2322;MQ=60;set=variant-variant3-variant4-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:30,36:66:99:962,0,730:10,20,12,24 chr1 11898849 . T G 1971.51 PASS AC=1;AF=0.536;AN=2;DP=2570;MQ=60;set=variant9-variant12-variant13-variant15-variant16-variant17-variant21-variant22-variant23-variant25-variant33-variant34-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:64,71:135:99:1733,0,1720:26,38,30,41 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 1/1:0,34:34:99:1175,102,0:0,0,27,7 chr1 11900385 . C T 1503.31 PASS AC=1;AF=0.536;AN=2;DP=1631;MQ=60;set=variant9-variant12-variant13-variant15-variant16-variant17-variant21-variant22-variant23-variant25-variant33-variant34-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:48,55:103:99:1381,0,1241:23,25,26,29 chr1 11900437 . T C 1322 PASS AC=1;AF=0.556;AN=2;DP=954;FractionInformativeReads=1;MQ=60;set=variant12-variant13-variant15-variant17-variant21-variant22-variant23-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:46,51:97:99:1181,0,1118:22,24,21,30 chr1 11900802 . T C 444 PASS AC=1;AF=0.536;AN=2;DP=728;MQ=60;set=variant9-variant12-variant13-variant15-variant16-variant17-variant21-variant22-variant23-variant25-variant33-variant34-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:19,25:44:99:668,0,409:8,11,10,15 chr1 11900825 . G T 517.63 PASS AC=1;AF=0.536;AN=2;DP=736;MQ=60;set=variant9-variant12-variant13-variant15-variant16-variant17-variant21-variant22-variant23-variant25-variant33-variant34-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:17,21:38:99:540,0,445:7,10,9,12 chr1 11901592 . T C 2302.18 PASS AC=1;AF=0.536;AN=2;DP=2353;MQ=60;set=variant9-variant12-variant13-variant15-variant16-variant17-variant21-variant22-variant23-variant25-variant33-variant34-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:84,73:157:99:1545,0,2088:36,48,34,39 chr1 11903010 . G A 3661.75 PASS AC=1;AF=0.536;AN=2;DP=2021;MQ=60;set=variant9-variant12-variant13-variant15-variant16-variant17-variant21-variant22-variant23-variant25-variant33-variant34-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:82,72:154:99:1817,0,2153:45,37,36,36 chr1 11905981 . A G 979.49 PASS AC=1;AF=0.533;AN=2;DP=1007;FractionInformativeReads=1;MQ=60;set=variant9-variant12-variant13-variant15-variant16-variant17-variant21-variant22-variant23-variant25-variant33-variant34-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:16,33:49:99:894,0,397:9,7,16,17 chr1 11906068 . A G 1343.5 PASS AC=1;AF=0.533;AN=2;DP=1643;MQ=60;set=variant9-variant12-variant13-variant15-variant16-variant17-variant21-variant22-variant23-variant25-variant33-variant34-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:38,46:84:99:1290,0,1014:22,16,22,24 chr1 11907603 . G A 1392.78 PASS AC=1;AF=0.556;AN=2;DP=1363;FractionInformativeReads=1;set=variant12-variant13-variant15-variant17-variant21-variant22-variant23-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:77,81:158:99:1967,0,1998:41,36,44,37 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 0/1:62,53:115:99:1247,0,1541:26,36,22,31 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 0/1:78,45:123:99:1070,0,1834:44,34,25,20 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 1/1:0,33:33:99:1209,99,0:0,0,14,19 chr1 11995176 . A G 698.29 PASS AC=1;AF=0.56;AN=2;DP=949;FractionInformativeReads=1;MQ=60;set=variant2-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,6:25:99:155,0,492:6,13,2,4 chr1 12056440 . C T 232.73 PASS AC=1;AF=0.688;AN=2;DP=755;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-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:237,0,192:0,5,0,6 chr1 12058606 . AAAAAC A 1326.88 PASS AC=1;AF=0.732;AN=2;DP=1288;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,16:38:99:606,0,1303:13,9,12,4 chr1 12062205 . A G 984 PASS AC=1;AF=0.732;AN=2;DP=2202;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,39:71:99:1033,0,907:9,23,12,27 chr1 12071680 . A G 3761.37 PASS AC=1;AF=0.732;AN=2;DP=4146;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,43:78:99:1141,0,869:20,15,17,26 chr1 12072518 . G C 2616.67 PASS AC=1;AF=0.73;AN=2;DP=3787;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,32:76:99:727,0,1293:20,24,15,17 chr1 12144219 . A G 109.69 PASS AC=1;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 0/1:15,5:20:98:98,0,412:10,5,4,1 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 0/1:26,23:49:99:856,0,1364:11,15,11,12 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 0/1:27,21:48:99:819,0,1389:11,16,11,10 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 0/1:10,7:17:99:259,0,382:3,7,2,5 chr1 12169988 . G A 173.37 PASS AC=1;AF=0.5;AN=2;DP=40;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,8:26:99:202,0,605:14,4,7,1 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 1/1:0,123:123:99:3606,368,0:0,0,64,59 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 0/1:42,38:80:99:943,0,1004:18,24,14,24 chr1 12183174 . A C 357.78 PASS AC=2;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 1/1:0,47:47:99:1500,141,0:0,0,28,19 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 0/1:15,25:40:99:759,0,435:12,3,22,3 chr1 12198635 . T C 1044.18 PASS AC=2;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 1/1:0,66:66:99:1898,197,0:0,0,30,36 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 1/1:0,45:45:99:1573,135,0:0,0,9,36 chr1 12248942 . A G 3468.32 PASS AC=2;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 1/1:0,106:106:99:4039,318,0:0,0,38,68 chr1 12248965 . A G 2292.58 PASS AC=2;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 1/1:0,61:61:99:2801,196,0:0,0,14,47 chr1 12249020 . C T 715.15 PASS AC=2;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 1/1:0,15:15:45:661,45,0:0,0,1,14 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 1/1:0,12:12:36:525,36,0:0,0,2,10 chr1 12251191 . T A 649.44 PASS AC=2;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 1/1:0,26:26:78:934,78,0:0,0,6,20 chr1 12251765 . T G 2813.6 PASS AC=2;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 1/1:0,105:105:99:3154,318,0:0,0,58,47 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 1/1:0,157:157:99:4816,470,0:0,0,89,68 chr1 12252333 . CTGTG CTGTGTG,C,CTG 269.89 PASS AC=0,1,1;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 2/3:14:90:0,0,12,2 chr1 12252892 . C T 557.11 PASS AC=2;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 1/1:0,17:17:51:505,51,0:0,0,10,7 chr1 12252955 . T G 1345.87 PASS AC=2;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 1/1:0,51:51:99:1744,153,0:0,0,35,16 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 0/1:14,15:29:99:477,0,343:5,9,3,12 chr1 12254201 . G A 1155.02 PASS AC=2;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 1/1:0,47:47:99:1727,141,0:0,0,13,34 chr1 12261972 . A G 1838.79 PASS AC=2;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 1/1:0,62:62:99:2013,186,0:0,0,31,31 chr1 12266591 . A G 336.68 PASS AC=2;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 1/1:0,12:12:36:405,36,0:0,0,9,3 chr1 12266612 . A G 98.3 PASS AC=2;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 1/1:0,12:12:36:397,36,0:0,0,9,3 chr1 12267265 . A G 633.28 PASS AC=2;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 1/1:1,44:45:99:1371,125,0:1,0,16,28 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 1/1:0,39:39:99:1313,117,0:0,0,12,27 chr1 12309478 . A G 1062.18 PASS AC=1;AF=0.5;AN=2;DP=72;FS=1.965;FractionInformativeReads=1;MQ=60;MQRankSum=-2.138;QD=14.75;ReadPosRankSum=-0.136;SOR=0.965;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:31,41:72:99:1090,0,725:14,17,16,25 chr1 12339619 . A T 658.98 PASS AC=1;AF=0.545;AN=2;DP=1381;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant14-variant15-variant19-variant21-variant22-variant23-variant27-variant29-variant30-variant31-variant33-variant36-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,24:53:99:554,0,670:16,13,10,14 chr1 12401868 . A C 1869.57 PASS AC=2;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 1/1:0,85:85:99:2691,255,0:0,0,55,30 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 1/1:0,28:28:84:1019,84,0:0,0,5,23 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 1/1:0,177:177:99:5265,530,0:0,0,89,88 chr1 12570579 . C CTG,CTGTG,CTGTGTG,CTGTGTGTGTG 473.63 PASS AC=2,0,0,0;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 1/1:26:24:0,2,7,17 chr1 12638964 . T C 3833.75 PASS AC=2;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 1/1:0,155:155:99:4671,464,0:0,0,75,80 chr1 12639018 . C T 3619.05 PASS AC=2;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 1/1:0,144:144:99:4751,430,0:0,0,75,69 chr1 12639168 . A G 4262.3 PASS AC=2;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 1/1:0,175:175:99:5570,525,0:0,0,85,90 chr1 12677525 . GA G 107.04 PASS AC=2;AF=0.786;AN=2;DP=133;FS=0;set=variant-variant2-variant4-variant8-variant23-variant29-variant36 GT:AD:DP:GQ:PL:SB 1/1:1,9:10:8:117,8,0:0,1,2,7 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 1/1:0,66:66:99:2260,198,0:0,0,46,20 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 1/1:0,160:160:99:4691,479,0:0,0,89,71 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 1/1:0,216:216:99:6309,647,0:0,0,103,113 chr1 12779560 . T C 6294.04 PASS AC=1;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 0/1:90,83:173:99:1802,0,2142:41,49,40,43 chr1 12779618 . T C 3901.77 PASS AC=1;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 0/1:54,52:106:99:1302,0,1390:21,33,19,33 chr1 12785093 . T G 3006.34 PASS AC=1;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 0/1:31,37:68:99:880,0,722:17,14,21,16 chr1 12785494 . G T 5028.71 PASS AC=1;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 0/1:57,71:128:99:1710,0,1262:25,32,35,36 chr1 12786070 . A G 1374.93 PASS AC=1;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 0/1:24,20:44:99:561,0,682:9,15,9,11 chr1 12786273 . T C 1799.13 PASS AC=1;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 0/1:32,38:70:99:1023,0,752:15,17,19,19 chr1 12786323 . C T 740.06 PASS AC=1;AF=0.5;AN=2;DP=566;MQ=60;set=variant11-variant12-variant19-variant23-variant29-variant31-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:47,31:78:99:785,0,1139:23,24,16,15 chr1 12786363 . C T 1871.6 PASS AC=1;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 0/1:31,43:74:99:1040,0,845:15,16,19,24 chr1 12786417 . A G 1421.88 PASS AC=1;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 0/1:33,32:65:99:779,0,853:18,15,13,19 chr1 12786444 . G A 1236.83 PASS AC=1;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 0/1:30,23:53:99:581,0,756:14,16,9,14 chr1 12787632 . C T 1817.7 PASS AC=1;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 0/1:23,31:54:99:821,0,588:12,11,14,17 chr1 12787980 . A G 1605.21 PASS AC=1;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 0/1:42,21:63:99:559,0,1204:25,17,11,10 chr1 12788113 . A G 883.99 PASS AC=1;AF=0.5;AN=2;DP=446;MQ=60;set=variant11-variant12-variant19-variant23-variant29-variant31-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:27,31:58:99:883,0,601:13,14,9,22 chr1 12788406 . G A 572.58 PASS AC=1;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 0/1:7,4:11:66:66,0,203:5,2,2,2 chr1 12820870 . T C 1612.88 PASS AC=1;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 0/1:43,39:82:99:1004,0,1173:17,26,15,24 chr1 12822162 . A G 277.08 PASS AC=1;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 0/1:2,4:6:70:121,0,70:0,2,1,3 chr1 12822586 . T C 255.13 PASS AC=1;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 0/1:2,4:6:31:121,0,31:1,1,3,1 chr1 12823667 . G A 2641.79 PASS AC=1;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 0/1:45,39:84:99:1050,0,1314:29,16,24,15 chr1 12835868 . T C 2269.28 PASS AC=1;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 0/1:65,51:116:99:1353,0,1612:31,34,26,25 chr1 12836250 . C T 1267.47 PASS AC=1;AF=0.5;AN=2;DP=82;FS=4.708;FractionInformativeReads=1;MQ=60;MQRankSum=1.661;QD=15.46;ReadPosRankSum=0.708;SOR=0.321;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:30,52:82:99:1296,0,876:8,22,20,32 chr1 12837463 . C T 2040.24 PASS AC=1;AF=0.556;AN=2;DP=1045;set=variant15-variant16-variant20-variant22-variant23-variant30-variant36-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:56,52:108:99:1379,0,1341:31,25,27,25 chr1 12837634 . T A,C 3692.81 PASS AC=1,0;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 0/1:137:99:36,33,35,33 chr1 12837840 . G C 2198.78 PASS AC=1;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 0/1:28,36:64:99:899,0,778:10,18,12,24 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 0/1:32,14:46:99:213,0,863:23,9,9,5 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 0/1:58,28:86:99:998,0,2411:37,21,16,12 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 0/1:57,28:85:99:995,0,2433:36,21,16,12 chr1 12854041 . T C 1681.45 PASS AC=1;AF=0.5;AN=2;DP=5169;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:69,29:98:99:1032,0,2676:42,27,16,13 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 0/1:82,23:105:99:259,0,3293:47,35,12,11 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 0/1:112,21:133:99:533,0,4800:59,53,9,12 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 0/1:115,21:136:99:533,0,4866:60,55,9,12 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 0/1:110,15:125:99:380,0,4645:57,53,6,9 chr1 12854530 . C G 6594.25 PASS AC=1;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 0/1:85,60:145:99:1278,0,2060:36,49,31,29 chr1 12854842 . G C 60.54 PASS AC=1;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 0/1:11,6:17:99:201,0,279:7,4,4,2 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 1/1:0,187:187:99:8233,566,0:0,0,80,107 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 1/1:0,175:175:99:7955,542,0:0,0,76,99 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 0/1:120,27:147:99:257,0,2735:54,66,13,14 chr1 12856079 . C T 135.54 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2116;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:78,16:94:99:134,0,1799:28,50,6,10 chr1 12887054 . T C,G 121.14 PASS AC=0,1;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 0/2:36:99:21,5,7,3 chr1 12887549 . T C 8709.88 PASS AC=1;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 0/1:158,155:313:99:3848,0,3797:78,80,79,76 chr1 12888601 . G GC 982.02 PASS AC=2;AF=0.943;AN=2;DP=2638;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1605,147,0:0,0,24,25 chr1 12888629 . A G 197.44 PASS AC=1;AF=0.5;AN=2;DP=1809;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant13-variant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant41-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,12:43:99:257,0,788:14,17,10,2 chr1 12898472 . C T 2121.05 PASS AC=1;AF=0.932;AN=2;DP=4750;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:51,52:103:99:1285,0,1363:30,21,27,25 chr1 12898654 . A G 1164.51 PASS AC=1;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 0/1:74,61:135:99:1287,0,1714:37,37,27,34 chr1 12898667 . C G 1413.79 PASS AC=1;AF=0.533;AN=2;DP=1945;set=variant2-variant6-variant11-variant12-variant16-variant19-variant21-variant23-variant28-variant29-variant30-variant32-variant33-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:71,49:120:99:1144,0,2701:35,36,20,29 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 0/1:46,64:110:99:1638,0,1762:18,28,31,33 chr1 12898775 . C G 429.9 PASS AC=2;AF=0.719;AN=2;DP=1121;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant20-variant21-variant23-variant25-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:2172,147,0:0,0,17,32 chr1 12898778 . T A 429.9 PASS AC=2;AF=0.719;AN=2;DP=1095;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant20-variant21-variant23-variant25-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:2136,144,0:0,0,17,30 chr1 12898833 . G C 231.03 PASS AC=1;AF=0.694;AN=2;DP=364;FractionInformativeReads=1;set=variant2-variant3-variant6-variant7-filterInvariant9-variant12-variant15-variant21-filterInvariant22-variant23-variant28-variant29-variant33-variant36-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:18,9:27:99:153,0,538:5,13,3,6 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 0/1:63,45:108:99:1739,0,4374:43,20,30,15 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 0/1:64,46:110:99:1730,0,4458:43,21,30,16 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 0/1:66,46:112:99:1730,0,4458:44,22,30,16 chr1 12907316 . T C 1544 PASS AC=1;AF=0.5;AN=2;DP=6705;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:92,49:141:99:1014,0,2374:55,37,26,23 chr1 12907350 . C T 2202.88 PASS AC=1;AF=0.5;AN=2;DP=7839;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:114,43:157:99:1455,0,4620:63,51,17,26 chr1 12907351 . A G 2244.87 PASS AC=1;AF=0.5;AN=2;DP=7873;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:114,42:156:99:1455,0,4620:63,51,16,26 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 0/1:132,36:168:99:1038,0,5630:70,62,13,23 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 0/1:141,34:175:99:1019,0,5907:76,65,11,23 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 0/1:141,33:174:99:994,0,5941:76,65,10,23 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 0/1:148,27:175:99:854,0,6011:78,70,6,21 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 0/1:157,18:175:99:288,0,6531:80,77,1,17 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 0/1:164,20:184:99:331,0,6628:81,83,3,17 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 0/1:162,22:184:99:426,0,6712:71,91,4,18 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 0/1:157,22:179:99:445,0,6632:66,91,4,18 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 0/1:153,20:173:99:370,0,6523:65,88,4,16 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 0/1:152,18:170:99:376,0,6439:65,87,4,14 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 0/1:152,19:171:99:376,0,6439:65,87,4,15 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 0/1:142,19:161:99:367,0,5980:61,81,4,15 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 0/1:140,19:159:99:370,0,5938:60,80,4,15 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 0/1:134,16:150:99:193,0,3610:58,76,3,13 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 0/1:117,14:131:99:233,0,4889:48,69,3,11 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 0/1:119,14:133:99:224,0,5028:49,70,3,11 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 0/1:120,14:134:99:221,0,5070:49,71,3,11 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 0/1:119,14:133:99:221,0,5070:48,71,3,11 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 0/1:109,14:123:99:230,0,4955:44,65,3,11 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 0/1:97,14:111:99:281,0,4232:40,57,3,11 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 0/1:98,14:112:99:284,0,4190:41,57,3,11 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 0/1:176,40:216:99:1147,0,7217:89,87,33,7 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 0/1:173,44:217:99:1306,0,7342:89,84,36,8 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 0/1:176,57:233:99:2017,0,7417:87,89,44,13 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 0/1:174,63:237:99:2122,0,7117:86,88,49,14 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 0/1:173,63:236:99:2122,0,7117:86,87,49,14 chr1 12907837 . C T 4253.12 PASS AC=1;AF=0.5;AN=2;DP=15041;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:159,121:280:99:3064,0,4363:76,83,85,36 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 0/1:204,173:377:99:4372,0,5433:128,76,91,82 chr1 12908236 . G T 2708.3 PASS AC=1;AF=0.5;AN=2;DP=8491;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:166,68:234:99:2147,0,8330:58,108,16,52 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 0/1:144,53:197:99:1778,0,7989:45,99,12,41 chr1 12918675 . CCAGCAG C 454.71 PASS AC=1;AF=0.55;AN=2;DP=454;MQ=60;set=variant2-variant8-variant12-variant21-variant23-variant28-variant29-variant33-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:13,17:30:99:660,0,1000:9,4,13,4 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 0/1:26,6:32:99:164,0,1565:20,6,5,1 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 0/1:28,6:34:99:164,0,1565:21,7,5,1 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 0/1:142,28:170:99:707,0,7500:46,96,16,12 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 0/1:113,27:140:99:724,0,6902:38,75,13,14 chr1 12942414 . G T 101.4 PASS AC=1;AF=0.5;AN=2;DP=1677;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:32,13:45:99:389,0,1433:3,29,1,12 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 0/1:27,5:32:99:129,0,1476:1,26,0,5 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 0/1:15,16:31:99:325,0,349:11,4,11,5 chr1 12987951 . C T 97.77 DRAGENHardSNP AC=1;AF=0.516;AN=2;DP=3156;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:61,42:103:99:700,0,1216:31,30,21,21 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 0/1:59,109:168:99:2660,0,1414:44,15,85,24 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 0/1:174,211:385:99:4355,0,3624:79,95,80,131 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 0/1:53,30:83:99:778,0,1364:18,35,0,30 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 0/1:44,14:58:99:291,0,1188:13,31,0,14 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 0/1:34,8:42:68:68,0,957:11,23,0,8 chr1 13013173 . A G 61.77 DRAGENHardSNP AC=1;AF=0.75;AN=2;DP=180;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:26,13:39:99:465,0,1951:15,11,2,11 chr1 13013178 . C T 49.73 DRAGENHardSNP AC=1;AF=0.722;AN=2;DP=160;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:28,13:41:99:459,0,2061:16,12,2,11 chr1 13013185 . T A 34.45 DRAGENHardSNP AC=1;AF=0.75;AN=2;DP=106;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:28,10:38:99:462,0,1938:18,10,1,9 chr1 13036587 . C T 2233.04 DRAGENHardSNP AC=1;AF=0.716;AN=2;DP=6391;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:42,116:158:99:2395,0,620:26,16,58,58 chr1 13036654 . C T 630.29 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2150;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:102,23:125:99:221,0,2190:45,57,9,14 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 0/1:124,50:174:99:1067,0,3244:68,56,33,17 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 0/1:170,58:228:99:947,0,5800:77,93,25,33 chr1 13052907 . T C 5232.75 PASS AC=1;AF=0.636;AN=2;DP=10166;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:90,88:178:99:2690,0,2088:36,54,31,57 chr1 13141561 . C T 86.58 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=540;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:119,0,252:9,2,5,2 chr1 13141835 . C T 567.97 DRAGENHardSNP AC=2;AF=0.733;AN=2;DP=1254;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:674,75,0:0,0,7,18 chr1 13182899 . A G 282.1 PASS AC=1;AF=0.5;AN=2;DP=443;set=variant2-variant3-variant4-filterInvariant5-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant20-variant23-variant24-variant26-filterInvariant30-variant37-variant40-variant41-variant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:73:73,0,162:4,0,2,1 chr1 13183187 . A G 56.44 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1314;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:83,6:89:86:86,0,5717:36,47,3,3 chr1 13183188 . T A 62.46 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1306;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:83,5:88:86:86,0,5717:36,47,2,3 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 0/1:77,6:83:59:59,0,5543:31,46,4,2 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 0/1:72,10:82:99:245,0,5131:28,44,8,2 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 0/1:63,16:79:99:521,0,4335:25,38,14,2 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 0/1:60,17:77:99:530,0,4114:23,37,15,2 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 0/1:58,19:77:99:659,0,3946:23,35,16,3 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 0/1:57,20:77:99:749,0,3822:22,35,17,3 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 0/1:55,22:77:99:755,0,3668:21,34,18,4 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 0/1:52,24:76:99:851,0,3368:20,32,20,4 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 0/1:51,24:75:99:851,0,3368:19,32,20,4 chr1 13183439 . T C 9192.24 PASS AC=2;AF=0.784;AN=2;DP=18306;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,275:275:99:8051,824,0:0,0,143,132 chr1 13183511 . T C 5032.46 PASS AC=1;AF=0.5;AN=2;DP=15315;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:85,150:235:99:5638,0,2844:44,41,56,94 chr1 13183528 . A C 4481.77 PASS AC=1;AF=0.5;AN=2;DP=13615;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:78,122:200:99:5116,0,2996:40,38,39,83 chr1 13183530 . A G 272.61 PASS AC=1;AF=0.5;AN=2;DP=4488;set=filterInvariant-filterInvariant6-filterInvariant7-filterInvariant11-variant14-filterInvariant16-filterInvariant18-filterInvariant21-filterInvariant22-variant23-variant29-filterInvariant33-filterInvariant40-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:157,38:195:99:671,0,5473:65,92,11,27 chr1 13183532 . C T 4088.45 PASS AC=1;AF=0.5;AN=2;DP=13070;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:76,114:190:99:4661,0,2957:37,39,35,79 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 0/1:77,112:189:99:4625,0,2876:38,39,34,78 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 0/1:76,48:124:99:1644,0,3058:35,41,3,45 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 0/1:74,36:110:99:1436,0,3014:34,40,1,35 chr1 13183631 . A T 126.66 PASS AC=1;AF=0.5;AN=2;DP=819;FractionInformativeReads=1;set=filterInvariant21-filterInvariant23-filterInvariant24-variant33-filterInvariant34-variant40 GT:AD:DP:GQ:PL:SB 0/1:111,13:124:99:202,0,4539:56,55,0,13 chr1 13183634 . G A 126.66 PASS AC=1;AF=0.5;AN=2;DP=803;FractionInformativeReads=1;set=filterInvariant21-filterInvariant23-filterInvariant24-variant33-filterInvariant34-variant40 GT:AD:DP:GQ:PL:SB 0/1:107,11:118:99:208,0,4475:55,52,0,11 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 0/1:24,8:32:99:102,0,959:6,18,4,4 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 0/1:8,20:28:99:657,0,276:4,4,5,15 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 0/1:307,51:358:99:337,0,7858:99,208,16,35 chr1 13219736 . ATTTTTTT ATT,ATTTT,ATTT,ATTTTT,AGTTTTTTTT,AGTTTTTTTTT,A,ATTTTTT,AGTTTTTTTTTTT 209.55 PASS AC=0,0,0,2,0,0,0,0,0;AF=0.019,0.056,0.037,0.259,0.056,0.056,0.019,0.093,0.019;AN=2;DP=972;set=variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant14-variant16-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant36-variant38-variant39-variant40-variant42-variant43 GT:DP:GQ:SB 4/4:5:15:0,0,0,5 chr1 13353904 . A C 1201.81 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=75;FS=0;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:2,2:4:37:78,0,37:1,1,1,1 chr1 13353910 . G C 70.68 PASS AC=1;AF=0.571;AN=2;DP=210;set=filterInvariant11-filterInvariant18-variant23-filterInvariant29-filterInvariant32-filterInvariant33-filterInvariant37 GT:AD:DP:GQ:PL:SB 0/1:0,2:2:37:78,0,37:0,0,1,1 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 0/1:14,5:19:94:94,0,363:11,3,4,1 chr1 13413926 . A G 184.77 DRAGENHardSNP AC=2;AF=0.625;AN=2;DP=86;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:130,12,0:0,0,4,0 chr1 13413961 . G C 811.55 DRAGENHardSNP AC=2;AF=0.66;AN=2;DP=877;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:620,69,0:0,0,16,7 chr1 13414059 . C T 3000.82 DRAGENHardSNP AC=2;AF=0.56;AN=2;DP=4085;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:2,65:67:99:1548,151,0:1,1,32,33 chr1 13448180 . A G 496.53 DRAGENHardSNP AC=1;AF=0.86;AN=2;DP=514;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:2,7:9:60:330,0,60:1,1,7,0 chr1 13448184 . C T 652.76 DRAGENHardSNP AC=1;AF=0.86;AN=2;DP=632;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:2,8:10:60:330,0,60:1,1,8,0 chr1 13448185 . G C 229.49 DRAGENHardSNP AC=1;AF=0.703;AN=2;DP=607;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:7,3:10:65:65,0,220:6,1,3,0 chr1 13448199 . C T 856.08 DRAGENHardSNP AC=2;AF=0.966;AN=2;DP=1358;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:2,21:23:20:576,20,0:1,1,17,4 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 1/1:0,96:96:99:2359,287,0:0,0,48,48 chr1 13448351 . T C 1765.7 DRAGENHardSNP AC=2;AF=0.943;AN=2;DP=3647;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:1743,198,0:0,0,26,40 chr1 13695787 . C G 1574.97 DRAGENHardSNP AC=2;AF=0.989;AN=2;DP=2527;FS=0;MQRankSum=-2.1;ReadPosRankSum=-0.853;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1353,150,0:0,0,34,16 chr1 13695816 . G A 2318.89 DRAGENHardSNP AC=2;AF=0.989;AN=2;DP=4360;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2432,276,0:0,0,58,34 chr1 13695974 . T C 960.66 DRAGENHardSNP AC=2;AF=0.989;AN=2;DP=2019;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1032,114,0:0,0,11,27 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 0/1:45,19:64:99:295,0,1902:15,30,19,0 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 0/1:50,19:69:99:271,0,2140:19,31,19,0 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 0/1:30,40:70:99:1054,0,762:19,11,24,16 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 0/1:40,32:72:99:897,0,1034:16,24,14,18 chr1 13937281 . T C 229.81 PASS AC=1;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 0/1:4,10:14:99:327,0,137:1,3,2,8 chr1 13940365 . CTTT CT,CTT,CTTTT,C 63.86 PASS AC=1,0,0,0;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 0/1:10:60:1,2,3,4 chr1 13940864 . C G 5238.77 PASS AC=1;AF=0.943;AN=2;DP=8146;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:86,88:174:99:2033,0,2106:42,44,47,41 chr1 13943653 . AT A,ATT 245.53 PASS AC=1,0;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 0/1:36:99:4,9,8,15 chr1 13943897 . T G 968.99 PASS AC=1;AF=0.682;AN=2;DP=902;set=variant-variant2-variant3-variant4-variant5-variant9-variant10-variant11-variant16-variant17-variant23-variant24-variant27-variant28-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:24,23:47:99:572,0,545:10,14,11,12 chr1 13944236 . C CTT 1897.62 PASS AC=1;AF=0.977;AN=2;DP=2092;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:16,10:26:99:372,0,666:11,5,5,5 chr1 14031732 . G C 3749.47 PASS AC=2;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 1/1:0,104:104:99:3322,311,0:0,0,63,41 chr1 14031756 . A C 4514.47 PASS AC=2;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 1/1:0,125:125:99:3723,372,0:0,0,67,58 chr1 14143003 . A G 1398.41 PASS AC=1;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 0/1:56,40:96:99:925,0,1212:31,25,22,18 chr1 14507057 . A G 1338.02 PASS AC=2;AF=0.526;AN=2;DP=2302;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant18-variant20-variant21-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant37-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:3583,345,0:0,0,56,59 chr1 14925105 . T G 443.87 PASS AC=2;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 1/1:0,24:24:72:775,72,0:0,0,14,10 chr1 15272687 . C T 808.97 PASS AC=2;AF=0.611;AN=2;DP=349;MQ=60;set=variant9-variant11-variant12-variant16-variant23-variant25-variant31-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:946,84,0:0,0,9,19 chr1 15272745 . T C 386.9 PASS AC=2;AF=0.7;AN=2;DP=164;FractionInformativeReads=1;MQ=60;set=variant9-variant11-variant12-variant16-variant23-variant25-variant31-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:541,39,0:0,0,2,11 chr1 15370427 . G A 520.64 PASS AC=1;AF=0.5;AN=2;DP=55;FS=1.187;FractionInformativeReads=1;MQ=60;MQRankSum=-0.499;QD=9.47;ReadPosRankSum=-0.219;SOR=0.97;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:35,20:55:99:549,0,939:24,11,15,5 chr1 15370458 . G C 727.08 PASS AC=1;AF=0.5;AN=2;DP=238;FractionInformativeReads=1;MQ=60;set=variant23-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,28:71:99:755,0,1073:25,18,20,8 chr1 15427783 . G T 75.23 PASS AC=1;AF=0.545;AN=2;DP=129;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant15-variant16-variant20-variant23-variant27-variant28-variant33-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:7,3:10:99:105,0,191:4,3,2,1 chr1 15427982 . G A 602.89 PASS AC=1;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 0/1:45,32:77:99:748,0,1139:24,21,18,14 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 1/1:0,43:43:99:1560,129,0:0,0,14,29 chr1 15438990 . G A 827.32 PASS AC=1;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 0/1:68,64:132:99:1486,0,1455:34,34,38,26 chr1 15439083 . A AAGGTCTTTTTTTTCTTCTCCCAGCGGC 1950.63 PASS AC=1;AF=0.684;AN=2;DP=3492;MQ=60;set=variant2-variant3-variant4-variant5-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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,17:54:99:511,0,2436:15,22,7,10 chr1 15441275 . C T 269.01 PASS AC=2;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 1/1:0,33:33:99:997,99,0:0,0,18,15 chr1 15441494 . G A 652.82 PASS AC=2;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 1/1:0,59:59:99:1732,174,0:0,0,31,28 chr1 15441926 . C T 636.82 PASS AC=2;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 1/1:0,99:99:99:3024,297,0:0,0,46,53 chr1 15442028 . T C 446.07 PASS AC=2;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 1/1:0,43:43:99:1363,128,0:0,0,17,26 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 0/1:20,23:43:99:584,0,554:7,13,10,13 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 0/1:40,36:76:99:980,0,1038:19,21,18,18 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 1/1:0,50:50:99:1656,150,0:0,0,23,27 chr1 15443426 . C T 1313.99 PASS AC=1;AF=0.5;AN=2;DP=880;FractionInformativeReads=1;MQ=60;set=variant3-variant12-variant16-variant19-variant20-variant23-variant27-variant28-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,29:65:99:725,0,879:17,19,16,13 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 0/1:25,32:57:99:747,0,645:14,11,15,17 chr1 15443631 . C G 1306.17 PASS AC=1;AF=0.5;AN=2;DP=1032;MQ=60;set=variant3-variant12-variant16-variant19-variant20-variant23-variant27-variant28-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,37:77:99:973,0,938:23,17,19,18 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 1/1:0,71:71:99:2174,213,0:0,0,31,40 chr1 15443859 . T C 608.99 PASS AC=2;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 1/1:0,59:59:99:1907,177,0:0,0,32,27 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 0/1:40,26:66:99:600,0,1049:22,18,13,13 chr1 15444288 . C T 735.99 PASS AC=2;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 1/1:0,60:60:99:1846,180,0:0,0,31,29 chr1 15444487 . G A 338.02 PASS AC=2;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 1/1:0,45:45:99:1410,134,0:0,0,16,29 chr1 15444563 . T C 201.9 PASS AC=2;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 1/1:0,17:17:51:578,51,0:0,0,4,13 chr1 15444643 . A G 87.74 PASS AC=2;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 1/1:0,4:4:12:180,12,0:0,0,0,4 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 0/1:14,12:26:99:461,0,976:7,7,3,9 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 0/1:14,12:26:99:461,0,976:7,7,3,9 chr1 15479283 . G A 422.34 PASS AC=1;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 0/1:13,10:23:99:247,0,358:6,7,3,7 chr1 15480286 . G C 1140.39 PASS AC=1;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 0/1:81,64:145:99:1428,0,1757:42,39,33,31 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 1/1:0,46:46:99:1567,138,0:0,0,11,35 chr1 15480493 . G T 79.67 PASS AC=1;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 0/1:7,5:12:99:189,0,279:3,4,1,4 chr1 15480494 . C A 79.67 PASS AC=1;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 0/1:7,5:12:99:189,0,279:3,4,1,4 chr1 15490865 . T A 1124.93 PASS AC=1;AF=0.529;AN=2;DP=1439;MQ=60;set=variant-variant3-variant6-variant9-variant12-variant15-variant17-variant18-variant19-variant22-variant23-variant28-variant31-variant32-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:51,44:95:99:1096,0,1232:28,23,24,20 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 1/1:0,158:158:99:4566,473,0:0,0,86,72 chr1 15497832 . T C 1525.62 PASS AC=1;AF=0.583;AN=2;DP=1871;MQ=60;set=variant3-variant6-variant14-variant16-variant20-variant23-variant26-variant27-variant29-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,74:149:99:1778,0,1789:31,44,35,39 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 1/1:0,122:122:99:3738,365,0:0,0,53,69 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 1/1:0,24:24:72:852,72,0:0,0,4,20 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 0/1:33,20:53:99:483,0,801:19,14,13,7 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 1/1:0,91:91:99:2974,273,0:0,0,54,37 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 0/1:155,171:326:99:3946,0,3709:67,88,72,99 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 0/1:22,28:50:99:729,0,570:10,12,15,13 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 0/1:14,29:43:99:815,0,433:5,9,17,12 chr1 15546872 . CAAA CA,CAA,C 1341.68 PASS AC=1,1,0;AF=0.341,0.466,0.011;AN=2;DP=3897;set=Intersection GT:DP:GQ:SB 1/2:52:99:1,1,37,13 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 0/1:2,4:6:31:110,0,31:1,1,3,1 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 0/1:3,7:10:51:149,0,51:2,1,4,3 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 0/1:5,7:12:99:143,0,154:5,0,3,4 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 0/1:5,8:13:99:185,0,173:5,0,4,4 chr1 15573775 . A G 498.51 PASS AC=2;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 1/1:0,15:15:45:569,45,0:0,0,10,5 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 0/1:21,17:38:99:398,0,485:11,10,8,9 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 0/1:6,8:14:99:174,0,134:2,4,3,5 chr1 15578195 . T C 299.56 PASS AC=2;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 1/1:0,31:31:92:1060,92,0:0,0,25,6 chr1 15578513 . A G 538.58 PASS AC=1;AF=0.5;AN=2;DP=141;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant16-variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:16,7:23:99:247,0,520:2,14,1,6 chr1 15616122 . C T 2237.18 PASS AC=1;AF=0.5;AN=2;DP=359;FractionInformativeReads=1;MQ=60;set=variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:88,91:179:99:2265,0,1945:42,46,44,47 chr1 15616139 . G A 1592.72 PASS AC=2;AF=0.589;AN=2;DP=5144;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant30-variant33-variant34-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,155:155:99:4543,463,0:0,0,72,83 chr1 15616183 . T C 3686.37 PASS AC=2;AF=0.625;AN=2;DP=4629;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3506,347,0:0,0,47,69 chr1 15671483 . G A 303.2 PASS AC=2;AF=0.633;AN=2;DP=932;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant34-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:86:897,86,0:0,0,19,10 chr1 15687059 . A G 492.92 PASS AC=1;AF=0.633;AN=2;DP=652;MQ=60;set=variant13-variant15-variant17-variant21-variant23-variant25-variant26-variant32-variant34-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,24:51:99:614,0,653:16,11,15,9 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 0/1:6,4:10:99:135,0,219:2,4,1,3 chr1 15701355 . T G 171.14 PASS AC=1;AF=0.5;AN=2;DP=54;FS=0;MQ=60;set=variant2-variant7-variant23-variant24-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:99:130,0,139:1,2,1,4 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 0/2:8:99:2,4,1,1 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 0/1:8,22:30:99:556,0,177:3,5,7,15 chr1 15707137 . C T 1479.34 PASS AC=1;AF=0.5;AN=2;DP=1363;FractionInformativeReads=1;MQ=60;set=variant4-variant16-variant17-variant22-variant23-variant24-variant26-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,52:113:99:1294,0,1435:26,35,27,25 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 0/1:25,17:42:99:392,0,691:9,16,9,8 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 0/1:73,47:120:99:1161,0,1731:38,35,21,26 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 0/1:50,79:129:99:1925,0,997:26,24,47,32 chr1 15709669 . C T 1825.35 PASS AC=1;AF=0.5;AN=2;DP=416;MQ=60;set=variant2-variant23-variant24 GT:AD:DP:GQ:PL:SB 0/1:85,30:115:99:621,0,2190:34,51,9,21 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 0/1:1,4:5:31:84,0,31:1,0,2,2 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 0/1:9,24:33:99:559,0,225:2,7,11,13 chr1 15710493 . CAT C 37.73 PASS AC=1;AF=0.5;AN=2;DP=93;MQ=60;set=variant-variant4-variant16-variant19-variant22-variant23-variant24-variant26-variant34-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:65:183,0,65:0,2,1,4 chr1 15714716 . G A 369.87 PASS AC=1;AF=0.5;AN=2;DP=282;FractionInformativeReads=1;MQ=60;set=variant4-variant16-variant17-variant22-variant23-variant24-variant26-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,17:29:99:434,0,378:1,11,4,13 chr1 15714774 . T A 91.78 PASS AC=1;AF=0.588;AN=2;DP=132;FS=0;MQ=60;set=variant-variant11-variant16-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant34-variant36-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:130,0,112:0,4,0,5 chr1 15714831 . C T,CCATT 691.48 PASS AC=1,0;AF=0.5,0.316;AN=2;DP=224;FS=0;MQ=60;set=variant11-variant18-variant20-variant3-variant22-variant23-variant25-variant29-variant31-variant32-variant34-variant36-variant38-variant39-variant40-variant4-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:3:13:0,0,3,0 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 0/1:12,5:17:85:85,0,316:8,4,2,3 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 0/1:8,16:24:99:591,0,223:1,7,2,14 chr1 15723843 . G A 1997.9 PASS AC=1;AF=0.594;AN=2;DP=3116;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant36-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:35,50:85:99:1255,0,839:23,12,32,18 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 0/1:130,99:229:99:2181,0,3108:68,62,48,51 chr1 15724033 . A G 4396.34 PASS AC=2;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 1/1:1,229:230:99:6596,678,0:1,0,110,119 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 1/1:0,76:76:99:2243,228,0:0,0,41,35 chr1 15755248 . C T 767.49 PASS AC=1;AF=0.563;AN=2;DP=561;FractionInformativeReads=1;MQ=60;set=variant2-variant18-variant21-variant23-variant24-variant29-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:17,43:60:99:1141,0,379:12,5,28,15 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 1/1:0,37:37:99:1317,111,0:0,0,22,15 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 0/1:19,37:56:99:922,0,512:15,4,27,10 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 0/1:9,8:17:99:265,0,315:7,2,7,1 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 1/1:0,149:149:99:4271,448,0:0,0,85,64 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 1/1:0,181:181:99:6742,545,0:0,0,103,78 chr1 15788269 . A C 4645.38 PASS AC=2;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 1/1:1,174:175:99:5285,515,0:0,1,84,90 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 0/1:165,139:304:99:3037,0,3918:83,82,68,71 chr1 15790013 . G A 4867.97 PASS AC=1;AF=0.611;AN=2;DP=2000;set=variant2-variant3-variant4-variant16-variant23-variant24-variant26-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:84,69:153:99:1585,0,2093:43,41,41,28 chr1 15808198 . C T 277.61 PASS AC=1;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 0/1:10,12:22:99:363,0,256:3,7,2,10 chr1 15808702 . C T 1180.25 PASS AC=1;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 0/1:30,28:58:99:803,0,951:25,5,22,6 chr1 15808767 . G A 2976.57 PASS AC=1;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 0/1:92,89:181:99:2159,0,2269:54,38,51,38 chr1 15808872 . G A 3193.08 PASS AC=1;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 0/1:127,120:247:99:2697,0,2925:56,71,56,64 chr1 15809876 . G A 3003.6 PASS AC=1;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 0/1:114,121:235:99:2998,0,2684:62,52,61,60 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 1/1:0,67:67:99:2191,201,0:0,0,41,26 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 1/1:0,178:178:99:5617,533,0:0,0,116,62 chr1 15813969 . A C 3785.15 PASS AC=1;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 0/1:45,43:88:99:1494,0,1435:5,40,3,40 chr1 15819768 . C A 1160.36 PASS AC=1;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 0/1:13,21:34:99:540,0,306:8,5,14,7 chr1 15820041 . C T 986.3 PASS AC=1;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 0/1:32,27:59:99:748,0,808:15,17,8,19 chr1 15820576 . T A 632.26 PASS AC=1;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 0/1:9,12:21:99:337,0,247:3,6,2,10 chr1 15820607 . A G 457.08 PASS AC=1;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 0/1:3,5:8:78:133,0,78:1,2,1,4 chr1 15820618 . A G 418.54 PASS AC=1;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 0/1:2,5:7:61:150,0,61:0,2,1,4 chr1 15822073 . A G 176.64 PASS AC=1;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 0/1:17,14:31:99:374,0,439:7,10,3,11 chr1 15832383 . G T 632.26 PASS AC=1;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 0/1:11,13:24:99:363,0,344:9,2,9,4 chr1 15832543 . T C 2538 PASS AC=1;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 0/1:44,40:84:99:902,0,1107:23,21,22,18 chr1 15834297 . G A 631.63 PASS AC=1;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 0/1:12,15:27:99:362,0,372:10,2,9,6 chr1 15834491 . G A 1589.46 PASS AC=1;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 0/1:25,19:44:99:413,0,721:9,16,9,10 chr1 15844615 . A G 2454.62 PASS AC=1;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 0/1:37,34:71:99:847,0,884:24,13,22,12 chr1 15844926 . C T 3375.96 PASS AC=1;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 0/1:45,38:83:99:988,0,1179:24,21,14,24 chr1 15845022 . C CTGAG 2249.87 PASS AC=1;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 0/1:35,17:52:99:608,0,1773:11,24,3,14 chr1 15850483 . G A 106.77 PASS AC=1;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 0/1:10,8:18:99:184,0,258:7,3,5,3 chr1 15850553 . C CGGGGGCG,CGAGGGCG 187.73 PASS AC=0,1;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 0/2:29:99:11,7,7,4 chr1 15850613 . G A 725.38 PASS AC=1;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 0/1:17,14:31:99:294,0,412:7,10,7,7 chr1 15850956 . G C 331.77 PASS AC=1;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 0/1:2,2:4:78:78,0,78:0,2,0,2 chr1 15850973 . TC T 313.29 PASS AC=1;AF=0.762;AN=2;DP=157;FS=0;FractionInformativeReads=1;set=variant8-variant11-variant12-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant25-variant27-variant28-variant31-variant34-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:78:78,0,78:0,2,0,2 chr1 15851045 . G C 57.04 PASS AC=1;AF=0.5;AN=2;DP=5;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.358;QD=11.41;ReadPosRankSum=-0.358;SOR=2.78;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:75:85,0,75:0,2,3,0 chr1 15851049 . CAGAA C 41.99 PASS AC=1;AF=0.5;AN=2;DP=7;FS=8.451;FractionInformativeReads=1;MQ=60;MQRankSum=0.937;QD=6;ReadPosRankSum=0.55;SOR=2.788;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:79:79,0,157:1,3,3,0 chr1 15851064 . A ATCCCCGCACTGACCTCACG 456.23 PASS AC=1;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 0/1:2,4:6:67:245,0,67:0,2,2,2 chr1 15853276 . T C 960.31 PASS AC=1;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 0/1:49,46:95:99:1234,0,1248:25,24,26,20 chr1 15853289 . T G 2671.28 PASS AC=1;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 0/1:54,49:103:99:1198,0,1330:28,26,25,24 chr1 15860563 . T A 273.53 PASS AC=1;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 0/1:2,7:9:65:166,0,65:2,0,4,3 chr1 15873386 . A G 1107.07 PASS AC=1;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 0/1:38,36:74:99:958,0,961:15,23,11,25 chr1 15873410 . CTTT CTT,CTTTT,CT,C 70.71 PASS AC=0,0,1,0;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 0/3:29:99:4,8,3,14 chr1 15874961 . T A 1176.39 PASS AC=1;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 0/1:40,55:95:99:1269,0,1008:14,26,22,33 chr1 15894959 . T C 2398.33 PASS AC=1;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 0/1:68,52:120:99:1273,0,1680:34,34,25,27 chr1 15897020 . C T 263.9 PASS AC=1;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 0/1:6,8:14:99:237,0,148:3,3,4,4 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 0/2:239:99:58,77,48,56 chr1 15899314 . AT ATTT,A 69.36 PASS AC=0,1;AF=0.026,0.553;AN=2;DP=284;set=variant3-variant4-variant5-variant8-variant10-variant11-filterInvariant14-variant15-variant19-variant22-variant23-variant25-variant29-variant31-variant32-variant33-variant39-variant40-variant42 GT:DP:GQ:SB 0/2:8:42:1,2,1,4 chr1 15899752 . C CA 170.68 PASS AC=1;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 0/1:9,7:16:99:139,0,199:9,0,7,0 chr1 15909624 . TGAGTACAG T 2482.96 PASS AC=1;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 0/1:38,24:62:99:887,0,1573:22,16,15,9 chr1 15909850 . C G 2429.36 PASS AC=1;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 0/1:59,36:95:99:700,0,1545:23,36,16,20 chr1 15909895 . A G 1315.96 PASS AC=1;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 0/1:36,20:56:99:480,0,975:13,23,6,14 chr1 15911010 . T G 1997.24 PASS AC=1;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 0/1:23,20:43:99:562,0,750:20,3,14,6 chr1 15911031 . T G 2264.77 PASS AC=1;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 0/1:30,27:57:99:766,0,764:21,9,20,7 chr1 15911349 . G A 884.93 PASS AC=1;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 0/1:58,27:85:99:635,0,1572:20,38,9,18 chr1 15911493 . A G 1948.36 PASS AC=1;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 0/1:38,34:72:99:836,0,1003:20,18,19,15 chr1 15911597 . A G 3182.06 PASS AC=1;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 0/1:41,40:81:99:846,0,1083:21,20,23,17 chr1 15911622 . A AG 3795.08 PASS AC=1;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 0/1:41,45:86:99:1343,0,1201:20,21,23,22 chr1 15911730 . T G 611.85 PASS AC=1;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 0/1:22,15:37:99:459,0,555:8,14,2,13 chr1 15959886 . C G 852.99 PASS AC=1;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 0/1:19,10:29:99:279,0,572:14,5,8,2 chr1 15978553 . CTTTTTTT CTTTTTT,CTTTTT,CT,CTT,CTTT,CTTTTTTTTT,C 60.25 PASS AC=2,0,0,0,0,0,0;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 1/1:6:8:1,0,0,5 chr1 15988957 . G A 1092.95 PASS AC=1;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 0/1:15,23:38:99:776,0,455:5,10,7,16 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 0/1:62,23:85:99:266,0,1037:40,22,20,3 chr1 15993338 . A G 714.13 PASS AC=1;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 0/1:35,25:60:99:549,0,863:12,23,10,15 chr1 16011005 . GGGC GGGCGGC,G 1973.66 PASS AC=1,0;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 0/1:90:99:26,18,31,15 chr1 16044584 . T G 1248.06 PASS AC=1;AF=0.5;AN=2;DP=112;FS=1.537;FractionInformativeReads=1;MQ=60;MQRankSum=-0.783;QD=11.14;ReadPosRankSum=0.748;SOR=0.503;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:56,56:112:99:1276,0,1273:22,34,25,31 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 1/1:0,11:11:33:378,33,0:0,0,8,3 chr1 16052121 . G A 520.14 PASS AC=1;AF=0.5;AN=2;DP=42;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.201;QD=12.38;ReadPosRankSum=1.535;SOR=0.482;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:21,21:42:99:548,0,665:4,17,5,16 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 0/1:12,11:23:99:426,0,770:2,10,4,7 chr1 16066773 . AT A 97.2 PASS AC=1;AF=0.5;AN=2;DP=42;FS=0;MQ=60;set=variant13-variant14-variant23 GT:AD:DP:GQ:PL:SB 0/1:2,10:12:11:174,0,11:1,1,3,7 chr1 16070763 . C T 1223.92 PASS AC=1;AF=0.5;AN=2;DP=79;FS=1.955;FractionInformativeReads=0.987;MQ=60;MQRankSum=0.71;QD=15.49;ReadPosRankSum=0.902;SOR=1.027;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:34,44:78:99:1252,0,952:20,14,29,15 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 0/1:24,23:47:99:471,0,587:8,16,9,14 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 0/1:18,20:38:99:432,0,510:4,14,7,13 chr1 16082976 . C T 160.06 PASS AC=1;AF=0.5;AN=2;DP=141;FractionInformativeReads=1;MQ=60;set=variant4-variant20-variant23-variant24-variant26-variant33-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:340,0,462:12,0,9,1 chr1 16090898 . G A 119.17 PASS AC=2;AF=0.625;AN=2;DP=350;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant10-variant11-variant13-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:543,48,0:0,0,12,4 chr1 16091074 . A G 305.15 PASS AC=2;AF=0.596;AN=2;DP=1379;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant10-variant11-variant13-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,48:49:99:1433,100,0:1,0,26,22 chr1 16097237 . G A 144.7 PASS AC=1;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 0/1:9,17:26:99:458,0,246:2,7,4,13 chr1 16111412 . TC T 450.17 PASS AC=1;AF=0.528;AN=2;DP=858;MQ=60;set=variant-variant3-variant6-variant7-variant10-variant11-variant13-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,18:40:99:554,0,700:10,12,8,10 chr1 16112326 . G A 804.19 PASS AC=1;AF=0.528;AN=2;DP=1646;MQ=60;set=variant-variant3-variant6-variant7-variant10-variant11-variant13-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,33:74:99:771,0,1001:23,18,16,17 chr1 16113037 . C T 280.56 PASS AC=1;AF=0.5;AN=2;DP=230;FractionInformativeReads=1;MQ=60;set=variant4-variant20-variant23-variant24-variant26-variant30-variant32-variant33-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,15:31:99:339,0,466:7,9,7,8 chr1 16200163 . A G 6033.08 PASS AC=1;AF=0.548;AN=2;DP=8566;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant12-variant14-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant27-variant30-variant31-variant33-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:194,181:375:99:4604,0,5156:102,92,100,81 chr1 16242620 . C A 935.27 PASS AC=1;AF=0.5;AN=2;DP=505;FractionInformativeReads=1;MQ=60;set=variant22-variant23-variant25-variant30-variant31-variant32 GT:AD:DP:GQ:PL:SB 0/1:48,36:84:99:841,0,1176:29,19,23,13 chr1 16245362 . G A 458.77 PASS AC=1;AF=0.5;AN=2;DP=254;FractionInformativeReads=1;MQ=60;set=variant22-variant23-variant25-variant30-variant31-variant32 GT:AD:DP:GQ:PL:SB 0/1:20,23:43:99:545,0,487:14,6,16,7 chr1 16255644 . C T 487.09 PASS AC=1;AF=0.5;AN=2;DP=268;FractionInformativeReads=1;MQ=60;set=variant22-variant23-variant25-variant30-variant31-variant32 GT:AD:DP:GQ:PL:SB 0/1:21,22:43:99:564,0,641:13,8,10,12 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 1/1:0,59:59:99:1791,177,0:0,0,31,28 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 1/1:0,131:131:99:4234,392,0:0,0,69,62 chr1 16260916 . C T 1102.64 PASS AC=1;AF=0.5;AN=2;DP=644;FractionInformativeReads=1;MQ=60;set=variant22-variant23-variant25-variant30-variant31-variant32 GT:AD:DP:GQ:PL:SB 0/1:48,38:86:99:1009,0,1268:30,18,22,16 chr1 16261814 . C A 3289.61 PASS AC=1;AF=0.5;AN=2;DP=579;FractionInformativeReads=1;MQ=60;set=variant23-variant39 GT:AD:DP:GQ:PL:SB 0/1:148,141:289:99:3318,0,3722:78,70,68,73 chr1 16262404 . C T 598.07 PASS AC=1;AF=0.5;AN=2;DP=377;FractionInformativeReads=1;MQ=60;set=variant22-variant23-variant25-variant30-variant31-variant32 GT:AD:DP:GQ:PL:SB 0/1:35,38:73:99:911,0,973:12,23,14,24 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 1/1:0,13:13:39:455,39,0:0,0,10,3 chr1 16264264 . G A 1963.26 PASS AC=1;AF=0.563;AN=2;DP=1163;MQ=60;set=variant6-variant20-variant22-variant23-variant25-variant30-variant31-variant32 GT:AD:DP:GQ:PL:SB 0/1:76,62:138:99:1649,0,2048:36,40,29,33 chr1 16265060 . CTTT CTT,CT,C 252.48 PASS AC=0,0,1;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 0/3:14:10:3,1,8,2 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 1/1:0,66:66:99:2031,198,0:0,0,29,37 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 1/1:0,43:43:99:1596,129,0:0,0,7,36 chr1 16271180 . T C 1698.29 PASS AC=1;AF=0.5;AN=2;DP=1029;MQ=60;set=variant13-variant22-variant23-variant25-variant30-variant31-variant32 GT:AD:DP:GQ:PL:SB 0/1:63,53:116:99:1260,0,1609:34,29,31,22 chr1 16271260 . G A 1496.52 PASS AC=1;AF=0.525;AN=2;DP=3983;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant12-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant27-variant30-variant31-variant33-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:83,83:166:99:1902,0,2134:52,31,42,41 chr1 16272250 . A G 937.23 PASS AC=2;AF=0.63;AN=2;DP=3721;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant12-variant13-variant14-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3532,348,0:0,0,68,48 chr1 16274769 . C T 1620.29 PASS AC=1;AF=0.5;AN=2;DP=1065;MQ=60;set=variant13-variant22-variant23-variant25-variant30-variant31-variant32 GT:AD:DP:GQ:PL:SB 0/1:56,65:121:99:1690,0,1345:27,29,38,27 chr1 16333142 . GAATA G 847.4 PASS AC=1;AF=0.556;AN=2;DP=861;MQ=60;set=variant2-variant5-variant8-variant9-variant12-variant14-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant27-variant31-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:22,19:41:99:732,0,1204:9,13,11,8 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 1/1:0,87:87:99:2783,261,0:0,0,33,54 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 0/1:10,22:32:99:371,0,168:5,5,12,10 chr1 16340460 . G T 302.94 PASS AC=1;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 0/1:13,19:32:99:518,0,327:8,5,14,5 chr1 16340761 . T C 768.32 PASS AC=1;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 0/1:34,37:71:99:1003,0,817:16,18,14,23 chr1 16340843 . TC T 1176.42 PASS AC=1;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 0/1:31,8:39:99:132,0,847:13,18,2,6 chr1 16340879 . T G 1175.45 PASS AC=1;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 0/1:29,10:39:99:267,0,877:13,16,5,5 chr1 16340951 . A T 866.65 PASS AC=1;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 0/1:25,9:34:99:222,0,650:12,13,7,2 chr1 16341354 . T G 1328.31 PASS AC=1;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 0/1:39,37:76:99:1085,0,840:20,19,17,20 chr1 16341649 . C T,G 545.24 PASS AC=1,0;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 0/1:48:99:11,14,10,13 chr1 16341733 . T C 894.05 PASS AC=1;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 0/1:19,23:42:99:654,0,632:11,8,13,10 chr1 16342237 . A G 765.02 PASS AC=1;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 0/1:24,24:48:99:591,0,597:11,13,9,15 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 1/1:0,127:127:99:3729,380,0:0,0,73,54 chr1 16344402 . G A 1576 PASS AC=1;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 0/1:83,75:158:99:1758,0,2074:48,35,41,34 chr1 16344494 . G A 1814.37 PASS AC=1;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 0/1:71,79:150:99:1760,0,1765:31,40,41,38 chr1 16344625 . C G 870.46 PASS AC=1;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 0/1:46,43:89:99:1107,0,1104:20,26,18,25 chr1 16344664 . G A 2930.76 PASS AC=1;AF=0.697;AN=2;DP=2455;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,38:74:99:987,0,896:17,19,19,19 chr1 16344730 . T C 1292.08 PASS AC=1;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 0/1:26,31:57:99:808,0,727:15,11,16,15 chr1 16344858 . C T 1104.04 PASS AC=1;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 0/1:52,58:110:99:1503,0,1440:23,29,31,27 chr1 16345208 . G A 703.75 PASS AC=1;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 0/1:38,38:76:99:937,0,864:17,21,18,20 chr1 16345619 . T C 726.7 PASS AC=1;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 0/1:36,41:77:99:1074,0,784:22,14,29,12 chr1 16346009 . G GC 4613.99 PASS AC=1;AF=0.697;AN=2;DP=4030;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,45:94:99:1144,0,1260:20,29,15,30 chr1 16348412 . T C 1720.79 PASS AC=1;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 0/1:19,13:32:99:310,0,458:8,11,4,9 chr1 16350123 . C G 223.62 PASS AC=1;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 0/1:19,9:28:99:124,0,534:11,8,5,4 chr1 16351275 . A G 99.4 PASS AC=1;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 0/1:14,17:31:99:500,0,352:10,4,14,3 chr1 16352937 . G A 2036.71 PASS AC=1;AF=0.708;AN=2;DP=5439;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,74:124:99:1819,0,1253:35,15,45,29 chr1 16353400 . T C 1909.22 PASS AC=1;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 0/1:14,23:37:99:759,0,448:2,12,3,20 chr1 16356501 . G A 638.79 PASS AC=1;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 0/1:37,34:71:99:871,0,910:18,19,16,18 chr1 16356583 . C T 2827.27 PASS AC=1;AF=0.697;AN=2;DP=2331;set=variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,30:60:99:707,0,805:10,20,12,18 chr1 16358148 . T C 5555.14 PASS AC=1;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 0/1:110,98:208:99:2282,0,2792:63,47,60,38 chr1 16358520 . T C 308.11 PASS AC=1;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 0/1:18,12:30:99:352,0,504:13,5,9,3 chr1 16358685 . C G 4536.03 PASS AC=1;AF=0.743;AN=2;DP=6496;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,66:149:99:1452,0,1951:40,43,28,38 chr1 16358808 . G A 789.25 PASS AC=1;AF=0.5;AN=2;DP=44;FS=4.911;FractionInformativeReads=1;MQ=60;MQRankSum=-1.754;QD=17.94;ReadPosRankSum=1.134;SOR=1.609;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:18,26:44:99:817,0,581:11,7,20,6 chr1 16358932 . T C 3158.63 PASS AC=1;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 0/1:87,86:173:99:2119,0,1933:46,41,51,35 chr1 16359051 . C A 800.37 PASS AC=1;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 0/1:46,66:112:99:1682,0,1140:14,32,27,39 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 1/1:1,111:112:99:4291,291,0:0,1,41,70 chr1 16359106 . C T 234.13 PASS AC=1;AF=0.714;AN=2;DP=2230;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,38:61:99:1078,0,612:6,17,9,29 chr1 16359123 . A G 480.75 PASS AC=1;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 0/1:17,20:37:99:661,0,561:2,15,2,18 chr1 16360033 . C A 428.89 PASS AC=1;AF=0.5;AN=2;DP=44;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.128;QD=9.75;ReadPosRankSum=0.752;SOR=0.686;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:21,23:44:99:457,0,466:10,11,11,12 chr1 16361737 . A G 37.69 PASS AC=1;AF=0.625;AN=2;DP=20;FS=0;FractionInformativeReads=1;set=variant21-variant23-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:72:136,0,72:0,1,2,0 chr1 16361748 . T C 57.3 PASS AC=1;AF=0.75;AN=2;DP=49;FractionInformativeReads=1;set=variant-filterInvariant7-filterInvariant16-variant21-variant22-variant23-variant25-variant32-variant39-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:1,5:6:69:167,0,69:0,1,5,0 chr1 16361875 . A G 1669.46 PASS AC=2;AF=0.943;AN=2;DP=2160;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1770,135,0:0,0,41,4 chr1 16361916 . G A 2068.07 PASS AC=1;AF=0.733;AN=2;DP=5308;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,75:124:99:1782,0,1215:36,13,47,28 chr1 16362109 . ACT A 445.85 PASS AC=1;AF=0.674;AN=2;DP=1424;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,11:32:99:379,0,2813:3,18,1,10 chr1 16362119 . T C 454.57 PASS AC=1;AF=0.674;AN=2;DP=1076;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,10:30:99:360,0,2776:3,17,0,10 chr1 16362125 . G C 454.57 PASS AC=1;AF=0.683;AN=2;DP=887;FractionInformativeReads=1;set=variant-filterInvariant2-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-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,9:27:99:321,0,2703:3,15,0,9 chr1 16362128 . C T 370.63 PASS AC=1;AF=0.688;AN=2;DP=802;FractionInformativeReads=1;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-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,7:23:99:327,0,2515:3,13,0,7 chr1 16362561 . C G 1341.54 PASS AC=1;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 0/1:80,46:126:99:1107,0,2204:56,24,34,12 chr1 16362621 . G A 3061.94 PASS AC=2;AF=1;AN=2;DP=14271;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,301:301:99:8882,897,0:0,0,176,125 chr1 16362661 . A C 4046.59 PASS AC=1;AF=0.743;AN=2;DP=14418;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:226,169:395:99:3777,0,5332:121,105,91,78 chr1 16366167 . G A 3246.48 PASS AC=1;AF=0.771;AN=2;DP=4221;set=variant-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-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,60:131:99:1470,0,1570:33,38,23,37 chr1 16366213 . T C 3332.5 PASS AC=1;AF=0.703;AN=2;DP=2462;set=variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,37:94:99:1032,0,1317:25,32,11,26 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 1/1:0,59:59:99:2280,180,0:0,0,19,40 chr1 16370314 . G T 873.88 PASS AC=2;AF=0.646;AN=2;DP=935;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant12-variant14-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant37-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:948,106,0:0,0,18,18 chr1 16370873 . C CACACAT,CACACACACAT,CACACACACACACAT,CACACACAT,CACACACACACAT 1073.12 PASS AC=0,1,1,0,0;AF=0.028,0.472,0.278,0.069,0.028;AN=2;DP=1020;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 2/3:11:99:0,0,8,3 chr1 16370899 . G A 453.98 PASS AC=2;AF=0.833;AN=2;DP=1922;set=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-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1352,134,0:0,0,30,15 chr1 16371067 . G T 4980.28 PASS AC=2;AF=0.846;AN=2;DP=7699;MQ=60;set=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-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,159:159:99:4764,475,0:0,0,80,79 chr1 16371872 . C G 789.58 PASS AC=2;AF=0.846;AN=2;DP=1424;MQ=60;set=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-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:849,81,0:0,0,16,11 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 1/1:0,32:32:96:1079,96,0:0,0,18,14 chr1 16372003 . G C 2609.65 PASS AC=2;AF=0.846;AN=2;DP=3315;FractionInformativeReads=1;MQ=60;set=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-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2123,198,0:0,0,42,24 chr1 16372283 . T G 894.74 PASS AC=2;AF=0.808;AN=2;DP=1315;MQ=60;set=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-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,40:42:68:1170,68,0:1,1,21,19 chr1 16372291 . G A 974.57 PASS AC=1;AF=0.5;AN=2;DP=165;FractionInformativeReads=1;MQ=60;set=variant15-variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:21,22:43:99:631,0,395:10,11,7,15 chr1 16373124 . A G 701.47 PASS AC=2;AF=0.902;AN=2;DP=3690;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-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2019,189,0:0,0,35,28 chr1 16373199 . CCTT C 1267.73 PASS AC=2;AF=0.89;AN=2;DP=3963;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-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:2644,178,0:0,0,24,35 chr1 16373282 . A G 328.54 PASS AC=2;AF=0.902;AN=2;DP=1577;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-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:798,66,0:0,0,4,18 chr1 16374504 . C G 937 PASS AC=1;AF=0.5;AN=2;DP=62;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.845;QD=15.11;ReadPosRankSum=0.801;SOR=0.603;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:23,39:62:99:965,0,542:13,10,21,18 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 1/1:0,76:76:99:2203,227,0:0,0,40,36 chr1 16374622 . C G 1999.53 PASS AC=2;AF=0.902;AN=2;DP=3682;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-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2408,221,0:0,0,39,35 chr1 16374656 . A G 1977.19 PASS AC=2;AF=0.902;AN=2;DP=3777;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-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2650,216,0:0,0,43,29 chr1 16374994 . C T 5605.65 PASS AC=2;AF=0.902;AN=2;DP=8652;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-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,198:198:99:6116,594,0:0,0,103,95 chr1 16375063 . C G 7741.67 PASS AC=2;AF=0.932;AN=2;DP=9680;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,210:210:99:9467,641,0:0,0,95,115 chr1 16375064 . A C 7741.67 PASS AC=2;AF=0.932;AN=2;DP=9653;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,213:213:99:9467,641,0:0,0,96,117 chr1 16375210 . G A 1759.66 PASS AC=1;AF=0.683;AN=2;DP=1635;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,28:46:99:720,0,536:8,10,11,17 chr1 16375354 . C T 3111.93 PASS AC=2;AF=0.902;AN=2;DP=5174;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-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,109:110:99:3301,318,0:0,1,68,41 chr1 16375838 . C G 6164.42 PASS AC=2;AF=0.902;AN=2;DP=6590;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-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,115:116:99:3494,337,0:0,1,44,71 chr1 16376191 . C T 704.28 PASS AC=2;AF=0.943;AN=2;DP=1774;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:1020,81,0:0,0,22,5 chr1 16376230 . A AT 1795.83 PASS AC=2;AF=0.943;AN=2;DP=3322;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:2543,172,0:0,0,38,18 chr1 16376232 . A T 1804.87 PASS AC=2;AF=0.943;AN=2;DP=3426;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:2543,172,0:0,0,38,19 chr1 16376238 . TC T 1275.67 PASS AC=2;AF=0.943;AN=2;DP=3627;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2029,192,0:0,0,40,24 chr1 16376278 . G A 1926.88 PASS AC=2;AF=0.943;AN=2;DP=5536;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:2894,290,0:0,0,51,46 chr1 16376319 . T C 2131.62 PASS AC=2;AF=0.943;AN=2;DP=6503;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:3572,351,0:0,0,54,63 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 1/1:34:99:0,0,10,24 chr1 16377108 . G C 3422.33 PASS AC=1;AF=0.579;AN=2;DP=7697;MQ=60;set=variant2-variant5-variant6-variant8-variant9-variant10-variant12-variant14-variant18-variant21-variant22-variant23-variant24-variant26-variant27-variant30-variant31-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:170,164:334:99:3783,0,4124:82,88,77,87 chr1 16377408 . C T 1955.05 PASS AC=1;AF=0.5;AN=2;DP=200;FS=1.136;FractionInformativeReads=1;MQ=50.19;MQRankSum=0.162;QD=9.78;ReadPosRankSum=-0.76;SOR=0.576;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:122,78:200:99:1983,0,3275:71,51,43,35 chr1 16378047 . G T 1890.46 PASS AC=1;AF=0.5;AN=2;DP=420;FractionInformativeReads=1;MQ=60;set=variant15-variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:75,58:133:99:1277,0,1916:29,46,26,32 chr1 16379008 . C T 766.28 PASS AC=2;AF=0.884;AN=2;DP=1916;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1305,117,0:0,0,12,27 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 1/1:0,270:270:99:7838,808,0:0,0,122,148 chr1 16380243 . A G 1336.4 PASS AC=1;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 0/1:68,73:141:99:2711,0,2426:21,47,22,51 chr1 16380252 . C T 1300.33 PASS AC=1;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 0/1:54,63:117:99:2603,0,2181:15,39,17,46 chr1 16381718 . T C 2390.06 PASS AC=2;AF=0.895;AN=2;DP=2036;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:2093,153,0:0,0,39,11 chr1 16381722 . C T 770.77 PASS AC=1;AF=0.661;AN=2;DP=1576;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,29:51:99:873,0,578:16,6,23,6 chr1 16381792 . T A 1861.34 PASS AC=1;AF=0.661;AN=2;DP=4677;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,74:138:99:2082,0,1517:37,27,51,23 chr1 16381816 . C T 2192.33 PASS AC=1;AF=0.661;AN=2;DP=6093;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,86:175:99:2363,0,2117:45,44,57,29 chr1 16382045 . T G 71.06 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=55;FS=64.686;FractionInformativeReads=0.964;MQ=60;MQRankSum=-0.535;QD=1.29;ReadPosRankSum=-1.906;SOR=5.417;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:39,14:53:99:99,0,946:30,9,0,14 chr1 16382086 . C T 728.64 PASS AC=1;AF=0.661;AN=2;DP=2481;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,45:90:99:1155,0,1161:29,16,24,21 chr1 16382730 . C T 144.4 PASS AC=1;AF=0.661;AN=2;DP=1158;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,25:52:99:954,0,986:23,4,24,1 chr1 16382791 . G C 647.07 PASS AC=1;AF=0.661;AN=2;DP=3556;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,59:123:99:1645,0,1639:46,18,46,13 chr1 16382827 . CTCT C 1935.16 PASS AC=1;AF=0.645;AN=2;DP=6422;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:117,91:208:99:3720,0,4714:68,49,56,35 chr1 16382831 . T A 1987.77 PASS AC=1;AF=0.645;AN=2;DP=6474;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:118,93:211:99:3727,0,4712:68,50,58,35 chr1 16382834 . T A 1987.9 PASS AC=1;AF=0.645;AN=2;DP=6702;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:117,101:218:99:3728,0,4711:66,51,61,40 chr1 16382877 . A G 4583.7 PASS AC=2;AF=0.907;AN=2;DP=13277;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,275:276:99:10286,819,0:0,1,131,144 chr1 16382880 . T A 1496.45 PASS AC=1;AF=0.621;AN=2;DP=9392;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:135,144:279:99:3334,0,3056:64,71,68,76 chr1 16383267 . A G 120.66 PASS AC=1;AF=0.603;AN=2;DP=1588;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:28,31:59:99:880,0,585:15,13,19,12 chr1 16383329 . T TC,TCC 277.71 PASS AC=2,0;AF=0.837,0.023;AN=2;DP=1504;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:35:99:0,0,4,31 chr1 16383336 . G C 286.77 PASS AC=2;AF=0.884;AN=2;DP=1423;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1581,108,0:0,0,3,31 chr1 16383348 . C T 88.72 PASS AC=1;AF=0.603;AN=2;DP=1102;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:8,24:32:99:899,0,252:0,8,1,23 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 1/1:0,36:36:99:1124,108,0:0,0,14,22 chr1 16383515 . C T 45.63 PASS AC=1;AF=0.611;AN=2;DP=465;FractionInformativeReads=1;set=variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-filterInvariant14-variant16-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:247,0,271:4,8,4,7 chr1 16383581 . G T 286.61 PASS AC=1;AF=0.573;AN=2;DP=680;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,13:14:3:494,0,3:1,0,7,6 chr1 16383605 . A G 408.7 PASS AC=1;AF=0.547;AN=2;DP=1076;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,19:22:57:747,0,57:3,0,16,3 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 1/1:0,86:86:99:2953,258,0:0,0,56,30 chr1 16383682 . G C 1616.54 PASS AC=1;AF=0.5;AN=2;DP=3735;set=variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,25:97:99:447,0,1919:47,25,16,9 chr1 16383742 . C G 1372.49 PASS AC=1;AF=0.602;AN=2;DP=6411;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:44,97:141:99:2240,0,763:24,20,45,52 chr1 16383914 . C T 152.62 PASS AC=1;AF=0.5;AN=2;DP=1320;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,12:30:99:283,0,468:5,13,3,9 chr1 16384986 . G T 367.58 PASS AC=1;AF=0.5;AN=2;DP=527;FractionInformativeReads=1;set=variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,8:11:99:327,0,239:2,1,7,1 chr1 16384998 . G C 343.5 PASS AC=1;AF=0.5;AN=2;DP=652;FractionInformativeReads=1;set=variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,10:14:99:408,0,276:3,1,9,1 chr1 16384999 . G A 343.5 PASS AC=1;AF=0.5;AN=2;DP=670;FractionInformativeReads=1;set=variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,10:14:99:408,0,276:3,1,9,1 chr1 16385042 . G A 588.54 PASS AC=1;AF=0.5;AN=2;DP=1396;set=variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-filterInvariant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:264,0,326:9,2,10,1 chr1 16385175 . G A 559.45 PASS AC=1;AF=0.634;AN=2;DP=5903;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,65:83:99:2216,0,215:8,10,30,35 chr1 16385184 . G A 3243.55 PASS AC=1;AF=0.5;AN=2;DP=4925;set=variant3-filterInvariant4-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,42:82:99:941,0,1140:17,23,20,22 chr1 16385248 . C T 833.72 PASS AC=1;AF=0.643;AN=2;DP=3161;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,29:35:92:1221,0,92:1,5,11,18 chr1 16385250 . A G 833.72 PASS AC=1;AF=0.778;AN=2;DP=3003;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,30:31:92:1221,0,92:1,0,11,19 chr1 16385323 . A G 855.92 PASS AC=2;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 1/1:0,9:9:27:405,27,0:0,0,3,6 chr1 16385330 . G T 806.49 PASS AC=2;AF=0.875;AN=2;DP=1479;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:405,27,0:0,0,3,6 chr1 16385797 . C G 1706 PASS AC=1;AF=0.64;AN=2;DP=4784;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,76:90:76:2275,0,76:7,7,54,22 chr1 16385815 . G A,C 848.3 PASS AC=1,0;AF=0.534,0.034;AN=2;DP=4231;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant37-variant39-variant41-variant42 GT:DP:GQ:SB 0/1:123:99:44,30,33,16 chr1 16385980 . G A 6015.28 PASS AC=2;AF=0.884;AN=2;DP=8526;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,143:143:99:4444,424,0:0,0,51,92 chr1 16386008 . T C 4832.98 PASS AC=2;AF=0.884;AN=2;DP=6486;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,110:110:99:3617,329,0:0,0,34,76 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 1/1:0,9:9:27:350,27,0:0,0,9,0 chr1 16386305 . G GC 889.27 PASS AC=2;AF=0.628;AN=2;DP=1798;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,27:29:29:831,29,0:1,1,19,8 chr1 16386416 . G A 1729.31 PASS AC=2;AF=0.884;AN=2;DP=4231;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,84:84:99:2261,248,0:0,0,38,46 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 1/1:0,72:72:99:2051,215,0:0,0,31,41 chr1 16386495 . C T 509.16 PASS AC=1;AF=0.645;AN=2;DP=1679;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,14:44:99:297,0,821:9,21,5,9 chr1 16388474 . G A 163.1 PASS AC=1;AF=0.571;AN=2;DP=746;FractionInformativeReads=1;set=variant-variant2-variant5-variant7-variant8-filterInvariant9-filterInvariant10-variant12-variant13-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:9,11:20:99:282,0,460:6,3,9,2 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 0/1:13,19:32:99:534,0,471:11,2,15,4 chr1 16388534 . C T 371.45 PASS AC=1;AF=0.571;AN=2;DP=2206;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-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:44,24:68:99:550,0,1047:26,18,17,7 chr1 16388556 . C T 4302.3 PASS AC=2;AF=0.814;AN=2;DP=5021;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:3840,265,0:0,0,53,32 chr1 16388565 . C G 2903.27 PASS AC=1;AF=0.629;AN=2;DP=4159;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,64:103:99:2346,0,1412:25,14,37,27 chr1 16388580 . C T,A 1105.58 PASS AC=1,0;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 0/1:116:99:45,28,27,16 chr1 16388646 . T C 5236.94 PASS AC=2;AF=0.909;AN=2;DP=7934;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,132:132:99:4234,395,0:0,0,64,68 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 0/1:46,53:99:99:1101,0,1095:20,26,23,30 chr1 16388737 . G A 782.08 PASS AC=1;AF=0.571;AN=2;DP=2167;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-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:39,29:68:99:701,0,1075:13,26,9,20 chr1 16388766 . C T 1575.79 PASS AC=2;AF=0.898;AN=2;DP=2429;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1793,150,0:0,0,14,36 chr1 16388852 . AC A 369.28 PASS AC=1;AF=0.63;AN=2;DP=628;set=variant-variant2-variant7-variant8-variant9-variant13-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,10:28:99:237,0,479:10,8,5,5 chr1 16388875 . GCCC GC,GCC,G 453.86 PASS AC=1,0,0;AF=0.557,0.057,0.1;AN=2;DP=818;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:18:84:3,2,7,6 chr1 16388904 . A T 268.01 PASS AC=1;AF=0.636;AN=2;DP=412;set=variant-variant2-variant7-variant8-variant9-variant13-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,5:17:99:168,0,491:2,10,2,3 chr1 16388909 . T C 306.77 PASS AC=1;AF=0.636;AN=2;DP=415;set=variant-variant2-variant7-variant8-variant9-variant13-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,5:18:99:168,0,491:2,11,2,3 chr1 16389026 . T C 261.15 PASS AC=1;AF=0.635;AN=2;DP=312;FractionInformativeReads=1;set=variant-variant2-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:118,0,116:1,2,1,3 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 1/1:0,51:51:99:1564,152,0:0,0,21,30 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 0/1:18,12:30:99:326,0,499:10,8,4,8 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 1/1:0,30:30:90:1311,90,0:0,0,18,12 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 0/1:22,24:46:99:680,0,583:9,13,7,17 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 0/1:12,11:23:99:362,0,378:4,8,4,7 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 0/1:12,18:30:99:678,0,566:4,8,4,14 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 0/1:12,18:30:99:677,0,568:4,8,4,14 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 1/1:0,38:38:99:1253,114,0:0,0,28,10 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 0/1:39,48:87:99:1109,0,875:19,20,26,22 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 0/1:33,28:61:99:790,0,968:8,25,6,22 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 0/1:4,9:13:99:366,0,184:2,2,4,5 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 0/1:6,6:12:98:98,0,155:2,4,3,3 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 0/1:15,28:43:99:973,0,387:12,3,22,6 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 0/1:21,20:41:99:650,0,611:15,6,15,5 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 1/1:0,95:95:99:2944,285,0:0,0,36,59 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 0/1:5,4:9:99:113,0,146:3,2,4,0 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 0/1:10,6:16:99:141,0,283:6,4,3,3 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 0/1:10,7:17:99:257,0,309:8,2,7,0 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 0/1:21,50:71:99:1253,0,395:9,12,23,27 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 0/1:41,29:70:99:691,0,942:18,23,10,19 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 1/1:0,17:17:51:645,51,0:0,0,14,3 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 1/1:0,51:51:99:1570,153,0:0,0,19,32 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 0/1:132,129:261:99:3936,0,4004:68,64,70,59 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 1/1:0,47:47:99:1747,141,0:0,0,9,38 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 0/1:17,5:22:78:78,0,447:6,11,2,3 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 0/1:30,10:40:99:184,0,912:16,14,4,6 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 0/1:65,52:117:99:1954,0,3206:30,35,23,29 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 0/1:19,23:42:99:497,0,490:8,11,10,13 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 0/1:51,56:107:99:1369,0,1257:26,25,29,27 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 0/1:11,7:18:99:168,0,292:4,7,3,4 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 0/1:17,8:25:99:169,0,438:11,6,4,4 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 1/1:0,37:37:99:1195,111,0:0,0,24,13 chr1 16621234 . G A,C 953.9 PASS AC=0,1;AF=0.375,0.125;AN=2;DP=303;FractionInformativeReads=1;MQ=60;set=variant18-variant23-variant31-variant38 GT:DP:GQ:SB 0/2:58:99:18,11,15,14 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 0/1:13,19:32:99:454,0,308:8,5,11,8 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 0/1:47,37:84:99:919,0,1196:18,29,16,21 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 0/1:11,5:16:99:170,0,428:4,7,2,3 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 0/1:107,89:196:99:1985,0,2488:56,51,45,44 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 0/1:50,64:114:99:1665,0,1329:27,23,31,33 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 0/1:94,88:182:99:1926,0,2099:47,47,44,44 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 0/1:31,30:61:99:733,0,735:16,15,16,14 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 0/1:49,48:97:99:1074,0,1294:25,24,24,24 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 0/1:54,55:109:99:1526,0,1404:26,28,29,26 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 0/1:49,58:107:99:1466,0,1177:22,27,29,29 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 0/1:8,5:13:99:147,0,127:4,4,4,1 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 0/1:23,36:59:99:1037,0,523:12,11,20,16 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 0/1:71,44:115:99:1674,0,3254:31,40,22,22 chr1 16730308 . G T 2002.16 PASS AC=1;AF=0.563;AN=2;DP=1314;MQ=60;set=variant5-variant9-variant21-variant23-variant26-variant28-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:58,70:128:99:1740,0,1504:25,33,27,43 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 0/1:42,33:75:99:821,0,983:21,21,11,22 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 0/1:10,15:25:99:438,0,227:3,7,5,10 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 1/1:0,57:57:99:2554,172,0:0,0,15,42 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 1/1:0,57:57:99:2554,172,0:0,0,15,42 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 0/1:26,24:50:99:756,0,675:10,16,4,20 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 1/1:0,45:45:99:1714,135,0:0,0,14,31 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 0/1:6,6:12:99:224,0,150:2,4,0,6 chr1 16735364 . CAAAAA CA,CAA,CAAA,CAAAA,C 127.81 PASS AC=0,0,2,0,0;AF=0.3,0.1,0.22,0.04,0.08;AN=2;DP=158;FS=0;set=variant2-variant3-variant4-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant33-variant36-variant40-variant41-variant44 GT:DP:GQ:SB 3/3:3:9:0,0,3,0 chr1 16736546 . C T 1070.97 PASS AC=1;AF=0.73;AN=2;DP=3700;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,52:77:99:1560,0,721:10,15,22,30 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 1/1:0,52:52:99:1651,156,0:0,0,30,22 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 0/1:50,10:60:99:180,0,1467:44,6,9,1 chr1 16862294 . A G 119.2 PASS AC=1;AF=0.5;AN=2;DP=814;set=filterInvariant3-filterInvariant6-filterInvariant18-variant23-filterInvariant32-filterInvariant38 GT:AD:DP:GQ:PL:SB 0/1:80,15:95:99:244,0,2887:67,13,13,2 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 0/1:48,49:97:99:1298,0,1416:41,7,41,8 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 0/1:193,67:260:99:1290,0,5125:146,47,56,11 chr1 16862454 . T G 19431.9 PASS AC=1;AF=0.5;AN=2;DP=59379;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:409,579:988:99:22278,0,15894:238,171,324,255 chr1 16862461 . T A 19801.3 PASS AC=1;AF=0.5;AN=2;DP=60743;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:298,715:1013:99:28197,0,10473:173,125,394,321 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 0/1:947,120:1067:99:1912,0,38408:510,437,68,52 chr1 16862502 . A G 24850.1 PASS AC=1;AF=0.5;AN=2;DP=67059;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:376,832:1208:99:19809,0,6845:187,189,415,417 chr1 16862638 . A G 484.05 PASS AC=1;AF=0.5;AN=2;DP=5741;set=filterInvariant18-filterInvariant23-filterInvariant24-variant31-variant33-filterInvariant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:539,88:627:99:563,0,14302:189,350,35,53 chr1 16862708 . T G 2252.72 PASS AC=1;AF=0.5;AN=2;DP=9082;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:70,96:166:99:3633,0,2677:19,51,12,84 chr1 16862712 . G T 2103.78 PASS AC=1;AF=0.5;AN=2;DP=8023;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:65,82:147:99:3493,0,2663:18,47,9,73 chr1 16862714 . T G 2112.33 PASS AC=1;AF=0.5;AN=2;DP=7572;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:60,78:138:99:3227,0,2567:16,44,9,69 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 0/1:49,17:66:99:380,0,1497:12,37,0,17 chr1 16863213 . C G 58.18 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=396;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:70,9:79:99:143,0,1908:45,25,9,0 chr1 16863229 . C T 126.62 PASS AC=1;AF=0.5;AN=2;DP=878;FractionInformativeReads=1;set=filterInvariant6-filterInvariant10-filterInvariant22-variant23-filterInvariant26-variant32-filterInvariant38 GT:AD:DP:GQ:PL:SB 0/1:93,15:108:99:386,0,3921:59,34,15,0 chr1 16863233 . A C 78 PASS AC=1;AF=0.5;AN=2;DP=1215;FractionInformativeReads=1;set=filterInvariant3-variant6-filterInvariant10-filterInvariant22-variant23-filterInvariant24-filterInvariant26-variant32-variant38 GT:AD:DP:GQ:PL:SB 0/1:99,21:120:99:626,0,4070:62,37,21,0 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 0/1:103,22:125:99:720,0,4145:63,40,22,0 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 0/1:139,33:172:99:920,0,5716:84,55,30,3 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 0/1:133,44:177:99:1456,0,5235:78,55,38,6 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 0/1:186,107:293:99:3927,0,7529:102,84,70,37 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 0/1:189,111:300:99:4309,0,7674:103,86,72,39 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 0/1:229,82:311:99:1512,0,8772:123,106,58,24 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 0/1:190,122:312:99:4512,0,7592:102,88,79,43 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 0/1:179,144:323:99:3982,0,4073:93,86,84,60 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 0/1:165,166:331:99:4191,0,3716:79,86,88,78 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 0/1:178,100:278:99:2174,0,4426:75,103,41,59 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 0/1:56,9:65:99:177,0,1823:10,46,0,9 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 0/1:167,208:375:99:5681,0,5411:119,48,146,62 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 0/1:387,102:489:99:1925,0,13962:264,123,67,35 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 0/1:668,156:824:99:2633,0,17758:411,257,97,59 chr1 16890598 . T A 13968 PASS AC=1;AF=0.534;AN=2;DP=55757;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:329,813:1142:99:29243,0,6668:141,188,379,434 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 0/1:568,572:1140:99:16401,0,18208:250,318,258,314 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 0/1:949,169:1118:99:1729,0,33839:424,525,75,94 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 0/1:788,149:937:99:1856,0,29353:342,446,58,91 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 0/1:376,525:901:99:13018,0,11022:154,222,226,299 chr1 16890671 . T C 17120.1 PASS AC=1;AF=0.545;AN=2;DP=34126;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:180,492:672:99:19874,0,5804:65,115,186,306 chr1 16890672 . G A 17120.1 PASS AC=1;AF=0.545;AN=2;DP=33755;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:176,489:665:99:19874,0,5804:65,111,184,305 chr1 16890760 . G A 1328.16 PASS AC=1;AF=0.511;AN=2;DP=8098;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:49,113:162:99:3925,0,1326:11,38,20,93 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 0/1:53,28:81:99:800,0,1572:43,10,22,6 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 0/1:112,15:127:99:176,0,3644:99,13,13,2 chr1 16891243 . C G 6249.01 PASS AC=2;AF=0.795;AN=2;DP=12817;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,241:241:99:7911,722,0:0,0,167,74 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 0/1:355,144:499:99:2827,0,9336:192,163,71,73 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 0/1:89,124:213:99:3893,0,2001:40,49,26,98 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 0/1:47,187:234:99:5272,0,703:31,16,39,148 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 0/1:145,37:182:99:570,0,4609:90,55,24,13 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 0/1:124,63:187:99:1454,0,3578:75,49,41,22 chr1 16892540 . A G 208.34 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=268;FS=4.468;FractionInformativeReads=1;MQ=54.78;MQRankSum=-4.269;QD=0.78;ReadPosRankSum=-1.173;SOR=0.981;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:235,33:268:99:237,0,6732:121,114,14,19 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 1/1:0,280:280:99:9188,841,0:0,0,140,140 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 0/1:265,28:293:99:379,0,10816:129,136,13,15 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 0/1:258,359:617:99:7961,0,5499:122,136,175,184 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 1/1:0,324:324:99:9556,968,0:0,0,181,143 chr1 16893721 . A C 853.81 PASS AC=1;AF=0.5;AN=2;DP=28631;set=filterInvariant2-filterInvariant4-filterInvariant6-filterInvariant7-filterInvariant12-filterInvariant13-variant14-filterInvariant23-filterInvariant28-filterInvariant30-filterInvariant32 GT:AD:DP:GQ:PL:SB 0/1:2821,340:3161:99:596,0,74288:1501,1320,180,160 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 0/1:380,551:931:99:16091,0,9804:98,282,125,426 chr1 16894289 . T C 147.64 PASS AC=1;AF=0.5;AN=2;DP=1903;set=filterInvariant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-variant13-variant14-filterInvariant16-variant17-variant23-variant25-filterInvariant26-filterInvariant28-variant30-variant32-filterInvariant36-filterInvariant38-filterInvariant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:73,16:89:99:215,0,1970:58,15,12,4 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 0/1:77,74:151:99:1557,0,1717:54,23,51,23 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 0/1:221,47:268:99:448,0,5212:135,86,26,21 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 0/1:100,159:259:99:3993,0,2131:45,55,49,110 chr1 16899669 . C T 50.3 PASS AC=2;AF=1;AN=2;DP=2;FS=0;FractionInformativeReads=1;MQ=38.01;QD=25.15;SOR=2.303;set=variant23 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:79,6,0:0,0,2,0 chr1 16899903 . G C 200.16 PASS AC=1;AF=0.531;AN=2;DP=171;FractionInformativeReads=1;set=variant3-variant4-variant5-variant6-variant7-variant11-variant16-variant17-variant18-variant19-variant22-variant23-variant26-variant28-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:105,0,157:2,4,1,3 chr1 16900883 . T G 62.88 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=4035;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:71,33:104:99:565,0,1506:40,31,18,15 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 0/1:23,36:59:99:826,0,473:6,17,2,34 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 0/1:17,25:42:99:574,0,366:5,12,1,24 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 0/1:84,30:114:99:994,0,3433:68,16,19,11 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 0/1:101,30:131:99:945,0,3902:78,23,19,11 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 0/1:290,62:352:99:568,0,7220:160,130,24,38 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 0/1:238,36:274:99:144,0,7869:90,148,13,23 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 0/1:101,162:263:99:4703,0,2301:39,62,55,107 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 0/1:72,35:107:99:613,0,2238:55,17,25,10 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 0/1:157,29:186:99:257,0,4072:109,48,19,10 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 0/1:142,95:237:99:2092,0,3461:71,71,33,62 chr1 16903630 . C T 87.65 PASS AC=1;AF=0.5;AN=2;DP=43;FS=0;FractionInformativeReads=1;set=variant23-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:14,5:19:99:116,0,455:12,2,4,1 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 0/1:27,20:47:99:636,0,769:20,7,19,1 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 0/1:37,32:69:99:1279,0,1468:27,10,27,5 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 0/1:38,40:78:99:1431,0,1410:28,10,32,8 chr1 16903770 . TAC T 768.47 PASS AC=1;AF=0.5;AN=2;DP=1514;set=variant7-variant8-filterInvariant23-filterInvariant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:223,25:248:99:335,0,9351:129,94,13,12 chr1 16903780 . C T 314.56 PASS AC=1;AF=0.5;AN=2;DP=5632;set=filterInvariant4-variant7-variant8-variant11-variant13-filterInvariant15-variant16-variant17-variant18-filterInvariant19-filterInvariant21-filterInvariant23-variant26-variant29-variant33-variant36-variant39-variant40-filterInvariant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:232,24:256:99:275,0,9522:132,100,12,12 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 0/1:66,45:111:99:1368,0,1566:31,35,0,45 chr1 16904073 . C A 60.06 PASS AC=1;AF=0.5;AN=2;DP=498;FractionInformativeReads=1;set=variant3-variant4-variant7-filterInvariant9-variant10-filterInvariant11-filterInvariant12-variant13-filterInvariant14-variant17-filterInvariant19-variant20-variant22-variant23-variant25-variant27-variant30-variant31-variant32-variant33-variant36-filterInvariant37-variant38-variant39-filterInvariant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,6:20:99:181,0,388:4,10,0,6 chr1 16905842 . A G 42.24 PASS AC=1;AF=0.571;AN=2;DP=89;FractionInformativeReads=1;set=variant5-variant11-variant12-variant13-variant15-filterInvariant18-variant19-variant21-variant23-variant29-variant31-variant34-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,5:14:99:135,0,319:7,2,4,1 chr1 16907110 . T C 3285.55 PASS AC=1;AF=0.5;AN=2;DP=8583;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:32,94:126:99:3175,0,933:26,6,83,11 chr1 16907117 . G C 123.85 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=150;FS=5.202;FractionInformativeReads=0.993;MQ=56.84;MQRankSum=3.353;QD=0.83;ReadPosRankSum=-1.293;SOR=0.216;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:132,17:149:99:152,0,5542:113,19,13,4 chr1 16907124 . A C 4836.66 PASS AC=1;AF=0.5;AN=2;DP=11837;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:45,129:174:99:4141,0,1225:35,10,105,24 chr1 16907204 . G A 200.23 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2873;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:575,82:657:99:474,0,15938:370,205,52,30 chr1 16907328 . G T 17721.3 PASS AC=1;AF=0.511;AN=2;DP=60220;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:300,707:1007:99:17036,0,5867:145,155,314,393 chr1 16907766 . A G 1790.32 PASS AC=1;AF=0.602;AN=2;DP=4209;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:34,29:63:99:813,0,902:23,11,28,1 chr1 16907854 . T A 6896.79 PASS AC=1;AF=0.5;AN=2;DP=25314;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:172,156:328:99:3716,0,4419:109,63,105,51 chr1 16907871 . C T 8073.31 PASS AC=1;AF=0.5;AN=2;DP=31480;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:219,199:418:99:4497,0,5711:140,79,123,76 chr1 16908034 . C G 395.69 PASS AC=1;AF=0.5;AN=2;DP=19589;set=filterInvariant2-filterInvariant3-filterInvariant4-variant7-filterInvariant8-filterInvariant10-filterInvariant11-variant12-filterInvariant13-filterInvariant16-filterInvariant17-variant18-filterInvariant19-filterInvariant22-variant23-variant24-filterInvariant26-filterInvariant29-filterInvariant33-filterInvariant34-variant36-filterInvariant37-filterInvariant39-variant40-filterInvariant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:337,72:409:99:1018,0,9465:125,212,27,45 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 0/1:133,21:154:99:255,0,4205:35,98,5,16 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 0/1:17,7:24:99:166,0,433:11,6,6,1 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 0/1:23,8:31:99:180,0,682:13,10,4,4 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 1/1:0,15:15:48:585,48,0:0,0,4,11 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 0/1:13,3:16:87:87,0,525:3,10,0,3 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 0/1:12,3:15:90:90,0,495:3,9,0,3 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 0/1:5,3:8:74:74,0,136:0,5,0,3 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 0/1:3,5:8:79:131,0,79:0,3,0,5 chr1 16910064 . A G 2984.01 PASS AC=1;AF=0.534;AN=2;DP=10210;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:118,46:164:99:794,0,2765:68,50,29,17 chr1 16910249 . T C 399.42 PASS AC=1;AF=0.5;AN=2;DP=1971;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-filterInvariant31-variant33-variant34-variant36-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,7:26:99:168,0,605:1,18,0,7 chr1 16910281 . A G 86.49 PASS AC=1;AF=0.5;AN=2;DP=73;FractionInformativeReads=1;set=variant8-variant23-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:130,0,216:1,5,0,4 chr1 16913416 . G C 310.32 PASS AC=1;AF=0.5;AN=2;DP=472;set=variant9-variant12-variant18-variant22-variant23-variant24-variant29-variant31-variant33-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:27,15:42:99:378,0,885:23,4,12,3 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 0/1:250,74:324:99:2515,0,10346:155,95,71,3 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 0/1:279,86:365:99:2643,0,11065:173,106,83,3 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 0/1:499,320:819:99:6793,0,13738:250,249,181,139 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 0/1:437,398:835:99:8279,0,10323:197,240,174,224 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 0/1:272,89:361:99:1743,0,11689:83,189,23,66 chr1 16914396 . C T 1199.27 PASS AC=1;AF=0.5;AN=2;DP=12760;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:164,182:346:99:6636,0,6724:51,113,48,134 chr1 16914415 . A G 712.43 PASS AC=1;AF=0.5;AN=2;DP=8760;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:122,114:236:99:4588,0,5764:33,89,22,92 chr1 16915609 . C T 94.14 DRAGENHardSNP AC=1;AF=0.667;AN=2;DP=98;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:5,4:9:76:76,0,205:3,2,4,0 chr1 16915611 . T C 32.95 DRAGENHardSNP AC=1;AF=0.569;AN=2;DP=281;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:6,5:11:92:92,0,178:5,1,4,1 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 0/1:37,53:90:99:1506,0,887:22,15,36,17 chr1 16916528 . G T 186.62 PASS AC=1;AF=0.5;AN=2;DP=1148;set=filterInvariant4-filterInvariant12-filterInvariant14-filterInvariant20-variant23-filterInvariant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:164,43:207:99:665,0,4506:75,89,29,14 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 0/1:124,77:201:99:1572,0,2806:54,70,40,37 chr1 16916603 . C A 3327.64 PASS AC=1;AF=0.693;AN=2;DP=7718;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:25,144:169:99:3608,0,351:6,19,60,84 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 0/1:106,22:128:99:361,0,3598:97,9,19,3 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 0/1:685,56:741:99:115,0,28696:299,386,12,44 chr1 16918502 . A G 5971.79 PASS AC=1;AF=0.5;AN=2;DP=21919;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:179,312:491:99:8125,0,3948:68,111,117,195 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 0/1:33,42:75:99:1192,0,902:18,15,28,14 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 0/1:37,52:89:99:1225,0,968:22,15,28,24 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 0/1:35,15:50:99:396,0,882:12,23,5,10 chr1 16950346 . A C 1661.22 PASS AC=1;AF=0.5;AN=2;DP=4872;set=variant9-filterInvariant18-filterInvariant22-variant23-variant24-variant29-variant31-variant32-variant33-filterInvariant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:313,96:409:99:1595,0,7508:164,149,46,50 chr1 16950509 . G C 127.34 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=359;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:118,11:129:64:64,0,6816:35,83,0,11 chr1 16950511 . G C 127.34 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=342;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:113,7:120:64:64,0,6816:32,81,0,7 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 0/1:266,98:364:99:1872,0,7638:184,82,62,36 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 0/1:262,38:300:99:390,0,8252:73,189,12,26 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 0/1:230,31:261:99:252,0,7489:60,170,10,21 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 0/1:147,43:190:99:764,0,3979:57,90,18,25 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 0/1:80,14:94:86:86,0,1958:34,46,7,7 chr1 16969381 . C T 2261.75 PASS AC=1;AF=0.523;AN=2;DP=14454;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:153,189:342:99:4894,0,3692:65,88,91,98 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 0/1:103,59:162:99:1483,0,3158:79,24,41,18 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 0/1:374,107:481:99:2445,0,9459:190,184,57,50 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 0/1:398,67:465:99:670,0,9797:195,203,23,44 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 0/1:595,398:993:99:9006,0,17965:318,277,223,175 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 0/1:852,208:1060:99:2821,0,27817:448,404,107,101 chr1 16973072 . T C 2030.55 PASS AC=1;AF=0.5;AN=2;DP=2940;set=variant7-variant8-variant23-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:425,81:506:99:1345,0,12645:165,260,26,55 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 0/1:338,77:415:99:1152,0,9132:170,168,39,38 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 0/1:358,60:418:99:464,0,10121:189,169,30,30 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 0/1:757,210:967:99:2273,0,16346:409,348,105,105 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 0/1:583,128:711:99:1338,0,13402:257,326,45,83 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 0/1:494,83:577:99:594,0,11455:209,285,25,58 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 0/1:413,84:497:99:757,0,9639:163,250,35,49 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 0/1:198,56:254:99:1160,0,5882:145,53,56,0 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 0/1:666,95:761:99:682,0,18132:357,309,51,44 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 0/1:599,282:881:99:7762,0,15244:291,308,113,169 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 0/1:650,142:792:99:1790,0,24240:301,349,50,92 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 0/1:340,347:687:99:8424,0,8542:211,129,203,144 chr1 16975093 . C T 1930.18 PASS AC=1;AF=0.5;AN=2;DP=11160;set=variant2-variant6-variant7-variant9-variant12-variant13-variant14-filterInvariant22-filterInvariant23-variant25-variant28-filterInvariant30-filterInvariant31-filterInvariant32-variant41 GT:AD:DP:GQ:PL:SB 0/1:614,100:714:99:1254,0,17013:309,305,40,60 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 0/1:636,138:774:99:1395,0,16447:307,329,66,72 chr1 16975230 . G C 5755.78 PASS AC=2;AF=0.705;AN=2;DP=33096;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:60,636:696:76:16597,76,0:31,29,286,350 chr1 16975278 . A ACC,ACCC,AC 74.98 PASS AC=1,0,0;AF=0.367,0.033,0.1;AN=2;DP=9698;set=filterInvariant3-variant5-variant6-filterInvariant8-variant9-filterInvariant10-variant23-filterInvariant24-variant25-variant27-filterInvariant29-filterInvariant33-filterInvariant38-variant39-filterInvariant42 GT:DP:GQ:SB 0/1:587:99:235,265,35,52 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 0/1:149,24:173:99:338,0,4705:90,59,15,9 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 0/1:135,19:154:99:117,0,3597:58,77,6,13 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 0/1:114,72:186:99:1744,0,2997:69,45,36,36 chr1 16976528 . G T 176.17 PASS AC=1;AF=0.5;AN=2;DP=789;FractionInformativeReads=1;set=variant2-filterInvariant3-filterInvariant7-filterInvariant12-filterInvariant23-variant25-variant28-filterInvariant34-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:60,8:68:66:66,0,2089:36,24,8,0 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 0/1:40,30:70:99:672,0,1120:25,15,23,7 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 0/1:113,45:158:99:1002,0,2866:76,37,32,13 chr1 16976585 . C T 519.88 PASS AC=1;AF=0.5;AN=2;DP=8614;set=variant-filterInvariant3-variant4-filterInvariant5-variant6-variant8-variant9-variant11-variant12-filterInvariant14-variant15-variant16-filterInvariant18-variant20-variant21-variant22-variant23-filterInvariant24-variant26-variant27-variant28-filterInvariant29-filterInvariant32-variant33-variant34-variant37-filterInvariant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:158,49:207:99:815,0,4110:104,54,34,15 chr1 16976620 . A G 1072.56 PASS AC=1;AF=0.5;AN=2;DP=7231;set=variant8-variant12-variant13-variant18-variant22-variant23-variant24-variant31-filterInvariant32-variant33-variant37-variant38-filterInvariant41-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:248,88:336:99:1407,0,6350:145,103,48,40 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 0/1:349,47:396:99:104,0,9752:196,153,25,22 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 0/1:129,280:409:99:6611,0,2929:65,64,145,135 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 0/1:79,75:154:99:1613,0,1917:34,45,31,44 chr1 17022952 . C A 11693.4 PASS AC=1;AF=0.932;AN=2;DP=20684;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:98,119:217:99:2803,0,2333:57,41,71,48 chr1 17023126 . C G 3163.33 PASS AC=1;AF=0.5;AN=2;DP=7371;set=variant3-variant4-variant6-variant12-variant14-filterInvariant18-variant22-variant23-variant24-variant28-variant32-variant33-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:116,124:240:99:2961,0,2969:56,60,57,67 chr1 17023511 . C A 13983.3 PASS AC=1;AF=0.659;AN=2;DP=12692;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:55,39:94:99:1067,0,1643:16,39,10,29 chr1 17023569 . T C 5032.01 PASS AC=1;AF=0.909;AN=2;DP=3717;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:24,10:34:99:304,0,782:6,18,1,9 chr1 17025951 . C T 769.89 PASS AC=1;AF=0.5;AN=2;DP=125;set=variant6-variant23 GT:AD:DP:GQ:PL:SB 0/1:15,27:42:99:847,0,419:10,5,21,6 chr1 17034041 . T C 14198.5 PASS AC=1;AF=0.693;AN=2;DP=15527;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:66,74:140:99:2015,0,1747:32,34,34,40 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 0/1:17,9:26:99:275,0,633:16,1,8,1 chr1 17044457 . G C 793.85 PASS AC=1;AF=0.875;AN=2;DP=2664;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:273,0,187:5,1,8,1 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 0/1:22,18:40:99:426,0,563:12,10,12,6 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 0/1:32,30:62:99:826,0,711:14,18,9,21 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 0/1:125,16:141:99:290,0,6522:83,42,10,6 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 0/1:141,17:158:99:269,0,6888:91,50,10,7 chr1 17083919 . G A 178.89 PASS AC=1;AF=0.524;AN=2;DP=1253;set=variant-variant3-filterInvariant6-variant8-variant11-variant12-variant13-variant15-variant16-variant18-variant22-variant23-variant24-variant27-variant28-variant30-variant34-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,63:125:99:1795,0,1487:27,35,18,45 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 0/1:120,20:140:99:198,0,3246:87,33,17,3 chr1 17084021 . C G 140.87 PASS AC=1;AF=0.5;AN=2;DP=4146;set=variant-filterInvariant4-filterInvariant6-variant8-filterInvariant11-filterInvariant15-filterInvariant17-filterInvariant21-filterInvariant23-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant38 GT:AD:DP:GQ:PL:SB 0/1:162,24:186:99:145,0,4156:112,50,18,6 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 0/1:11,24:35:99:744,0,271:10,1,10,14 chr1 17084859 . A G 43.12 PASS AC=1;AF=0.5;AN=2;DP=170;FractionInformativeReads=1;set=filterInvariant8-variant23-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:56,10:66:99:173,0,1825:50,6,10,0 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 0/1:306,46:352:99:235,0,7772:193,113,32,14 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 0/1:343,117:460:99:1944,0,8452:209,134,69,48 chr1 17085165 . G C,T 1891.84 PASS AC=1,0;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 0/1:196:99:53,60,46,37 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 0/1:664,298:962:99:5527,0,27835:377,287,199,99 chr1 17085427 . T C 8636.79 PASS AC=1;AF=0.5;AN=2;DP=51112;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:570,547:1117:99:17132,0,13689:320,250,330,217 chr1 17085502 . T C 16196 PASS AC=1;AF=0.5;AN=2;DP=54761;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:738,494:1232:99:11879,0,16386:351,387,238,256 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 0/1:730,348:1078:99:10523,0,27761:331,399,149,199 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 0/1:679,260:939:99:8789,0,26646:287,392,98,162 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 0/1:636,82:718:99:1363,0,26092:250,386,26,56 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 0/1:377,191:568:99:5510,0,10141:162,215,91,100 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 0/1:422,144:566:99:2150,0,16128:183,239,64,80 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 0/2:541:99:179,203,60,99 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 0/1:359,79:438:99:961,0,9824:175,184,24,55 chr1 17085834 . G T 5877.73 PASS AC=1;AF=0.807;AN=2;DP=18352;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:118,219:337:99:5139,0,2353:57,61,113,106 chr1 17085995 . G GC 334.5 PASS AC=1;AF=0.5;AN=2;DP=1127;set=variant3-variant4-variant6-variant12-variant14-variant22-variant23-variant24-variant28-variant31-variant32-variant33-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:30,28:58:99:675,0,726:3,27,1,27 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 1/1:0,56:56:99:1908,168,0:0,0,25,31 chr1 17087072 . G A 3215.89 PASS AC=1;AF=0.5;AN=2;DP=8816;set=variant3-variant4-variant18-filterInvariant22-variant23-variant24-variant28-filterInvariant32-filterInvariant33-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:544,134:678:99:1803,0,14345:256,288,66,68 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 0/1:455,118:573:99:2085,0,12184:230,225,65,53 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 0/1:575,47:622:99:345,0,24061:263,312,42,5 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 0/1:570,55:625:99:685,0,24388:258,312,47,8 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 0/1:553,70:623:99:1086,0,23674:257,296,58,12 chr1 17087365 . C G 7328.19 PASS AC=1;AF=0.511;AN=2;DP=34433;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:81,609:690:99:19218,0,683:44,37,371,238 chr1 17087459 . A G 1414.48 PASS AC=1;AF=0.5;AN=2;DP=9873;set=filterInvariant4-filterInvariant18-filterInvariant23-filterInvariant28-filterInvariant32-filterInvariant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:1235,143:1378:99:181,0,40543:665,570,76,67 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 0/1:859,546:1405:99:11078,0,23492:457,402,294,252 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 0/1:1469,174:1643:99:188,0,47232:685,784,81,93 chr1 17087541 . GGTGCT G 10847.3 PASS AC=1;AF=0.5;AN=2;DP=78083;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:950,574:1524:99:21085,0,38020:429,521,264,310 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 0/1:659,599:1258:99:18514,0,16145:281,378,243,356 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 0/1:843,285:1128:99:5038,0,30968:346,497,114,171 chr1 17087640 . A C 289.82 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2162;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:585,78:663:99:318,0,15843:199,386,22,56 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 0/1:234,83:317:99:1865,0,6498:60,174,19,64 chr1 17091129 . G A 341.95 PASS AC=1;AF=0.5;AN=2;DP=1403;set=variant3-variant4-variant6-variant12-variant14-variant22-variant23-variant24-variant28-variant31-variant32-variant33-variant37-filterInvariant38-filterInvariant39 GT:AD:DP:GQ:PL:SB 0/1:40,23:63:99:507,0,1122:13,27,9,14 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 0/1:110,28:138:99:987,0,4590:65,45,21,7 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 0/1:126,34:160:99:1158,0,4972:74,52,25,9 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 0/1:149,53:202:99:1776,0,3833:88,61,37,16 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 0/1:152,64:216:99:2290,0,6396:82,70,42,22 chr1 17197610 . G A 821.17 PASS AC=1;AF=0.5;AN=2;DP=3579;set=variant5-variant8-filterInvariant14-filterInvariant22-variant23-filterInvariant26-filterInvariant27-filterInvariant31-filterInvariant32-filterInvariant39 GT:AD:DP:GQ:PL:SB 0/1:171,52:223:99:856,0,6989:92,79,34,18 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 0/1:157,67:224:99:2329,0,6458:78,79,44,23 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 0/1:159,67:226:99:2320,0,6554:78,81,44,23 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 0/1:166,72:238:99:2107,0,3944:77,89,39,33 chr1 17197690 . T G 718.7 PASS AC=1;AF=0.5;AN=2;DP=13678;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:129,87:216:99:3253,0,4827:58,71,45,42 chr1 17197694 . G A 667.42 PASS AC=1;AF=0.5;AN=2;DP=13199;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:121,87:208:99:3265,0,4731:52,69,44,43 chr1 17197710 . G C 520.04 PASS AC=1;AF=0.5;AN=2;DP=11298;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:92,71:163:99:2741,0,3454:35,57,33,38 chr1 17197715 . G A 541.82 PASS AC=1;AF=0.5;AN=2;DP=10737;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:85,68:153:99:2595,0,3389:31,54,30,38 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 0/1:111,16:127:90:90,0,4150:35,76,5,11 chr1 17197758 . C G 355.1 PASS AC=1;AF=0.5;AN=2;DP=5775;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:42,42:84:99:1625,0,1607:8,34,11,31 chr1 17197764 . G A,C 303.47 PASS AC=0,1;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 0/2:69:99:8,24,11,26 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 0/1:26,40:66:99:1643,0,968:4,22,10,30 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 0/1:24,34:58:99:1478,0,938:3,21,9,25 chr1 17197779 . G A 223.4 PASS AC=1;AF=0.5;AN=2;DP=3837;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:26,30:56:99:1265,0,995:3,23,8,22 chr1 17197798 . A G 122.32 PASS AC=1;AF=0.5;AN=2;DP=2488;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:16,22:38:99:728,0,572:1,15,4,18 chr1 17197817 . C A 109.62 PASS AC=1;AF=0.5;AN=2;DP=1840;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:13,20:33:99:801,0,486:1,12,4,16 chr1 17197818 . C G 112.63 PASS AC=1;AF=0.5;AN=2;DP=1821;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:13,20:33:99:801,0,486:1,12,4,16 chr1 17248500 . A G 5266.57 PASS AC=1;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 0/1:76,88:164:99:2159,0,2043:51,25,54,34 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 1/1:0,231:231:99:6900,691,0:0,0,134,97 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 0/1:33,30:63:99:866,0,780:13,20,5,25 chr1 17250573 . T C 283.05 PASS AC=2;AF=0.963;AN=2;DP=453;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-variant32-variant33-variant34-variant36-variant37-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 17251055 . C T 2247.32 PASS AC=1;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 0/1:30,38:68:99:914,0,740:14,16,15,23 chr1 17265171 . A G 111.02 PASS AC=1;AF=0.514;AN=2;DP=2616;set=filterInvariant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,22:43:99:514,0,436:8,13,10,12 chr1 17265327 . A G 332.97 PASS AC=1;AF=0.5;AN=2;DP=6879;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,51:97:99:1179,0,958:25,21,27,24 chr1 17266648 . C T 1375.5 PASS AC=1;AF=0.5;AN=2;DP=1269;FractionInformativeReads=1;MQ=60;set=variant9-variant12-variant18-variant23-variant29-variant31-variant33-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:40,35:75:99:733,0,1000:15,25,13,22 chr1 17267302 . A G 143.28 PASS AC=1;AF=0.5;AN=2;DP=2281;MQ=60;set=variant-filterInvariant2-variant3-variant4-variant5-variant7-variant9-variant11-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,21:41:99:454,0,428:10,10,10,11 chr1 17273493 . A C 1209.71 PASS AC=1;AF=0.514;AN=2;DP=4121;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,18:54:99:364,0,974:14,22,10,8 chr1 17280022 . A T 700.22 PASS AC=1;AF=0.556;AN=2;DP=368;FractionInformativeReads=1;set=variant9-variant12-variant18-variant23-variant29-variant31-variant33-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:30,24:54:99:878,0,5348:13,17,9,15 chr1 17280025 . T C 697.18 PASS AC=1;AF=0.556;AN=2;DP=352;FractionInformativeReads=1;set=variant9-variant12-variant18-variant23-variant29-variant31-variant33-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:28,22:50:99:923,0,5312:12,16,7,15 chr1 17280045 . T C 433.35 PASS AC=1;AF=0.556;AN=2;DP=276;FractionInformativeReads=1;set=variant9-variant12-variant18-variant23-variant29-variant31-variant33-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:24,15:39:99:600,0,5362:10,14,5,10 chr1 17280051 . T C 400.39 PASS AC=1;AF=0.556;AN=2;DP=258;FractionInformativeReads=1;set=variant9-variant12-variant18-variant23-variant29-variant31-variant33-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:23,14:37:99:561,0,5294:9,14,4,10 chr1 17280057 . G A 406.41 PASS AC=1;AF=0.556;AN=2;DP=226;FractionInformativeReads=1;set=variant9-variant12-variant18-variant23-variant29-variant31-variant33-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:18,13:31:99:483,0,5158:6,12,3,10 chr1 17280061 . G T 412.43 PASS AC=1;AF=0.556;AN=2;DP=209;FractionInformativeReads=1;set=variant9-variant12-variant18-variant23-variant29-variant31-variant33-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:16,13:29:99:495,0,4657:6,10,3,10 chr1 17280074 . AG A 208.5 PASS AC=1;AF=0.556;AN=2;DP=169;FractionInformativeReads=1;set=variant9-variant12-variant18-variant23-variant29-variant31-variant33-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:15,8:23:99:333,0,4229:6,9,1,7 chr1 17280077 . CCA C 211.51 PASS AC=1;AF=0.556;AN=2;DP=163;FractionInformativeReads=1;set=variant9-variant12-variant18-variant23-variant29-variant31-variant33-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:14,8:22:99:291,0,4232:5,9,1,7 chr1 17280085 . C T 190.59 PASS AC=1;AF=0.556;AN=2;DP=127;FractionInformativeReads=1;set=variant9-variant12-variant18-variant23-variant29-variant31-variant33-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:306,0,3311:3,7,1,7 chr1 17280107 . T C 31.66 PASS AC=1;AF=0.563;AN=2;DP=83;FS=0;FractionInformativeReads=1;set=variant9-variant18-variant23-variant29-variant31-variant33-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:231,0,2432:1,5,0,6 chr1 17280118 . G T 133.71 PASS AC=1;AF=0.571;AN=2;DP=56;FS=0;FractionInformativeReads=1;set=variant18-variant23-variant29-variant31-variant33-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:198,0,1593:0,4,0,5 chr1 17280120 . G T 133.71 PASS AC=1;AF=0.571;AN=2;DP=54;FS=0;FractionInformativeReads=1;set=variant18-variant23-variant29-variant31-variant33-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:198,0,1593:0,4,0,4 chr1 17281003 . T C 1167.54 PASS AC=1;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 0/1:19,11:30:99:303,0,545:5,14,3,8 chr1 17281759 . C CG 1257.37 PASS AC=1;AF=0.556;AN=2;DP=773;MQ=60;set=variant9-variant12-variant18-variant23-variant29-variant31-variant33-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:61,29:90:99:609,0,1594:30,31,14,15 chr1 17282425 . G A 379.2 PASS AC=1;AF=0.5;AN=2;DP=187;FractionInformativeReads=1;MQ=60;set=variant18-variant23-variant29-variant31-variant33-variant38 GT:AD:DP:GQ:PL:SB 0/1:13,11:24:99:258,0,319:8,5,7,4 chr1 17282573 . G A 1399.19 PASS AC=1;AF=0.5;AN=2;DP=552;FractionInformativeReads=1;MQ=60;set=variant18-variant23-variant29-variant31-variant33-variant38 GT:AD:DP:GQ:PL:SB 0/1:35,53:88:99:1391,0,869:23,12,33,20 chr1 17285022 . A G 1073.35 PASS AC=1;AF=0.5;AN=2;DP=382;FractionInformativeReads=1;MQ=60;set=variant18-variant23-variant29-variant31-variant33-variant38 GT:AD:DP:GQ:PL:SB 0/1:22,20:42:99:487,0,550:13,9,13,7 chr1 17285298 . C T 774.32 PASS AC=1;AF=0.5;AN=2;DP=430;FractionInformativeReads=1;MQ=60;set=variant18-variant23-variant29-variant31-variant33-variant38 GT:AD:DP:GQ:PL:SB 0/1:32,33:65:99:974,0,803:16,16,14,19 chr1 17285464 . A G 144.85 PASS AC=1;AF=0.5;AN=2;DP=104;FractionInformativeReads=1;MQ=60;set=variant18-variant23-variant29-variant31-variant33-variant38 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:264,0,243:2,7,0,7 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 0/1:8,7:15:99:172,0,217:5,3,5,2 chr1 17287639 . C T 266.22 PASS AC=1;AF=0.5;AN=2;DP=185;FractionInformativeReads=1;MQ=60;set=variant18-variant23-variant29-variant31-variant33-variant38 GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:409,0,313:7,6,4,11 chr1 17292678 . G A 1681.24 PASS AC=1;AF=0.5;AN=2;DP=462;FractionInformativeReads=1;MQ=60;set=variant23-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,65:135:99:1709,0,1836:26,44,20,45 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 1/1:0,121:121:99:3674,362,0:0,0,45,76 chr1 17297289 . C T 328.65 PASS AC=1;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 0/1:8,6:14:99:140,0,198:3,5,2,4 chr1 17299014 . A C 1770.26 PASS AC=1;AF=0.898;AN=2;DP=2468;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:7,49:56:30:1114,0,30:4,3,26,23 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 0/2:62:99:28,16,11,7 chr1 17314870 . G C 3113.31 PASS AC=1;AF=0.5;AN=2;DP=291;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.288;QD=10.7;ReadPosRankSum=-1.6;SOR=0.69;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:151,140:291:99:3142,0,3673:70,81,65,75 chr1 17316010 . A AT 406.79 PASS AC=1;AF=0.5;AN=2;DP=30;FS=0;FractionInformativeReads=0.967;MQ=60;MQRankSum=1.375;QD=13.56;ReadPosRankSum=-1.898;SOR=0.776;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:14,15:29:99:444,0,401:11,3,12,3 chr1 17328301 . T C 161.25 PASS AC=2;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 1/1:0,11:11:33:320,33,0:0,0,6,5 chr1 17331676 . A G 506.5 PASS AC=2;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 1/1:1,47:48:98:1460,98,0:1,0,20,27 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 1/1:1,12:13:33:443,33,0:1,0,10,2 chr1 17345113 . G C 298.55 PASS AC=1;AF=0.5;AN=2;DP=529;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant11-variant18-variant21-variant23-variant24-variant27-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,12:34:99:273,0,556:12,10,7,5 chr1 17359386 . T C 297.52 PASS AC=1;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 0/1:23,10:33:99:257,0,675:17,6,8,2 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 1/1:0,91:91:99:2700,273,0:0,0,39,52 chr1 17371152 . T C 444.83 PASS AC=1;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 0/1:5,5:10:99:192,0,154:4,1,5,0 chr1 17371223 . C T 597.28 PASS AC=1;AF=0.5;AN=2;DP=529;MQ=60;set=variant2-variant7-variant11-variant18-variant21-variant23-variant24-variant27-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,21:48:99:587,0,725:18,9,15,6 chr1 17371494 . C T 76.42 PASS AC=1;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 0/1:2,3:5:77:79,0,77:0,2,2,1 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 1/1:1,99:100:99:2904,287,0:1,0,45,54 chr1 17393708 . AG A 216.15 PASS AC=1;AF=0.595;AN=2;DP=386;set=variant2-variant4-variant8-variant9-variant15-variant16-variant18-variant21-variant23-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant36-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:82:108,0,82:4,2,3,5 chr1 17393709 . G A 144.6 PASS AC=1;AF=0.55;AN=2;DP=169;set=variant-variant3-variant11-variant16-variant17-variant21-variant23-variant24-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:82:82,0,108:3,5,4,2 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 1/1:0,35:35:99:1299,105,0:0,0,20,15 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 1/1:0,39:39:99:1169,117,0:0,0,18,21 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 1/1:0,43:43:99:1414,129,0:0,0,22,21 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 1/1:0,38:38:99:1788,120,0:0,0,22,16 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 1/1:0,42:42:99:1839,126,0:0,0,25,17 chr1 17394880 . C T 616.69 PASS AC=1;AF=0.5;AN=2;DP=238;FractionInformativeReads=1;MQ=60;set=variant23-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,28:78:99:645,0,1385:23,27,13,15 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 1/1:0,193:193:99:6165,577,0:0,0,99,94 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 1/1:0,216:216:99:6394,644,0:0,0,101,115 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 1/1:0,22:22:66:810,66,0:0,0,18,4 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 1/1:0,86:86:99:2420,257,0:0,0,37,49 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 1/1:0,54:54:99:2377,163,0:0,0,22,32 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 1/1:0,52:52:99:2352,160,0:0,0,21,31 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 1/1:0,31:31:93:1135,93,0:0,0,23,8 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 1/1:0,118:118:99:3709,353,0:0,0,62,56 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 1/1:1,127:128:99:3986,373,0:1,0,63,64 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 1/1:0,126:126:99:3997,377,0:0,0,66,60 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 1/1:0,177:177:99:5175,529,0:0,0,88,89 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 1/1:0,166:166:99:4791,495,0:0,0,66,100 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 1/1:0,76:76:99:2422,228,0:0,0,23,53 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 1/1:0,71:71:99:2133,213,0:0,0,36,35 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 1/1:0,39:39:99:1118,117,0:0,0,17,22 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 1/1:0,20:20:60:657,60,0:0,0,6,14 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 1/1:0,7:7:21:274,21,0:0,0,2,5 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 1/1:0,6:6:18:208,18,0:0,0,1,5 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 1/1:0,80:80:99:2371,239,0:0,0,32,48 chr1 17418883 . A G 1443.29 PASS AC=2;AF=0.92;AN=2;DP=1757;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1634,111,0:0,0,26,11 chr1 17418894 . A G 702.69 PASS AC=2;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 1/1:0,41:41:99:1780,123,0:0,0,29,12 chr1 17419066 . T C 688.47 PASS AC=2;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 1/1:0,100:100:99:2864,298,0:0,0,40,60 chr1 17422226 . C T 190.14 PASS AC=2;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 1/1:0,20:20:60:762,60,0:0,0,15,5 chr1 17422302 . T C 834.87 PASS AC=2;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 1/1:0,60:60:99:1902,180,0:0,0,33,27 chr1 17431277 . G T 667.04 PASS AC=2;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 1/1:0,22:22:66:652,66,0:0,0,14,8 chr1 17431618 . A G 2723.54 PASS AC=2;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 1/1:0,93:93:99:2879,279,0:0,0,38,55 chr1 17431681 . C A 1451.29 PASS AC=2;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 1/1:0,37:37:99:1254,110,0:0,0,9,28 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 1/1:0,84:84:99:2511,251,0:0,0,44,40 chr1 17550303 . T C 1328.27 PASS AC=2;AF=0.684;AN=2;DP=1392;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant13-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant30-variant33-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2578,270,0:0,0,40,50 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 0/1:5,3:8:99:108,0,201:0,5,0,3 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 1/1:0,35:35:99:1117,104,0:0,0,14,21 chr1 17555401 . G A 87.35 PASS AC=1;AF=0.5;AN=2;DP=21;FS=2.128;FractionInformativeReads=1;MQ=60;MQRankSum=1.051;QD=4.16;ReadPosRankSum=-0.895;SOR=1.688;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:15,6:21:99:116,0,395:9,6,5,1 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 0/1:9,20:29:99:599,0,263:8,1,15,5 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 0/1:40,53:93:99:1437,0,870:22,18,30,23 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 0/1:17,13:30:99:399,0,428:6,11,2,11 chr1 17600822 . A G 309.95 PASS AC=1;AF=0.542;AN=2;DP=208;MQ=60;set=variant2-variant5-variant6-variant10-variant11-variant12-variant18-variant19-variant23-variant24-variant26-variant41 GT:AD:DP:GQ:PL:SB 0/1:11,14:25:99:358,0,306:9,2,10,4 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 0/1:38,62:100:99:1532,0,947:20,18,26,36 chr1 17601165 . C T 1033.87 PASS AC=1;AF=0.545;AN=2;DP=1105;MQ=60;set=variant2-variant5-variant6-variant11-variant12-variant18-variant19-variant23-variant24-variant26-variant41 GT:AD:DP:GQ:PL:SB 0/1:46,50:96:99:1302,0,1186:22,24,24,26 chr1 17603472 . G T 276.08 PASS AC=1;AF=0.55;AN=2;DP=245;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant12-variant18-variant19-variant23-variant24-variant26-variant41 GT:AD:DP:GQ:PL:SB 0/1:10,14:24:99:462,0,265:4,6,3,11 chr1 17609448 . G T 2001.63 PASS AC=1;AF=0.661;AN=2;DP=3289;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant25-variant27-variant29-variant30-variant31-variant32-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,73:136:99:1612,0,1555:34,29,41,32 chr1 17610030 . C T 800.81 PASS AC=1;AF=0.5;AN=2;DP=650;MQ=60;set=variant2-variant5-variant11-variant12-variant18-variant19-variant23-variant24-variant26-variant41 GT:AD:DP:GQ:PL:SB 0/1:34,46:80:99:1015,0,1014:13,21,22,24 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 0/1:33,30:63:99:797,0,742:15,18,14,16 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 0/1:11,13:24:99:500,0,381:9,2,9,4 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 1/1:0,24:24:72:709,72,0:0,0,11,13 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 1/1:0,23:23:69:711,69,0:0,0,10,13 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 1/1:0,10:10:30:355,30,0:0,0,3,7 chr1 17657534 . G A 1199.59 PASS AC=1;AF=0.632;AN=2;DP=3838;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,45:71:99:1142,0,735:14,12,20,25 chr1 17657616 . T C 1083.32 PASS AC=1;AF=0.635;AN=2;DP=3343;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-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,39:79:99:887,0,959:18,22,15,24 chr1 17660499 . G C 2846.71 PASS AC=1;AF=0.635;AN=2;DP=4126;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-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,41:102:99:934,0,1652:34,27,23,18 chr1 17660660 . G A 3084.97 PASS AC=1;AF=0.635;AN=2;DP=3744;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-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,47:87:99:1152,0,1039:15,25,20,27 chr1 17660697 . T C 2043.46 PASS AC=1;AF=0.635;AN=2;DP=2763;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-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,34:61:99:898,0,695:10,17,12,22 chr1 17661128 . A C 5226.38 PASS AC=1;AF=0.697;AN=2;DP=5434;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-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,56:124:99:1331,0,1537:33,35,29,27 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 0/1:27,17:44:99:355,0,648:14,13,9,8 chr1 17662541 . A C 668.48 PASS AC=1;AF=0.703;AN=2;DP=898;FractionInformativeReads=1;MQ=60;set=variant-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-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,10:21:99:306,0,398:11,0,8,2 chr1 17662639 . T C 2837.79 PASS AC=1;AF=0.635;AN=2;DP=4830;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-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,52:122:99:1145,0,1756:44,26,30,22 chr1 17662662 . T C 3360.5 PASS AC=1;AF=0.697;AN=2;DP=5938;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-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:88,57:145:99:1408,0,2204:54,34,35,22 chr1 17662751 . C G 3397.09 PASS AC=1;AF=0.697;AN=2;DP=6094;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-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:96,58:154:99:1314,0,2456:46,50,28,30 chr1 17662804 . C T 2753.24 PASS AC=1;AF=0.697;AN=2;DP=4092;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-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,49:122:99:1246,0,2007:29,44,18,31 chr1 17662907 . A T 2107.85 PASS AC=1;AF=0.697;AN=2;DP=2249;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-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,28:59:99:646,0,860:15,16,11,17 chr1 17664770 . A G 812.07 PASS AC=1;AF=0.697;AN=2;DP=975;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-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:329,0,370:0,11,0,9 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 0/1:14,11:25:99:217,0,334:6,8,6,5 chr1 17666545 . GCGCACACACA GCACACA,GCACA,GCACACACACACACA,GCACACACGCACACACA,GCACACACACACACACA,G 383.24 PASS AC=1,0,0,0,0,0;AF=0.656,0.016,0.016,0.031,0.016,0.031;AN=2;DP=411;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant38-variant39-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:13:99:2,4,1,6 chr1 17666547 . G A 177.49 PASS AC=1;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 0/1:7,6:13:99:149,0,273:1,6,2,4 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 0/1:7,6:13:99:138,0,186:5,2,4,2 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 0/1:22,23:45:99:613,0,555:15,7,15,8 chr1 17674537 . C A 2400.38 PASS AC=1;AF=0.6;AN=2;DP=4335;MQ=60;set=variant-variant3-variant4-variant7-variant8-variant9-variant11-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,58:109:99:1274,0,1382:28,23,29,29 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 1/1:0,70:70:99:2306,210,0:0,0,20,50 chr1 17707798 . C T 1094.39 PASS AC=2;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 1/1:0,18:18:53:689,53,0:0,0,2,16 chr1 17708349 . G A 1009.46 PASS AC=2;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 1/1:1,34:35:59:1265,59,0:1,0,31,3 chr1 17714710 . A C 761.87 PASS AC=1;AF=0.609;AN=2;DP=577;MQ=60;set=variant-variant4-variant5-variant9-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant27-variant28-variant29-variant32-variant33-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:209,0,147:4,1,6,1 chr1 17714864 . T C 1275.48 PASS AC=1;AF=0.579;AN=2;DP=1779;MQ=60;set=variant-variant4-variant9-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant27-variant28-variant29-variant33-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,37:81:99:1014,0,1016:25,19,24,13 chr1 17715081 . C T 2459.13 PASS AC=1;AF=0.609;AN=2;DP=1889;MQ=60;set=variant-variant4-variant5-variant9-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant27-variant28-variant29-variant32-variant33-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,43:81:99:1161,0,1023:13,25,18,25 chr1 17715135 . T C 2106.39 PASS AC=1;AF=0.609;AN=2;DP=1230;MQ=60;set=variant-variant4-variant5-variant9-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant27-variant28-variant29-variant32-variant33-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,22:48:99:720,0,753:13,13,10,12 chr1 17715475 . T C 1389.06 PASS AC=1;AF=0.609;AN=2;DP=749;MQ=60;set=variant-variant4-variant5-variant9-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant27-variant28-variant29-variant32-variant33-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,13:20:99:412,0,218:2,5,2,11 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 0/1:3,10:13:99:307,0,99:2,1,6,4 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 1/1:0,59:59:99:2092,178,0:0,0,24,35 chr1 17718750 . C T 514.13 PASS AC=1;AF=0.609;AN=2;DP=657;MQ=60;set=variant-variant4-variant5-variant9-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant27-variant28-variant29-variant32-variant33-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,14:25:99:420,0,270:4,7,4,10 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 0/1:56,47:103:99:1152,0,1289:32,24,31,16 chr1 17720439 . T C 4316.55 PASS AC=2;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 1/1:0,138:138:99:4259,412,0:0,0,74,64 chr1 17720545 . C T 1881.31 PASS AC=1;AF=0.563;AN=2;DP=1151;MQ=60;set=variant4-variant10-variant13-variant23-variant28-variant33-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:85,56:141:99:1340,0,2198:36,49,26,30 chr1 17720615 . A C 2479.76 PASS AC=2;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 1/1:0,102:102:99:3354,305,0:0,0,47,55 chr1 17720686 . AG A 788.69 PASS AC=2;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 1/1:0,47:47:99:1490,141,0:0,0,24,23 chr1 17721388 . C T 252.51 PASS AC=2;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 1/1:1,12:13:29:397,29,0:1,0,8,4 chr1 17721695 . GTTT GTT,G,GT,GTTTT 1277.23 PASS AC=1,1,0,0;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 2/1:29:99:0,0,6,23 chr1 17721707 . T G 1347.98 PASS AC=1;AF=0.614;AN=2;DP=930;set=variant-variant4-variant5-variant9-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant27-variant28-variant29-variant32-variant33-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,14:30:99:448,0,581:4,12,3,11 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 0/1:6,10:16:99:388,0,222:1,5,0,10 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 0/1:18,14:32:99:533,0,725:15,3,11,3 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 0/1:21,10:31:99:303,0,617:5,16,1,9 chr1 17725011 . T C 52.67 PASS AC=2;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 1/1:0,9:9:27:280,27,0:0,0,4,5 chr1 17725358 . C G 515.71 PASS AC=2;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 1/1:0,76:76:99:2141,228,0:0,0,30,46 chr1 17738570 . AC A 3424.64 PASS AC=1;AF=0.619;AN=2;DP=3061;MQ=60;set=variant-variant4-variant5-variant9-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant27-variant29-variant32-variant33-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,60:116:99:1787,0,1644:33,23,33,27 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 0/1:9,8:17:99:187,0,277:6,3,5,3 chr1 17739820 . T C 1537.04 PASS AC=2;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 1/1:0,70:70:99:2140,210,0:0,0,26,44 chr1 17740357 . G A 283.54 PASS AC=1;AF=0.619;AN=2;DP=550;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant9-variant10-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant27-variant29-variant32-variant33-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:228,0,282:2,6,0,6 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 0/1:17,30:47:99:818,0,423:12,5,20,10 chr1 17907505 . A G 513.75 PASS AC=2;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 1/1:0,20:20:60:731,60,0:0,0,3,17 chr1 17907575 . C T 66.22 PASS AC=2;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 1/1:0,3:3:9:111,9,0:0,0,0,3 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 1/1:0,5:5:15:161,15,0:0,0,2,3 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 1/1:0,2:2:6:73,6,0:0,0,1,1 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 1/1:0,20:20:57:606,57,0:0,0,16,4 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 0/1:47,36:83:99:770,0,1141:29,18,19,17 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 1/1:0,140:140:99:4146,419,0:0,0,70,70 chr1 18017522 . T C 1960.66 PASS AC=2;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 1/1:0,46:46:99:1336,138,0:0,0,28,18 chr1 18017558 . A G 3148.13 PASS AC=2;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 1/1:0,56:56:99:1813,167,0:0,0,32,24 chr1 18017704 . C T 2430.23 PASS AC=2;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 1/1:0,59:59:99:1819,177,0:0,0,21,38 chr1 18021406 . T C 3104.12 PASS AC=2;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 1/1:0,119:119:99:3710,356,0:0,0,72,47 chr1 18023154 . A G 291.22 PASS AC=2;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 1/1:0,24:24:72:841,72,0:0,0,19,5 chr1 18023290 . C T 2120.58 PASS AC=2;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 1/1:0,107:107:99:3252,318,0:0,0,57,50 chr1 18023365 . C T 3592.28 PASS AC=2;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 1/1:0,128:128:99:4053,381,0:0,0,65,63 chr1 18023509 . T C 2590.79 PASS AC=2;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 1/1:0,90:90:99:2910,270,0:0,0,39,51 chr1 18023690 . A G 3854.74 PASS AC=2;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 1/1:0,139:139:99:4246,417,0:0,0,74,65 chr1 18023997 . G GC 2815.45 PASS AC=2;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 1/1:0,70:70:99:2596,211,0:0,0,29,41 chr1 18149476 . G A 1529.77 PASS AC=1;AF=0.5;AN=2;DP=212;MQ=60;set=variant9-variant23 GT:AD:DP:GQ:PL:SB 0/1:39,44:83:99:1348,0,1101:29,10,34,10 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 1/1:0,11:11:33:370,33,0:0,0,6,5 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 0/1:3,6:9:99:202,0,110:0,3,1,5 chr1 18554345 . T C 366.12 PASS AC=1;AF=0.583;AN=2;DP=1380;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant7-variant11-variant12-variant14-variant18-variant19-variant20-variant21-variant23-variant24-variant28-variant29-variant31-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,30:61:99:718,0,814:19,12,20,10 chr1 18554356 . C T 369.75 PASS AC=1;AF=0.583;AN=2;DP=1604;MQ=60;set=variant-variant2-variant5-variant7-variant11-variant12-variant14-variant18-variant19-variant20-variant21-variant23-variant24-variant28-variant29-variant31-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,36:67:99:823,0,761:18,13,21,15 chr1 18661583 . T C 1307.65 PASS AC=1;AF=0.55;AN=2;DP=620;MQ=60;set=variant3-variant10-variant12-variant13-variant17-variant23-variant30-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:28,14:42:99:346,0,814:11,17,3,11 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 1/1:0,12:12:36:407,36,0:0,0,3,9 chr1 18703458 . C T 3703.02 PASS AC=1;AF=0.5;AN=2;DP=285;FS=0.431;FractionInformativeReads=1;MQ=60;MQRankSum=-1.223;QD=12.99;ReadPosRankSum=0.605;SOR=0.732;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:128,157:285:99:3731,0,2858:64,64,80,77 chr1 18703523 . A G 7486.33 PASS AC=2;AF=0.696;AN=2;DP=5897;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant12-variant13-variant16-variant18-variant19-variant22-variant23-variant24-variant28-variant30-variant32-variant34-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,213:213:99:8999,641,0:0,0,87,126 chr1 18703538 . G C 6270.49 PASS AC=2;AF=0.705;AN=2;DP=4848;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant12-variant13-variant16-variant18-variant19-variant22-variant23-variant24-variant28-variant32-variant34-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,181:181:99:8067,548,0:0,0,69,112 chr1 18704862 . A G 4971.26 PASS AC=2;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 1/1:0,146:146:99:4444,436,0:0,0,61,85 chr1 18807536 . G T 1310.8 PASS AC=1;AF=0.5;AN=2;DP=1445;MQ=60;set=variant11-variant12-variant13-variant16-variant19-variant22-variant23-variant24-variant29-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:65,47:112:99:967,0,1630:32,33,24,23 chr1 18807620 . G C 1159.32 PASS AC=1;AF=0.5;AN=2;DP=1237;MQ=60;set=variant11-variant12-variant13-variant16-variant19-variant22-variant23-variant24-variant29-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:53,43:96:99:1143,0,1338:24,29,18,25 chr1 18807755 . G A 1749.41 PASS AC=1;AF=0.5;AN=2;DP=1159;MQ=60;set=variant11-variant12-variant13-variant16-variant19-variant22-variant23-variant24-variant29-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,52:94:99:1382,0,1044:25,17,32,20 chr1 18807781 . C T 1977.19 PASS AC=1;AF=0.5;AN=2;DP=1368;MQ=60;set=variant11-variant12-variant13-variant16-variant19-variant22-variant23-variant24-variant29-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:59,60:119:99:1480,0,1536:33,26,38,22 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 0/1:104,109:213:99:2648,0,2642:57,47,57,52 chr1 18808056 . G C 5388.1 PASS AC=1;AF=0.5;AN=2;DP=4072;MQ=60;set=variant11-variant12-variant13-variant16-variant19-variant22-variant23-variant24-variant29-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:162,124:286:99:4537,0,8698:81,81,59,65 chr1 18808069 . A G 5486.75 PASS AC=1;AF=0.5;AN=2;DP=3977;MQ=60;set=variant11-variant12-variant13-variant16-variant19-variant22-variant23-variant24-variant29-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:158,122:280:99:4488,0,8604:77,81,56,66 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 0/1:84,87:171:99:2087,0,2066:43,41,44,43 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 0/1:44,56:100:99:1499,0,1030:19,25,24,32 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 0/1:52,68:120:99:1786,0,1172:24,28,31,37 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 0/1:56,45:101:99:1292,0,1458:22,34,19,26 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 0/1:28,18:46:99:645,0,1566:12,16,10,8 chr1 18810349 . G C 1604 PASS AC=1;AF=0.5;AN=2;DP=858;FractionInformativeReads=1;MQ=60;set=variant11-variant12-variant13-variant16-variant19-variant22-variant23-variant24-variant29-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,17:46:99:645,0,1566:13,16,9,8 chr1 18811121 . G A 690.15 PASS AC=1;AF=0.5;AN=2;DP=500;MQ=60;set=variant11-variant12-variant13-variant16-variant19-variant22-variant23-variant24-variant29-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,9:28:99:233,0,478:9,10,3,6 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 0/1:18,16:34:99:485,0,530:10,8,7,9 chr1 18957546 . G A 175.66 PASS AC=1;AF=0.5;AN=2;DP=106;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant14-variant18-variant19-variant21-variant22-variant23-variant28-variant39 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:175,0,140:3,3,4,3 chr1 19071153 . C CGGAT,CGGATGGAT 127.32 PASS AC=1,1;AF=0.462,0.25;AN=2;DP=385;set=variant-variant5-variant6-variant8-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant40-variant44 GT:DP:GQ:SB 1/2:11:99:0,0,11,0 chr1 19071183 . A AATGG,G,AATGGATGG 699.95 PASS AC=1,0,0;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 0/1:17:99:9,1,6,1 chr1 19071752 . T C 339.76 PASS AC=1;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 0/1:14,23:37:99:639,0,400:7,7,10,13 chr1 19072926 . A G 269.05 PASS AC=1;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 0/1:13,13:26:99:374,0,402:5,8,7,6 chr1 19075225 . A G 2525.49 PASS AC=1;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 0/1:79,56:135:99:1299,0,1970:45,34,31,25 chr1 19175846 . T C 500.93 PASS AC=1;AF=0.55;AN=2;DP=408;FractionInformativeReads=1;MQ=60;set=variant5-variant13-variant23-variant26-variant30-variant31-variant32-variant33-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:34,20:54:99:469,0,818:22,12,12,8 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 0/1:8,2:10:60:60,0,243:3,5,0,2 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 1/1:0,115:115:99:3455,345,0:0,0,64,51 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 0/1:42,38:80:99:933,0,1052:19,23,12,26 chr1 19186320 . G C 1359.12 PASS AC=1;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 0/1:31,24:55:99:787,0,771:14,17,7,17 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 0/1:16,24:40:99:639,0,379:9,7,15,9 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 0/1:23,25:48:99:804,0,594:11,12,15,10 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 0/1:30,40:70:99:1034,0,706:18,12,22,18 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 0/1:37,45:82:99:1743,0,2182:18,19,19,26 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 0/1:38,45:83:99:1743,0,2182:19,19,19,26 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 0/1:62,43:105:99:1050,0,1627:33,29,28,15 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 0/1:74,66:140:99:1580,0,1814:39,35,37,29 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 0/1:30,17:47:99:491,0,778:14,16,7,10 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 0/1:66,67:133:99:1500,0,1518:34,32,32,35 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 0/1:28,23:51:99:516,0,719:16,12,16,7 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 0/1:11,10:21:99:320,0,263:4,7,1,9 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 0/1:4,7:11:99:229,0,117:0,4,0,7 chr1 19201928 . C T 1564.41 PASS AC=1;AF=0.563;AN=2;DP=986;FractionInformativeReads=1;MQ=60;set=variant10-variant13-variant23-variant26-variant30-variant31-variant32-variant40 GT:AD:DP:GQ:PL:SB 0/1:54,35:89:99:776,0,1365:29,25,17,18 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 0/1:39,71:110:99:1682,0,854:18,21,36,35 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 1/1:0,97:97:99:3001,291,0:0,0,50,47 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 0/1:42,34:76:99:769,0,996:17,25,16,18 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 0/1:33,29:62:99:1091,0,1764:11,22,13,16 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 0/1:31,28:59:99:1058,0,1712:10,21,12,16 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 0/1:39,48:87:99:1229,0,899:17,22,24,24 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 1/1:0,16:16:48:522,48,0:0,0,6,10 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 1/1:0,17:17:51:554,51,0:0,0,6,11 chr1 19205672 . T G 1363.58 PASS AC=1;AF=0.565;AN=2;DP=2087;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant10-variant12-variant13-variant14-variant16-variant17-variant22-variant23-variant24-variant26-variant30-variant31-variant32-variant34-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,23:67:99:588,0,1175:26,18,15,8 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 1/1:0,41:41:99:1935,129,0:0,0,24,17 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 1/1:0,26:26:78:847,78,0:0,0,18,8 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 1/1:0,82:82:99:2694,244,0:0,0,58,24 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 1/1:0,297:297:99:8777,888,0:0,0,176,121 chr1 19223571 . A G 300.62 PASS AC=1;AF=0.5;AN=2;DP=120;FractionInformativeReads=1;MQ=60;set=variant10-variant23 GT:AD:DP:GQ:PL:SB 0/1:25,33:58:99:896,0,647:9,16,10,23 chr1 19231800 . G A 2586.81 PASS AC=1;AF=0.5;AN=2;DP=677;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant18-variant21-variant23 GT:AD:DP:GQ:PL:SB 0/1:63,47:110:99:1161,0,1511:38,25,31,16 chr1 19243589 . A G 2939.97 PASS AC=1;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 0/1:44,56:100:99:1300,0,998:17,27,22,34 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 1/1:0,76:76:99:2362,228,0:0,0,32,44 chr1 19401405 . G A 1159.43 PASS AC=1;AF=0.593;AN=2;DP=4558;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:75,74:149:99:1747,0,1869:38,37,33,41 chr1 19404176 . G A 96.2 PASS AC=1;AF=0.62;AN=2;DP=257;FractionInformativeReads=1;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:94:94,0,118:3,2,3,1 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 0/1:34,34:68:99:761,0,909:18,16,16,18 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 0/1:6,3:9:99:108,0,163:4,2,3,0 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 0/1:81,51:132:99:1093,0,1991:43,38,24,27 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 0/1:21,25:46:99:713,0,608:7,14,7,18 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 0/1:17,22:39:99:608,0,348:10,7,17,5 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 0/1:27,40:67:99:1026,0,697:15,12,23,17 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 0/1:16,9:25:99:207,0,441:5,11,2,7 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 0/1:7,8:15:99:225,0,238:1,6,2,6 chr1 19439838 . C A 864.41 PASS AC=1;AF=0.5;AN=2;DP=66;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.56;QD=13.1;ReadPosRankSum=1.668;SOR=0.654;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:30,36:66:99:893,0,678:17,13,20,16 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 0/1:65,62:127:99:1581,0,1657:32,33,33,29 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 0/1:6,8:14:99:311,0,232:6,0,8,0 chr1 19441594 . C G 988.65 PASS AC=1;AF=0.5;AN=2;DP=265;FractionInformativeReads=1;MQ=60;set=variant11-variant17-variant20-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:27,18:45:99:479,0,756:9,18,4,14 chr1 19441689 . ACATG A 240.61 PASS AC=1;AF=0.5;AN=2;DP=107;MQ=60;set=variant11-variant17-variant20-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:131,0,259:4,3,2,3 chr1 19444552 . G A 252.92 PASS AC=1;AF=0.5;AN=2;DP=115;FractionInformativeReads=1;MQ=60;set=variant11-variant17-variant20-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:16,9:25:99:258,0,417:6,10,2,7 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 0/1:5,7:12:99:267,0,183:5,0,7,0 chr1 19447819 . T C 1754.92 PASS AC=1;AF=0.5;AN=2;DP=349;FractionInformativeReads=1;MQ=60;set=variant11-variant17-variant20-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:31,31:62:99:1065,0,1521:14,17,12,19 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 0/1:27,28:55:99:988,0,1504:13,14,12,16 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 0/1:40,39:79:99:952,0,1034:23,17,24,15 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 0/1:3,4:7:75:104,0,75:1,2,1,3 chr1 19450938 . G A 389.86 PASS AC=1;AF=0.5;AN=2;DP=81;FractionInformativeReads=1;MQ=60;set=variant11-variant17-variant20-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:7,13:20:99:403,0,246:7,0,9,4 chr1 19454560 . C T 455.36 PASS AC=1;AF=0.5;AN=2;DP=32;FS=3.467;FractionInformativeReads=1;MQ=60;MQRankSum=-0.264;QD=14.23;ReadPosRankSum=-1.322;SOR=1.577;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:15,17:32:99:484,0,447:9,6,13,4 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 0/1:11,19:30:99:458,0,203:5,6,9,10 chr1 19474216 . GCTCAATATCC G 357.96 PASS AC=1;AF=0.5;AN=2;DP=84;FractionInformativeReads=1;MQ=60;set=variant11-variant17-variant20-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:4,16:20:99:660,0,335:3,1,12,4 chr1 19474975 . T G 1279.91 PASS AC=1;AF=0.589;AN=2;DP=2428;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,31:74:99:715,0,1033:25,18,20,11 chr1 19481184 . C T 312.97 PASS AC=1;AF=0.5;AN=2;DP=80;FractionInformativeReads=1;MQ=60;set=variant11-variant17-variant20-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:153,0,226:5,1,4,2 chr1 19483209 . A G 439.54 PASS AC=1;AF=0.6;AN=2;DP=1139;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,19:27:99:490,0,206:7,1,11,8 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 0/1:14,12:26:99:374,0,474:1,13,2,10 chr1 19487656 . T C 1647.36 PASS AC=1;AF=0.583;AN=2;DP=4116;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:50,63:113:99:1661,0,1358:20,30,26,37 chr1 19489275 . G A 199.33 PASS AC=1;AF=0.589;AN=2;DP=354;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:141,0,151:1,3,0,4 chr1 19491514 . G C 430.82 PASS AC=1;AF=0.5;AN=2;DP=103;FractionInformativeReads=1;MQ=60;set=variant11-variant17-variant20-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:255,0,271:2,6,1,6 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 0/1:35,42:77:99:1001,0,946:16,19,23,19 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 0/1:31,34:65:99:899,0,904:17,14,18,16 chr1 19499873 . G T 836.23 PASS AC=1;AF=0.5;AN=2;DP=384;MQ=60;set=variant11-variant17-variant20-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:33,32:65:99:862,0,829:17,16,17,15 chr1 19499954 . G A 618.98 PASS AC=1;AF=0.5;AN=2;DP=465;FractionInformativeReads=1;MQ=60;set=variant11-variant17-variant20-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:30,43:73:99:1170,0,909:13,17,20,23 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 0/1:17,22:39:99:612,0,471:12,5,15,7 chr1 19504306 . C G 267 PASS AC=1;AF=0.5;AN=2;DP=190;FractionInformativeReads=1;MQ=60;set=variant11-variant17-variant20-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:19,25:44:99:570,0,434:7,12,11,14 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 0/1:79,64:143:99:1571,0,1918:43,36,37,27 chr1 19513570 . TTA T 35.63 PASS AC=2;AF=0.885;AN=2;DP=59;FS=0;MQ=60;set=variant14-variant15-variant17-variant23-variant24-variant28-variant29-variant31-variant33-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:73,6,0:0,0,1,1 chr1 19518659 . G A 376.26 PASS AC=1;AF=0.589;AN=2;DP=1464;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,28:58:99:734,0,930:23,7,20,8 chr1 19519782 . C T 411.9 PASS AC=1;AF=0.589;AN=2;DP=803;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,9:21:99:235,0,374:10,2,7,2 chr1 19545053 . C T 447.76 PASS AC=1;AF=0.5;AN=2;DP=191;FractionInformativeReads=1;MQ=60;set=variant11-variant17-variant20-variant23-variant27-variant34 GT:AD:DP:GQ:PL:SB 0/1:19,8:27:99:139,0,480:11,8,4,4 chr1 19545140 . CAA C 788.92 PASS AC=1;AF=0.5;AN=2;DP=178;MQ=60;set=variant11-variant17-variant20-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:23,17:40:99:643,0,908:14,9,11,6 chr1 19545484 . A AAAAAC,AAAAAAC 530.13 PASS AC=1,0;AF=0.567,0.017;AN=2;DP=1936;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant36-variant39-variant40-variant43 GT:DP:GQ:SB 0/1:48:99:6,13,13,16 chr1 19549759 . G A 266.63 PASS AC=1;AF=0.586;AN=2;DP=538;FractionInformativeReads=1;set=variant-variant2-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:274,0,351:9,0,8,2 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 0/1:10,9:19:99:249,0,347:1,9,2,7 chr1 19557281 . G C 224.78 PASS AC=1;AF=0.5;AN=2;DP=104;FractionInformativeReads=1;MQ=60;set=variant11-variant17-variant20-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:284,0,432:10,3,8,1 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 0/1:11,6:17:99:170,0,364:7,4,4,2 chr1 19558018 . C T 692.59 PASS AC=1;AF=0.5;AN=2;DP=343;FractionInformativeReads=1;MQ=60;set=variant11-variant17-variant20-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:39,36:75:99:789,0,907:17,22,15,21 chr1 19558096 . A T 406.3 PASS AC=1;AF=0.5;AN=2;DP=135;FractionInformativeReads=1;MQ=60;set=variant11-variant17-variant20-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:20,15:35:99:317,0,553:6,14,6,9 chr1 19559729 . A G 558.28 PASS AC=1;AF=0.5;AN=2;DP=288;FractionInformativeReads=1;MQ=60;set=variant4-variant11-variant17-variant20-variant23-variant27-variant34 GT:AD:DP:GQ:PL:SB 0/1:12,25:37:99:673,0,357:3,9,10,15 chr1 19563461 . CAAAAA CAA,CAAA,CAAAA,CA,CAAAAAA,C 122.48 PASS AC=1,0,0,0,0,0;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 0/1:8:82:3,2,3,0 chr1 19565338 . C T 1926.45 PASS AC=1;AF=0.5;AN=2;DP=598;FractionInformativeReads=1;MQ=60;set=variant4-variant11-variant17-variant20-variant23-variant27-variant34 GT:AD:DP:GQ:PL:SB 0/1:53,46:99:99:1761,0,3068:27,26,21,25 chr1 19565344 . C G 1395.16 PASS AC=1;AF=0.569;AN=2;DP=2545;FractionInformativeReads=1;set=variant-variant2-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:55,46:101:99:1780,0,3045:28,27,21,25 chr1 19566627 . A G 492.42 PASS AC=1;AF=0.5;AN=2;DP=174;FractionInformativeReads=1;MQ=60;set=variant4-variant11-variant17-variant20-variant23-variant27-variant34 GT:AD:DP:GQ:PL:SB 0/1:9,11:20:99:310,0,222:5,4,6,5 chr1 19568722 . G C 177.11 PASS AC=1;AF=0.569;AN=2;DP=1028;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,15:31:99:365,0,418:10,6,9,6 chr1 19568972 . A G 430.63 PASS AC=1;AF=0.569;AN=2;DP=1739;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,26:52:99:643,0,641:11,15,10,16 chr1 19570426 . C G 562.05 PASS AC=1;AF=0.5;AN=2;DP=302;FractionInformativeReads=1;MQ=60;set=variant11-variant17-variant20-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:22,22:44:99:655,0,496:12,10,15,7 chr1 19578192 . G A 2406.15 PASS AC=1;AF=0.662;AN=2;DP=7750;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,94:176:99:2329,0,2239:40,42,56,38 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 0/1:29,35:64:99:884,0,687:16,13,19,16 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 0/1:35:99:4,13,7,11 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 0/1:15,18:33:99:687,0,609:5,10,6,12 chr1 19582563 . G A 1599.12 PASS AC=2;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 1/1:0,136:136:99:4091,408,0:0,0,58,78 chr1 19583330 . G C 579.31 PASS AC=1;AF=0.538;AN=2;DP=516;MQ=60;set=variant2-variant5-variant10-variant12-variant13-variant15-variant16-variant23-variant27-variant34-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,20:34:99:553,0,235:6,8,11,9 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 1/1:0,30:30:90:1051,90,0:0,0,19,11 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 0/1:32,35:67:99:865,0,852:14,18,16,19 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 0/1:23,30:53:99:985,0,867:9,14,14,16 chr1 19583734 . G A 734.38 PASS AC=1;AF=0.662;AN=2;DP=2136;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,24:53:99:694,0,1156:14,15,9,15 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 0/1:43,52:95:99:1434,0,1072:14,29,22,30 chr1 19584578 . T C 1181.79 PASS AC=1;AF=0.5;AN=2;DP=683;MQ=60;set=variant11-variant17-variant20-variant21-variant23-variant31 GT:AD:DP:GQ:PL:SB 0/1:60,42:102:99:950,0,1507:22,38,17,25 chr1 19585207 . G A 1945.58 PASS AC=1;AF=0.5;AN=2;DP=1065;FractionInformativeReads=1;set=variant4-variant11-variant17-variant20-variant21-variant23-variant31 GT:AD:DP:GQ:PL:SB 0/1:61,78:139:99:2049,0,1621:34,27,36,42 chr1 19585545 . G A 185.02 PASS AC=2;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 1/1:2,22:24:22:747,22,0:1,1,3,19 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 0/1:14,13:27:99:324,0,430:9,5,9,4 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 0/1:40,23:63:99:468,0,984:18,22,11,12 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 0/1:52,30:82:99:717,0,1282:32,20,19,11 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 0/1:48,39:87:99:981,0,1458:12,36,12,27 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 0/1:20,22:42:99:618,0,495:12,8,14,8 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 0/1:26,32:58:99:751,0,581:14,12,19,13 chr1 19597420 . G T 1538.04 PASS AC=1;AF=0.536;AN=2;DP=1869;set=variant2-variant5-variant10-variant12-variant13-variant15-variant16-variant17-variant23-variant27-variant34-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,43:101:99:962,0,1459:26,32,20,23 chr1 19609254 . T C 1834.13 PASS AC=1;AF=0.83;AN=2;DP=9083;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:84,113:197:99:2533,0,1952:43,41,57,56 chr1 19609437 . T C 115.21 PASS AC=1;AF=0.556;AN=2;DP=231;FractionInformativeReads=1;set=variant4-filterInvariant10-variant12-variant16-variant17-variant23-variant27-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:16,7:23:99:205,0,450:7,9,0,7 chr1 19611241 . T C 692.34 PASS AC=1;AF=0.818;AN=2;DP=5419;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:50,59:109:99:1455,0,1144:24,26,27,32 chr1 19612492 . C T 3513.78 PASS AC=1;AF=0.5;AN=2;DP=298;FS=2.482;FractionInformativeReads=1;MQ=59.5;MQRankSum=0.557;QD=11.79;ReadPosRankSum=-0.798;SOR=0.569;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:148,150:298:99:3542,0,3518:79,69,75,75 chr1 19632757 . C T 773.3 PASS AC=1;AF=0.5;AN=2;DP=207;MQ=60;set=variant20-variant21-variant23-variant31 GT:AD:DP:GQ:PL:SB 0/1:16,18:34:99:472,0,397:5,11,5,13 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 1/1:0,87:87:99:2740,261,0:0,0,50,37 chr1 19638643 . G GCCGGGGGCCCCGGGGGCC,GCCGGGGGCC 543.23 PASS AC=0,1;AF=0.111,0.444;AN=2;DP=559;MQ=60;set=variant3-variant4-variant7-variant10-variant20-variant21-variant23-variant26-variant28-variant30-variant31-variant32-variant36-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/2:31:99:8,9,6,8 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 1/1:0,61:61:99:1995,183,0:0,0,38,23 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 0/1:16,5:21:99:150,0,562:13,3,5,0 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 0/1:77,53:130:99:1244,0,1836:39,38,31,22 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 0/1:20,25:45:99:892,0,756:6,14,10,15 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 0/1:10,21:31:99:808,0,525:2,8,7,14 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 0/1:5,10:15:99:350,0,184:0,5,3,7 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 0/1:48,62:110:99:1526,0,1223:30,18,32,30 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 0/1:24,38:62:99:1432,0,920:13,11,17,21 chr1 19652132 . T G 1098.78 PASS AC=1;AF=0.732;AN=2;DP=1493;MQ=60;set=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-filterInvariant30-variant-variant32 GT:AD:DP:GQ:PL:SB 0/1:38,24:62:99:448,0,1467:17,21,11,13 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 0/1:27,37:64:99:1457,0,886:13,14,15,22 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 0/1:16,19:35:99:592,0,439:11,5,13,6 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 0/1:17,15:32:99:517,0,665:1,16,6,9 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 0/1:30,35:65:99:887,0,934:14,16,21,14 chr1 19746332 . A T 562.59 PASS AC=1;AF=0.542;AN=2;DP=485;FractionInformativeReads=1;MQ=60;set=variant8-variant13-variant15-variant17-variant22-variant23-variant28-variant29-variant30-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,23:43:99:546,0,404:10,10,11,12 chr1 19775566 . G A 803.61 PASS AC=1;AF=0.542;AN=2;DP=719;FractionInformativeReads=1;MQ=60;set=variant8-variant13-variant15-variant17-variant22-variant23-variant28-variant29-variant30-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,30:55:99:790,0,714:10,15,13,17 chr1 19775811 . G A 238.83 PASS AC=1;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 0/1:15,17:32:99:463,0,327:6,9,6,11 chr1 19934634 . G A 528.32 PASS AC=1;AF=0.5;AN=2;DP=193;FractionInformativeReads=1;MQ=60;set=variant13-variant23-variant28-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:17,18:35:99:664,0,564:14,3,17,1 chr1 19934900 . G A 2892.21 PASS AC=2;AF=0.556;AN=2;DP=3324;set=variant3-variant5-variant8-variant11-variant12-variant13-variant14-variant17-variant18-variant20-variant23-variant27-variant28-variant29-variant32-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,170:170:99:5230,507,0:0,0,74,96 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 1/1:0,19:19:57:689,57,0:0,0,14,5 chr1 19954014 . G T 1028.74 PASS AC=2;AF=0.556;AN=2;DP=824;MQ=60;set=variant3-variant5-variant8-variant11-variant12-variant13-variant14-variant17-variant18-variant20-variant23-variant27-variant28-variant29-variant32-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1412,126,0:0,0,18,24 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 1/1:0,126:126:99:4123,378,0:0,0,38,88 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 1/1:0,25:25:75:766,75,0:0,0,16,9 chr1 19970727 . C G 355.9 PASS AC=2;AF=0.55;AN=2;DP=432;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant8-variant11-variant12-variant13-variant14-variant17-variant18-variant20-variant23-variant24-variant27-variant28-variant29-variant32-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:674,72,0:0,0,10,14 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 1/1:0,78:78:99:2637,235,0:0,0,41,37 chr1 20027034 . ATCT A 543.6 PASS AC=1;AF=0.629;AN=2;DP=637;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,11:16:99:447,0,177:4,1,11,0 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 0/1:12,3:15:91:91,0,422:12,0,3,0 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 0/1:26,37:63:99:973,0,630:9,17,16,21 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 0/1:19,33:52:99:867,0,400:8,11,13,20 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 0/1:22,19:41:99:567,0,530:9,13,6,13 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 0/1:6,6:12:99:150,0,140:2,4,3,3 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 0/1:57,45:102:99:988,0,1396:30,27,26,19 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 0/1:31,30:61:99:769,0,707:13,18,12,18 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 0/1:9,15:24:99:368,0,318:9,0,10,5 chr1 20140581 . C T 1059.17 PASS AC=1;AF=0.5;AN=2;DP=315;FractionInformativeReads=1;MQ=60;set=variant-variant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:44,52:96:99:1190,0,1095:24,20,25,27 chr1 20141283 . C T 1905.7 PASS AC=1;AF=0.5;AN=2;DP=677;MQ=60;set=variant5-variant16-variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:78,71:149:99:1779,0,1958:39,39,30,41 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 0/1:133,119:252:99:2474,0,3400:62,71,56,63 chr1 20141761 . G A 393.94 PASS AC=1;AF=0.5;AN=2;DP=128;FractionInformativeReads=1;MQ=60;set=variant10-variant23-variant30 GT:AD:DP:GQ:PL:SB 0/1:16,24:40:99:557,0,478:5,11,9,15 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 1/1:0,4:4:12:150,12,0:0,0,1,3 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 1/1:0,41:41:99:1187,122,0:0,0,25,16 chr1 20224152 . G A 648.57 PASS AC=1;AF=0.5;AN=2;DP=759;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant15-variant16-variant18-variant23-variant36-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,29:52:99:780,0,581:9,14,8,21 chr1 20233226 . A G 334.09 PASS AC=1;AF=0.5;AN=2;DP=204;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant15-variant16-variant18-variant23-variant36-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:234,0,192:0,5,0,6 chr1 20236027 . A G 809.13 PASS AC=1;AF=0.5;AN=2;DP=569;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant15-variant16-variant18-variant23-variant36-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,28:54:99:715,0,698:16,10,18,10 chr1 20236731 . A G 837.42 PASS AC=1;AF=0.548;AN=2;DP=1406;MQ=60;set=variant-variant2-variant4-variant9-variant12-variant15-variant16-variant17-variant18-variant22-variant23-variant25-variant26-variant28-variant33-variant34-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,21:48:99:614,0,721:13,14,10,11 chr1 20237881 . AT ATT,ATTT,A 318.35 PASS AC=1,0,0;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 0/1:51:99:2,12,10,27 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 1/1:0,50:50:99:1465,150,0:0,0,26,24 chr1 20238373 . G A 485.81 PASS AC=1;AF=0.5;AN=2;DP=568;MQ=60;set=variant-variant2-variant4-variant15-variant16-variant18-variant23-variant36-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,28:50:99:664,0,582:12,10,14,14 chr1 20238576 . A AT 842.85 PASS AC=1;AF=0.5;AN=2;DP=675;MQ=60;set=variant-variant2-variant4-variant15-variant16-variant18-variant23-variant36-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,28:56:99:771,0,795:12,16,16,12 chr1 20238860 . C G 518.01 PASS AC=1;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 0/1:28,20:48:99:542,0,794:16,12,9,11 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 0/1:59,56:115:99:1317,0,1586:28,31,30,26 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 0/1:21,18:39:99:693,0,1154:17,4,15,3 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 0/1:21,22:43:99:803,0,1142:17,4,18,4 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 0/1:47,59:106:99:1430,0,1033:26,21,37,22 chr1 20250336 . A G 198.66 PASS AC=2;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 1/1:0,9:9:27:396,27,0:0,0,3,6 chr1 20250339 . A G 198.66 PASS AC=2;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 1/1:0,8:8:24:360,24,0:0,0,3,5 chr1 20304857 . G A 432.84 PASS AC=1;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 0/1:35,24:59:99:573,0,906:21,14,16,8 chr1 20304926 . G A 1171.95 PASS AC=1;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 0/1:53,41:94:99:1030,0,1449:29,24,24,17 chr1 20305065 . C T 2739.19 PASS AC=1;AF=0.817;AN=2;DP=3602;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-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,34:76:99:1044,0,1286:21,21,15,19 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 2/2:16:48:0,0,4,12 chr1 20306146 . G C 416.87 PASS AC=1;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 0/1:24,12:36:99:238,0,582:11,13,5,7 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 1/1:0,35:35:99:1107,105,0:0,0,23,12 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 0/1:15,17:32:99:378,0,380:12,3,11,6 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 0/1:62,42:104:99:893,0,1509:33,29,22,20 chr1 20438701 . C T 111.22 PASS AC=1;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 0/1:6,4:10:69:69,0,183:5,1,2,2 chr1 20439313 . C G 1061.3 PASS AC=1;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 0/1:60,40:100:99:969,0,1575:31,29,20,20 chr1 20439522 . T A 826.76 PASS AC=1;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 0/1:24,30:54:99:863,0,650:12,12,20,10 chr1 20440041 . A G 701.54 PASS AC=1;AF=0.5;AN=2;DP=191;MQ=60;set=variant19-variant23-variant30-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,20:28:99:545,0,202:5,3,9,11 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 1/1:0,114:114:99:3380,340,0:0,0,52,62 chr1 20442583 . A G 209.18 PASS AC=1;AF=0.5;AN=2;DP=97;FractionInformativeReads=1;MQ=60;set=variant5-variant9-variant13-variant14-variant15-variant18-variant23-variant39 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:221,0,229:5,2,6,1 chr1 20442587 . T C 94.89 PASS AC=2;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 1/1:0,16:16:48:648,48,0:0,0,12,4 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 1/1:0,18:18:54:585,54,0:0,0,3,15 chr1 20466830 . T C 1189.88 PASS AC=1;AF=0.5;AN=2;DP=611;FractionInformativeReads=1;MQ=60;set=variant12-variant13-variant17-variant19-variant20-variant23-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,26:65:99:523,0,976:16,23,12,14 chr1 20476391 . C T 3580.07 PASS AC=1;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 0/1:57,96:153:99:2323,0,1294:28,29,46,50 chr1 20487743 . C T 262.21 PASS AC=1;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 0/1:7,5:12:99:108,0,143:4,3,2,3 chr1 20488689 . T C 30.19 PASS AC=1;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 0/1:11,10:21:99:293,0,268:7,4,8,2 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 0/1:26,18:44:99:377,0,627:15,11,8,10 chr1 20490518 . T C 923.22 PASS AC=1;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 0/1:61,79:140:99:1847,0,1435:29,32,37,42 chr1 20501442 . T C 962.83 PASS AC=1;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 0/1:29,48:77:99:1339,0,646:15,14,25,23 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 1/1:0,2:2:6:82,6,0:0,0,2,0 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 1/1:1,92:93:99:2448,267,0:1,0,42,50 chr1 20518226 . G A 785.63 PASS AC=1;AF=0.556;AN=2;DP=650;MQ=60;set=variant13-variant16-variant20-variant23-variant27-variant29-variant31-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:37,15:52:99:391,0,1125:16,21,6,9 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 0/1:48,58:106:99:1407,0,1168:28,20,28,30 chr1 20617658 . A AGTGTGTGT,AGTGTGTGTGT,AGTGT,AGTGTGTGTGTGT,AGT,ACTGTGTGT,AGTGTGT 31.48 PASS AC=0,0,1,0,0,0,0;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 0/3:18:99:3,7,2,6 chr1 20617671 . A G 40.45 PASS AC=1;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 0/1:12,9:21:99:323,0,558:3,9,3,6 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 0/1:52,84:136:99:2062,0,1329:29,23,47,37 chr1 20637374 . T C 452.09 PASS AC=1;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 0/1:34,26:60:99:649,0,928:12,22,9,17 chr1 20640969 . G A 2325.21 PASS AC=1;AF=0.5;AN=2;DP=448;MQ=60;set=variant23-variant24 GT:AD:DP:GQ:PL:SB 0/1:87,95:182:99:2353,0,2076:39,48,44,51 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 0/1:7,8:15:99:234,0,229:6,1,6,2 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 0/1:16,9:25:99:280,0,439:11,5,9,0 chr1 20645086 . T A 1667.62 PASS AC=1;AF=0.563;AN=2;DP=1607;MQ=60;set=variant2-variant15-variant16-variant19-variant23-variant26-variant32-variant33 GT:AD:DP:GQ:PL:SB 0/1:100,93:193:99:2060,0,2462:41,59,39,54 chr1 20649814 . T C 1758.66 PASS AC=1;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 0/1:68,64:132:99:1569,0,1694:43,25,34,30 chr1 20657352 . T C 1475.11 PASS AC=1;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 0/1:66,52:118:99:1232,0,1673:35,31,26,26 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 0/1:3,4:7:97:118,0,97:1,2,1,3 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 0/1:55,59:114:99:1425,0,1196:28,27,33,26 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 0/1:44,51:95:99:1208,0,994:24,20,32,19 chr1 20671961 . G A 1384.4 PASS AC=1;AF=0.639;AN=2;DP=2408;MQ=60;set=variant-variant3-variant4-variant6-variant11-variant13-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant27-variant31-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,56:114:99:1383,0,1346:28,30,23,33 chr1 20672101 . C T 166.62 PASS AC=1;AF=0.639;AN=2;DP=650;MQ=60;set=variant-variant3-variant4-variant6-variant11-variant13-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant27-variant31-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,15:32:99:337,0,478:6,11,8,7 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 0/1:6,10:16:99:321,0,180:1,5,2,8 chr1 20680718 . G A 1287.28 PASS AC=1;AF=0.633;AN=2;DP=1566;MQ=60;set=variant-variant3-variant4-variant6-variant11-variant13-variant17-variant20-variant22-variant23-variant24-variant27-variant31-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,47:109:99:1203,0,1907:35,27,23,24 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 0/1:45,30:75:99:711,0,1429:32,13,17,13 chr1 20681004 . G C 69.48 PASS AC=1;AF=0.542;AN=2;DP=166;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant11-variant13-variant17-variant22-variant23-variant27-variant31-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:111,0,115:3,3,2,3 chr1 20809349 . CGTGT CGTGTGT,CGT,CGTGTGTGTGTGTGT,CGTGTGTGTGTGT,CGTGTGTGTGT,CGTGTGTGT,C 3059.03 PASS AC=1,0,0,0,0,0,0;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 0/1:123:99:37,37,20,29 chr1 20826685 . T A 1321.23 PASS AC=1;AF=0.6;AN=2;DP=1232;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant9-variant10-variant11-variant19-variant21-variant23-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,27:60:99:1034,0,1851:17,16,12,15 chr1 20826686 . C A 1321.23 PASS AC=1;AF=0.6;AN=2;DP=1227;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant9-variant10-variant11-variant19-variant21-variant23-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,27:60:99:1034,0,1851:17,16,12,15 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 0/1:24,31:55:99:1230,0,927:13,11,16,15 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 0/1:51,40:91:99:803,0,1247:29,22,21,19 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 0/1:42,26:68:99:629,0,1043:20,22,12,14 chr1 20827216 . C T 1284.01 PASS AC=1;AF=0.567;AN=2;DP=1165;MQ=60;set=variant6-variant9-variant10-variant11-variant23-variant26-variant28-variant29-variant32-variant33-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,27:66:99:695,0,1111:18,21,14,13 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 0/1:11,17:28:99:480,0,243:7,4,13,4 chr1 20829808 . TA T 580.52 PASS AC=1;AF=0.567;AN=2;DP=568;MQ=60;set=variant6-variant9-variant10-variant11-variant23-variant26-variant28-variant29-variant31-variant32-variant33-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,9:24:99:179,0,331:6,9,2,7 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 0/1:82,54:136:99:1235,0,2251:33,49,22,32 chr1 20834738 . G C 308.71 PASS AC=1;AF=0.567;AN=2;DP=602;MQ=60;set=variant6-variant9-variant10-variant11-variant23-variant26-variant28-variant29-variant32-variant33-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,27:42:99:669,0,407:3,12,9,18 chr1 20915418 . C G 1064.63 PASS AC=1;AF=0.729;AN=2;DP=1234;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant12-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant28-variant29-variant32-variant33-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,24:49:99:515,0,585:12,13,13,11 chr1 20915531 . A G 1429.41 PASS AC=1;AF=0.614;AN=2;DP=1519;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant12-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant28-variant29-variant32-variant33-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,28:56:99:743,0,687:18,10,13,15 chr1 20915589 . TC T 1389.1 PASS AC=1;AF=0.729;AN=2;DP=2554;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,28:66:99:775,0,1120:21,17,17,11 chr1 20915701 . A C 599.93 PASS AC=1;AF=0.587;AN=2;DP=1921;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant12-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,45:95:99:1113,0,1160:20,30,21,24 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 1/1:0,95:95:99:2918,284,0:0,0,55,40 chr1 20944889 . G A 598.01 PASS AC=1;AF=0.575;AN=2;DP=1899;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant8-variant9-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant27-variant28-variant34-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,43:84:99:1002,0,947:21,20,24,19 chr1 20944909 . G A 536.13 PASS AC=1;AF=0.575;AN=2;DP=2110;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant8-variant9-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant27-variant28-variant34-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,44:88:99:1035,0,1061:24,20,25,19 chr1 20944922 . C T 553.91 PASS AC=1;AF=0.575;AN=2;DP=2197;MQ=60;set=variant-variant4-variant6-variant8-variant9-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant27-variant28-variant34-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,46:93:99:1133,0,1109:25,22,26,20 chr1 20945055 . C T 709.4 PASS AC=1;AF=0.575;AN=2;DP=2024;MQ=60;set=variant-variant4-variant6-variant8-variant9-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant27-variant28-variant34-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,36:88:99:870,0,1253:28,24,18,18 chr1 20945252 . G GC 244.49 PASS AC=1;AF=0.575;AN=2;DP=1226;MQ=60;set=variant-variant4-variant6-variant8-variant9-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant27-variant28-variant34-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,18:53:99:412,0,955:15,20,9,9 chr1 20945452 . A G 323.57 PASS AC=1;AF=0.575;AN=2;DP=542;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant8-variant9-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant27-variant28-variant34-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,17:28:99:536,0,295:2,9,4,13 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 0/1:31,28:59:99:717,0,770:15,16,19,9 chr1 20960385 . A T 1198.82 PASS AC=1;AF=0.5;AN=2;DP=493;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant22-variant23-variant40 GT:AD:DP:GQ:PL:SB 0/1:42,30:72:99:710,0,1072:15,27,13,17 chr1 20964328 . A G 83.95 PASS AC=1;AF=0.886;AN=2;DP=1103;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:7,11:18:99:387,0,223:4,3,10,1 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 0/1:2,3:5:75:120,0,75:2,0,3,0 chr1 20971980 . CA CAA,CAAAA,CAAA,CAAAAA,C 116.03 PASS AC=0,0,1,0,0;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 0/3:19:98:4,2,8,5 chr1 20972048 . G A 656.75 PASS AC=1;AF=0.886;AN=2;DP=3429;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:30,29:59:99:777,0,850:15,15,18,11 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 0/1:17,23:40:99:625,0,392:10,7,13,10 chr1 20976759 . C T 85.73 PASS AC=1;AF=0.886;AN=2;DP=878;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:131,0,241:6,3,4,2 chr1 20977221 . A T 983.42 PASS AC=1;AF=0.886;AN=2;DP=3264;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:30,40:70:99:1049,0,830:14,16,15,25 chr1 20977365 . C G 608.8 PASS AC=1;AF=0.886;AN=2;DP=2815;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:23,31:54:99:798,0,675:10,13,18,13 chr1 20977449 . G T 854.27 PASS AC=1;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 0/1:33,43:76:99:1148,0,747:16,17,24,19 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 0/1:55,69:124:99:1835,0,1532:38,17,35,34 chr1 20978058 . G A 1538.04 PASS AC=1;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 0/1:63,51:114:99:1513,0,1978:12,51,10,41 chr1 20978832 . T C 954.21 PASS AC=1;AF=0.886;AN=2;DP=5274;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:54,63:117:99:1516,0,1229:30,24,36,27 chr1 20979307 . G GT 1700.62 PASS AC=1;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 0/1:83,74:157:99:1998,0,2364:39,44,37,37 chr1 20980922 . G A 267.76 PASS AC=1;AF=0.5;AN=2;DP=478;MQ=60;set=variant-variant4-variant6-variant8-variant16-variant22-variant23-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,22:45:99:524,0,659:14,9,7,15 chr1 20981768 . G T 116.23 PASS AC=1;AF=0.5;AN=2;DP=22;FS=0;FractionInformativeReads=1;MQ=60;set=variant4-variant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:66:66,0,78:2,0,2,0 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 1/1:0,13:13:39:442,39,0:0,0,10,3 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 1/1:1,230:231:99:6675,682,0:0,1,119,111 chr1 20991197 . T G 101.43 PASS AC=1;AF=0.5;AN=2;DP=23;FS=50.171;FractionInformativeReads=1;MQ=60;MQRankSum=-0.155;QD=4.41;ReadPosRankSum=-3.256;SOR=3.744;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:10,13:23:50:130,0,50:10,0,1,12 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 0/1:4,5:9:99:157,0,146:0,4,1,4 chr1 20992819 . G C 920.03 PASS AC=1;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 0/1:53,46:99:99:1110,0,1261:23,30,21,25 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 1/1:0,28:28:84:996,84,0:0,0,7,21 chr1 20997072 . A G 1170.11 PASS AC=1;AF=0.5;AN=2;DP=655;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant15-variant22-variant23-variant30-variant40 GT:AD:DP:GQ:PL:SB 0/1:55,37:92:99:916,0,1329:20,35,13,24 chr1 20998849 . C T 72.31 PASS AC=1;AF=0.5;AN=2;DP=215;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant10-variant11-variant12-variant21-variant23-variant28-variant31-variant32-variant33-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,9:18:99:286,0,257:2,7,0,9 chr1 21016487 . C T 424.04 PASS AC=1;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 0/1:10,10:20:99:225,0,229:6,4,5,5 chr1 21024860 . C A 1343.36 PASS AC=1;AF=0.5;AN=2;DP=171;FractionInformativeReads=1;MQ=60;set=variant8-variant23 GT:AD:DP:GQ:PL:SB 0/1:38,44:82:99:1160,0,877:23,15,29,15 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 0/1:72,68:140:99:1435,0,1833:43,29,37,31 chr1 21040151 . G A 870.97 PASS AC=1;AF=0.563;AN=2;DP=398;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant13-variant16-variant20-variant23-variant27-variant34 GT:AD:DP:GQ:PL:SB 0/1:37,23:60:99:625,0,945:12,25,6,17 chr1 21044219 . A C 1205.19 PASS AC=1;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 0/1:62,68:130:99:1717,0,1361:25,37,25,43 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 1/1:0,10:10:30:372,30,0:0,0,6,4 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 0/1:82,60:142:99:1360,0,2125:40,42,23,37 chr1 21058655 . G A 49.73 PASS AC=2;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 1/1:0,7:7:21:226,21,0:0,0,5,2 chr1 21091861 . G T 1633.48 PASS AC=2;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 1/1:0,78:78:99:2457,234,0:0,0,53,25 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 1/1:0,30:30:90:925,90,0:0,0,11,19 chr1 21151506 . G A 319.2 PASS AC=1;AF=0.5;AN=2;DP=60;FS=0;FractionInformativeReads=1;MQ=60;set=variant8-variant23 GT:AD:DP:GQ:PL:SB 0/1:8,18:26:99:569,0,186:6,2,14,4 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 1/1:0,56:56:99:1786,168,0:0,0,31,25 chr1 21167659 . A G 49.73 PASS AC=1;AF=0.5;AN=2;DP=4;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.026;QD=12.43;ReadPosRankSum=1.026;SOR=0.693;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:75:78,0,75:0,2,0,2 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 1/1:0,24:24:72:911,72,0:0,0,19,5 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 1/1:0,21:21:63:680,63,0:0,0,15,6 chr1 21180181 . C T 404.05 PASS AC=2;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 1/1:0,38:38:99:1205,114,0:0,0,14,24 chr1 21180250 . G A 172.12 PASS AC=2;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 1/1:0,15:15:45:474,45,0:0,0,5,10 chr1 21188703 . A T 1079.77 PASS AC=2;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 1/1:0,76:76:99:2287,227,0:0,0,44,32 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 1/1:0,37:37:99:1113,111,0:0,0,16,21 chr1 21191430 . A G 383.05 PASS AC=2;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 1/1:0,32:32:96:1028,96,0:0,0,15,17 chr1 21220375 . T G 43.74 PASS AC=2;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 1/1:0,10:10:30:362,30,0:0,0,2,8 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 0/1:45:99:12,24,3,6 chr1 21314765 . T C 1638.5 PASS AC=1;AF=0.5;AN=2;DP=239;MQ=60;set=variant-variant23 GT:AD:DP:GQ:PL:SB 0/1:45,56:101:99:1277,0,910:24,21,32,24 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 1/1:0,93:93:99:2756,279,0:0,0,49,44 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 1/1:0,27:27:81:895,81,0:0,0,18,9 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 1/1:0,37:37:99:1155,111,0:0,0,24,13 chr1 21554573 . C T 784.65 PASS AC=1;AF=0.5;AN=2;DP=206;MQ=60;set=variant3-variant8-variant16-variant17-variant23 GT:AD:DP:GQ:PL:SB 0/1:20,16:36:99:418,0,513:6,14,4,12 chr1 21564970 . T C 245.17 PASS AC=1;AF=0.5;AN=2;DP=22;FractionInformativeReads=1;MQ=60;set=variant8-variant23 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:57:149,0,57:2,2,1,4 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 0/1:9,7:16:99:264,0,314:8,1,7,0 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 0/1:63,58:121:99:1585,0,1684:42,21,43,15 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 0/1:6,6:12:99:153,0,181:5,1,3,3 chr1 21616932 . G T 475.89 PASS AC=1;AF=0.563;AN=2;DP=297;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant16-variant17-variant20-variant23-variant27-variant41 GT:AD:DP:GQ:PL:SB 0/1:22,17:39:99:327,0,428:11,11,10,7 chr1 21671943 . T G 327.82 PASS AC=1;AF=0.641;AN=2;DP=1981;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant28-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,29:69:99:621,0,1015:23,17,13,16 chr1 21671973 . G A 682.53 PASS AC=1;AF=0.563;AN=2;DP=496;MQ=60;set=variant8-variant14-variant16-variant20-variant23-variant27-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,39:66:99:836,0,642:11,16,20,19 chr1 21751116 . G C 178.1 PASS AC=1;AF=0.536;AN=2;DP=423;set=filterInvariant4-variant8-variant13-filterInvariant14-filterInvariant16-filterInvariant18-filterInvariant21-variant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant29-filterInvariant30-variant36 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:189,0,111:4,1,6,1 chr1 21751142 . A G 1146.87 PASS AC=1;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 0/1:18,14:32:99:320,0,411:13,5,10,4 chr1 21751214 . G A 3577.5 PASS AC=1;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 0/1:62,62:124:99:1409,0,1173:32,30,40,22 chr1 21752681 . C T 782.98 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1375;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:48,26:74:99:508,0,1060:29,19,18,8 chr1 21752746 . G A 1167.28 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1668;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:60,40:100:99:775,0,2045:34,26,25,15 chr1 21752752 . G A 2652.98 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1870;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:65,41:106:99:1519,0,2513:38,27,26,15 chr1 21752762 . T A 2862.21 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1954;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:65,47:112:99:1655,0,2443:38,27,29,18 chr1 21754920 . G T 1733.3 PASS AC=1;AF=0.5;AN=2;DP=1589;FractionInformativeReads=1;set=variant4-variant8-variant14-variant16-variant21-variant22-variant23-variant25-variant29-variant30-variant36 GT:AD:DP:GQ:PL:SB 0/1:73,56:129:99:1113,0,1588:39,34,30,26 chr1 21754996 . C T 3200.4 PASS AC=2;AF=0.989;AN=2;DP=4876;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2660,278,0:0,0,39,54 chr1 21755055 . C A 1546.59 PASS AC=1;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 0/1:20,16:36:99:443,0,506:5,15,5,11 chr1 21755142 . C T 407.21 PASS AC=1;AF=0.536;AN=2;DP=335;FractionInformativeReads=1;set=variant3-variant6-variant8-variant9-variant14-variant17-variant19-variant20-variant23-variant27-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,10:17:99:360,0,239:4,3,8,2 chr1 21755345 . T C 1993.36 PASS AC=1;AF=0.538;AN=2;DP=2095;set=variant4-variant8-variant14-variant16-variant18-variant21-variant22-variant23-variant24-variant25-variant29-variant30-variant36 GT:AD:DP:GQ:PL:SB 0/1:120,52:172:99:1061,0,3226:52,68,21,31 chr1 21755408 . A G 938.19 PASS AC=1;AF=0.5;AN=2;DP=993;set=variant4-variant8-variant14-variant16-variant21-variant23-variant25-variant29-variant30-variant36 GT:AD:DP:GQ:PL:SB 0/1:97,27:124:99:453,0,2664:39,58,10,17 chr1 21755453 . G A 1047.64 PASS AC=1;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 0/1:61,11:72:99:204,0,1633:23,38,1,10 chr1 21755517 . C T 49.52 PASS AC=1;AF=0.5;AN=2;DP=216;FractionInformativeReads=1;set=variant4-filterInvariant8-filterInvariant14-variant16-variant21-variant23-variant25-variant29-variant30-variant36 GT:AD:DP:GQ:PL:SB 0/1:34,7:41:99:155,0,1255:11,23,3,4 chr1 21755539 . C A 379.14 PASS AC=1;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 0/1:26,8:34:99:208,0,1054:7,19,4,4 chr1 21755756 . G C 4868.3 PASS AC=1;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 0/1:97,101:198:99:2280,0,2422:57,40,59,42 chr1 21755867 . A G 5568.25 PASS AC=1;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 0/1:114,93:207:99:2202,0,2717:52,62,42,51 chr1 21755906 . G A 4328.42 PASS AC=1;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 0/1:103,79:182:99:1759,0,2569:44,59,35,44 chr1 21756008 . G T 1587.13 PASS AC=1;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 0/1:36,37:73:99:827,0,854:15,21,14,23 chr1 21756069 . G A 848.77 PASS AC=1;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 0/1:10,23:33:99:631,0,308:3,7,7,16 chr1 21766776 . G C 2136.29 PASS AC=1;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 0/1:104,106:210:99:2400,0,2439:51,53,57,49 chr1 21766813 . T TA 2686.65 PASS AC=1;AF=0.5;AN=2;DP=207;FS=3.175;FractionInformativeReads=0.995;MQ=60;MQRankSum=1.295;QD=12.98;ReadPosRankSum=1.184;SOR=0.945;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:117,89:206:99:2724,0,3743:58,59,39,50 chr1 21795432 . G GA 1829.98 PASS AC=1;AF=0.5;AN=2;DP=1748;MQ=60;set=variant3-variant6-variant9-variant14-variant17-variant18-variant20-variant23-variant24-variant27-variant28-variant34-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,47:104:99:1562,0,1989:19,38,14,33 chr1 21797221 . A G 412 PASS AC=1;AF=0.5;AN=2;DP=41;FS=2.858;FractionInformativeReads=1;MQ=60;MQRankSum=1.457;QD=10.05;ReadPosRankSum=-0.013;SOR=0.297;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:25,16:41:99:440,0,687:9,16,8,8 chr1 21799489 . T C 3046.81 PASS AC=1;AF=0.817;AN=2;DP=4170;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-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,43:78:99:1089,0,847:16,19,14,29 chr1 21799823 . A G 1072.45 PASS AC=1;AF=0.793;AN=2;DP=1856;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-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,16:39:99:489,0,859:22,1,14,2 chr1 21801346 . G A 1783.8 PASS AC=1;AF=0.817;AN=2;DP=2240;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-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,38:60:99:866,0,500:11,11,20,18 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 1/1:0,126:126:99:3742,377,0:0,0,57,69 chr1 21805730 . A G 3152.45 PASS AC=1;AF=0.817;AN=2;DP=4365;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-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,32:69:99:926,0,907:25,12,24,8 chr1 21805978 . G A 1998.63 PASS AC=1;AF=0.817;AN=2;DP=3233;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-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,33:61:99:995,0,864:8,20,9,24 chr1 21806525 . A T 1554.6 PASS AC=1;AF=0.5;AN=2;DP=1320;set=variant3-variant6-variant9-variant14-variant17-variant20-variant23-variant24-variant27-variant28-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,55:100:99:1527,0,1256:34,11,38,17 chr1 21806751 . C T 1746.51 PASS AC=1;AF=0.824;AN=2;DP=775;set=variant3-variant6-variant9-variant14-variant17-variant18-variant20-variant23-variant24-variant27-variant28-variant34-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,21:59:99:661,0,1105:12,26,3,18 chr1 21807521 . A T 312.71 PASS AC=1;AF=0.5;AN=2;DP=892;set=variant3-filterInvariant5-filterInvariant6-filterInvariant9-filterInvariant13-variant14-filterInvariant17-filterInvariant18-filterInvariant20-variant23-filterInvariant24-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant40-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,22:51:99:407,0,870:6,23,10,12 chr1 21808159 . G A 1222.52 DRAGENHardSNP AC=1;AF=0.525;AN=2;DP=5615;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:58,37:95:99:661,0,1378:32,26,15,22 chr1 21808207 . A C 840.85 DRAGENHardSNP AC=1;AF=0.528;AN=2;DP=3229;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:67,21:88:99:307,0,1495:31,36,6,15 chr1 21808223 . T C 637.76 DRAGENHardSNP AC=1;AF=0.529;AN=2;DP=2147;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:66,13:79:99:127,0,1507:30,36,4,9 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 0/1:22:99:4,9,2,7 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 0/1:33,26:59:99:613,0,807:19,14,16,10 chr1 21889635 . T C 2897.73 PASS AC=1;AF=0.955;AN=2;DP=7280;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:68,71:139:99:1766,0,1448:36,32,36,35 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 1/1:0,34:34:99:1079,102,0:0,0,26,8 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 0/1:24,23:47:99:604,0,654:7,17,8,15 chr1 21900891 . G A 1014.58 PASS AC=1;AF=0.966;AN=2;DP=963;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:10,15:25:99:472,0,251:6,4,12,3 chr1 21901025 . T TAC 2120.86 PASS AC=1;AF=0.717;AN=2;DP=4039;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant25-variant26-variant29-variant31-variant34-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,56:116:99:1866,0,2037:37,23,30,26 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 1/1:0,31:31:93:1130,93,0:0,0,8,23 chr1 21902950 . C A 191.06 PASS AC=1;AF=0.538;AN=2;DP=302;MQ=60;set=variant-variant3-variant5-variant6-variant12-variant13-variant14-variant17-variant23-variant24-variant27-variant34-variant41 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:407,0,298:9,2,9,3 chr1 21904206 . C T 2004.06 PASS AC=1;AF=0.607;AN=2;DP=2123;MQ=60;set=variant2-variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant23-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant36-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,41:73:99:1094,0,984:11,21,12,29 chr1 21904267 . A G 689.61 PASS AC=2;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 1/1:0,54:54:99:1789,162,0:0,0,25,29 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 0/1:23,16:39:99:435,0,490:11,12,7,9 chr1 21905007 . G A 230.37 PASS AC=1;AF=0.5;AN=2;DP=72;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant23-variant24-variant27 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:195,0,156:0,4,0,5 chr1 21922893 . CG C 1895.97 PASS AC=1;AF=0.591;AN=2;DP=1354;MQ=60;set=variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant29-variant32-variant33-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,31:46:99:874,0,350:10,5,15,16 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 1/1:0,7:7:21:306,21,0:0,0,1,6 chr1 21926187 . C T 40.71 PASS AC=1;AF=0.688;AN=2;DP=460;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant31-variant32-variant33-variant36-variant37-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:9,4:13:99:128,0,205:5,4,0,4 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 0/1:28,41:69:99:1114,0,855:5,23,10,31 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 1/1:0,122:122:99:3407,365,0:0,0,60,62 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 0/1:11,17:28:99:436,0,252:2,9,2,15 chr1 21932530 . C A 2269.11 PASS AC=2;AF=0.807;AN=2;DP=3315;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1463,137,0:0,0,32,14 chr1 21934667 . G A 619.76 PASS AC=1;AF=0.662;AN=2;DP=2505;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,40:64:99:906,0,601:12,12,22,18 chr1 21935433 . G T 1057.33 PASS AC=1;AF=0.69;AN=2;DP=3172;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant29-variant32-variant33-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,21:58:99:593,0,941:19,18,10,11 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 0/1:6,16:22:93:284,0,93:6,0,11,5 chr1 21938375 . T G 723.78 PASS AC=1;AF=0.581;AN=2;DP=1870;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,36:63:99:944,0,684:12,15,16,20 chr1 21939493 . G C 1167.84 PASS AC=1;AF=0.586;AN=2;DP=2517;FractionInformativeReads=1;set=variant2-variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant36-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,39:80:99:1031,0,1142:28,13,27,12 chr1 21939741 . G C 1893.76 PASS AC=1;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 0/1:50,43:93:99:1013,0,1300:15,35,15,28 chr1 21940555 . C T 57.15 PASS AC=1;AF=0.625;AN=2;DP=1533;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,14:44:99:292,0,717:13,17,6,8 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 0/1:34,33:67:99:724,0,805:19,15,18,15 chr1 21944352 . A G 511.03 PASS AC=1;AF=0.574;AN=2;DP=1720;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant29-variant32-variant33-variant34-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:24,32:56:99:824,0,580:15,9,21,11 chr1 21945614 . C T 300.67 PASS AC=1;AF=0.5;AN=2;DP=218;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant17-variant22-variant23-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,12:38:99:254,0,718:10,16,3,9 chr1 21946396 . T C 164.69 PASS AC=1;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 0/1:11,10:21:99:277,0,315:8,3,7,3 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 1/1:0,29:29:87:954,87,0:0,0,19,10 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 1/1:0,7:7:21:201,21,0:0,0,2,5 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 1/1:1,152:153:99:4363,412,0:0,1,64,88 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 1/1:0,78:78:99:2347,233,0:0,0,32,46 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 1/1:0,8:8:24:319,24,0:0,0,7,1 chr1 22005511 . T C 3000.83 PASS AC=1;AF=0.5;AN=2;DP=469;FractionInformativeReads=1;MQ=60;set=variant18-variant23 GT:AD:DP:GQ:PL:SB 0/1:97,80:177:99:1812,0,2206:44,53,34,46 chr1 22005665 . C T 344.05 PASS AC=1;AF=0.545;AN=2;DP=1041;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant9-variant11-variant14-variant15-variant17-variant18-variant19-variant23-variant24-variant25-variant26-variant29-variant30-variant34-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,19:32:99:541,0,317:1,12,10,9 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 1/1:0,16:16:48:551,48,0:0,0,13,3 chr1 22013771 . G A 601.14 PASS AC=1;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 0/1:29,29:58:99:714,0,678:13,16,12,17 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 1/1:3:9:0,0,1,2 chr1 22030189 . T C 964.95 PASS AC=1;AF=0.591;AN=2;DP=909;MQ=60;set=variant3-variant5-variant6-variant7-variant9-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant31-variant33-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:444,0,377:7,9,6,11 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 0/1:18,16:34:99:339,0,394:12,6,9,7 chr1 22050649 . C A 880.68 PASS AC=1;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 0/1:57,44:101:99:1110,0,1649:26,31,19,25 chr1 22054262 . T C 746.99 PASS AC=1;AF=0.571;AN=2;DP=430;FractionInformativeReads=1;MQ=60;set=variant7-variant8-variant15-variant17-variant23-variant25-variant26-variant29-variant30-variant34-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,17:26:99:652,0,278:8,1,17,0 chr1 22054427 . C A 3968.56 PASS AC=1;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 0/1:147,171:318:99:4329,0,3438:87,60,94,77 chr1 22063149 . G A 818.23 PASS AC=1;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 0/1:27,30:57:99:776,0,678:14,13,8,22 chr1 22082923 . G A 144.4 PASS AC=1;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 0/1:4,5:9:99:154,0,154:4,0,4,1 chr1 22082967 . CAA CA,C,CAAA 238.1 PASS AC=0,1,0;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 0/2:26:99:5,3,14,4 chr1 22084145 . T C 990.84 PASS AC=1;AF=0.545;AN=2;DP=1028;MQ=60;set=variant5-variant9-variant18-variant19-variant20-variant22-variant23-variant24-variant31-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:52,35:87:99:780,0,1293:28,24,18,17 chr1 22109796 . C T 2209.67 PASS AC=1;AF=0.545;AN=2;DP=2035;MQ=60;set=variant5-variant9-variant18-variant19-variant20-variant22-variant23-variant24-variant31-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:86,96:182:99:2193,0,2008:42,44,49,47 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 1/1:0,37:37:99:1231,111,0:0,0,14,23 chr1 22139141 . C T 549.75 PASS AC=1;AF=0.531;AN=2;DP=861;MQ=60;set=variant-variant9-variant10-variant18-variant19-variant21-variant22-variant23-variant24-variant27-variant28-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,13:29:99:297,0,435:6,10,5,8 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 1/1:0,96:96:99:3162,288,0:0,0,45,51 chr1 22147764 . A G 757.25 PASS AC=1;AF=0.5;AN=2;DP=1052;MQ=60;set=variant-variant7-variant8-variant10-variant12-variant13-variant17-variant18-variant20-variant23-variant25-variant26-variant29-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,19:31:99:579,0,360:9,3,15,4 chr1 22148164 . G A 1014.46 PASS AC=1;AF=0.5;AN=2;DP=1148;MQ=60;set=variant-variant7-variant8-variant10-variant12-variant13-variant17-variant18-variant20-variant23-variant25-variant26-variant29-variant32-variant33-variant36-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,32:56:99:869,0,746:5,19,8,24 chr1 22149183 . G C 589.84 PASS AC=1;AF=0.5;AN=2;DP=1086;MQ=60;set=variant-variant7-variant8-variant10-variant12-variant13-variant17-variant18-variant20-variant23-variant25-variant26-variant29-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,16:39:99:503,0,757:16,7,10,6 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 1/1:0,306:306:99:9056,917,0:0,0,158,148 chr1 22150118 . C T 1514.17 PASS AC=1;AF=0.5;AN=2;DP=1134;FractionInformativeReads=1;MQ=60;set=variant-variant10-variant13-variant23-variant29-variant33-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,72:148:99:1736,0,1979:34,42,32,40 chr1 22150257 . C T 982.87 PASS AC=1;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 0/1:47,58:105:99:1414,0,1263:24,23,25,33 chr1 22154845 . A G 2185.75 PASS AC=1;AF=0.5;AN=2;DP=4719;MQ=60;set=variant-variant7-variant8-variant10-variant12-variant13-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant29-variant32-variant33-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,91:178:99:2248,0,2148:35,52,35,56 chr1 22154987 . G A 705.06 PASS AC=1;AF=0.5;AN=2;DP=1123;MQ=60;set=variant-variant7-variant8-variant10-variant12-variant13-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant29-variant32-variant33-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,27:43:99:743,0,457:5,11,14,13 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 1/1:0,12:12:36:507,36,0:0,0,10,2 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 1/1:0,337:337:99:10131,1004,0:0,0,162,175 chr1 22158363 . G A 896.55 PASS AC=1;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 0/1:41,26:67:99:578,0,1003:16,25,10,16 chr1 22160020 . C T 1922.22 PASS AC=1;AF=0.5;AN=2;DP=1664;MQ=60;set=variant5-variant18-variant19-variant20-variant22-variant23-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:92,93:185:99:2299,0,2399:46,46,44,49 chr1 22160148 . C T 580.97 PASS AC=1;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 0/1:30,38:68:99:1086,0,847:9,21,11,27 chr1 22163402 . G A 1973.11 PASS AC=1;AF=0.5;AN=2;DP=1120;FractionInformativeReads=1;MQ=60;set=variant-variant10-variant13-variant23-variant29-variant33-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,81:158:99:1854,0,1752:45,32,36,45 chr1 22168216 . C T 805.83 PASS AC=1;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 0/1:45,32:77:99:820,0,1224:19,26,12,20 chr1 22170879 . G A 993.24 PASS AC=1;AF=0.5;AN=2;DP=312;MQ=60;set=variant-variant10-variant13-variant23-variant29-variant33-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,23:46:99:682,0,688:6,17,5,18 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 1/1:0,11:11:33:401,33,0:0,0,9,2 chr1 22174426 . T G 2634.23 PASS AC=1;AF=0.5;AN=2;DP=6828;MQ=60;set=variant-variant7-variant8-variant10-variant12-variant13-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant29-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:112,108:220:99:2740,0,2789:53,59,50,58 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 1/1:0,91:91:99:2759,273,0:0,0,37,54 chr1 22177119 . A G 266.75 PASS AC=1;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 0/1:8,11:19:99:366,0,269:1,7,2,9 chr1 22179673 . T C 1294.29 PASS AC=1;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 0/1:71,69:140:99:1825,0,1934:20,51,23,46 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 1/1:0,86:86:99:2588,257,0:0,0,41,45 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 1/1:0,64:64:99:1857,191,0:0,0,35,29 chr1 22183739 . A G 2671.26 PASS AC=1;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 0/1:128,103:231:99:2447,0,3117:59,69,52,51 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 1/1:0,55:55:99:2016,165,0:0,0,32,23 chr1 22190826 . G GC 181.29 PASS AC=1;AF=0.526;AN=2;DP=486;MQ=60;set=variant-variant7-variant8-variant10-variant12-variant13-variant15-variant17-variant20-variant23-variant25-variant26-variant32-variant33-variant36-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,17:29:99:439,0,305:5,7,5,12 chr1 22191454 . G A 2395.87 PASS AC=1;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 0/1:157,72:229:99:1522,0,3870:72,85,32,40 chr1 22198955 . G A 854.3 PASS AC=1;AF=0.5;AN=2;DP=695;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant13-variant23-variant26-variant29-variant32-variant33-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,23:45:99:578,0,608:13,9,13,10 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 1/1:0,74:74:99:2354,220,0:0,0,41,33 chr1 22199245 . C T 1730.45 PASS AC=1;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 0/1:53,58:111:99:1383,0,1335:26,27,27,31 chr1 22199821 . G A 1308.45 PASS AC=1;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 0/1:24,17:41:99:358,0,725:18,6,10,7 chr1 22200067 . A G 491.86 PASS AC=1;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 0/1:44,33:77:99:739,0,1157:16,28,13,20 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 1/1:0,65:65:99:2032,194,0:0,0,23,42 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 1/1:0,30:30:90:982,90,0:0,0,18,12 chr1 22201438 . C T 1669.88 PASS AC=1;AF=0.55;AN=2;DP=1488;MQ=60;set=variant5-variant18-variant20-variant21-variant22-variant23-variant28-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:67,56:123:99:1364,0,1716:38,29,33,23 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 1/1:0,69:69:99:2246,207,0:0,0,48,21 chr1 22203259 . A G 111 PASS AC=1;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 0/1:10,9:19:99:286,0,270:4,6,0,9 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 1/1:0,15:15:45:613,45,0:0,0,10,5 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 1/1:0,30:30:90:1065,90,0:0,0,22,8 chr1 22205755 . C A 275.02 PASS AC=1;AF=0.5;AN=2;DP=127;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant13-variant23-variant26-variant29-variant33-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:169,0,282:1,7,1,5 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 1/1:0,110:110:99:3505,330,0:0,0,57,53 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 1/1:0,221:221:99:6674,660,0:0,0,99,122 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 1/1:0,84:84:99:2783,252,0:0,0,32,52 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 1/1:0,127:127:99:5678,384,0:0,0,68,59 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 1/1:0,40:40:99:1196,119,0:0,0,12,28 chr1 22211222 . T C 6222.06 PASS AC=1;AF=0.886;AN=2;DP=8824;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:113,92:205:99:2089,0,2713:67,46,52,40 chr1 22214046 . C T 1659.14 PASS AC=1;AF=0.55;AN=2;DP=1641;MQ=60;set=variant5-variant18-variant20-variant21-variant22-variant23-variant28-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:76,90:166:99:2257,0,1783:35,41,38,52 chr1 22214127 . A G 1689.59 PASS AC=1;AF=0.596;AN=2;DP=4049;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant16-variant19-variant21-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,55:137:99:1303,0,2103:36,46,20,35 chr1 22214409 . G A 486.41 PASS AC=1;AF=0.5;AN=2;DP=68;FS=2.059;FractionInformativeReads=1;MQ=60;MQRankSum=-1.458;QD=7.15;ReadPosRankSum=-1.117;SOR=0.978;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:42,26:68:99:515,0,908:23,19,16,10 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 1/1:0,133:133:99:4033,397,0:0,0,81,52 chr1 22216279 . C T 406.9 PASS AC=1;AF=0.56;AN=2;DP=1340;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant12-variant13-variant16-variant19-variant21-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant36-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,24:60:99:636,0,940:22,14,19,5 chr1 22216574 . C A 652.52 PASS AC=1;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 0/1:51,37:88:99:934,0,1351:25,26,18,19 chr1 22216604 . C G 573.46 PASS AC=1;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 0/1:37,34:71:99:771,0,1070:19,18,16,18 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 1/1:0,171:171:99:5064,511,0:0,0,82,89 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 1/1:0,40:40:99:1321,120,0:0,0,26,14 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 1/1:0,6:6:18:270,18,0:0,0,4,2 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 1/1:0,6:6:18:270,18,0:0,0,4,2 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 1/1:0,18:18:54:663,54,0:0,0,16,2 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 1/1:0,47:47:99:1750,140,0:0,0,20,27 chr1 22307340 . C T 1079.65 PASS AC=2;AF=0.966;AN=2;DP=1454;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:536,45,0:0,0,12,3 chr1 22307358 . C G 1413.84 PASS AC=2;AF=0.966;AN=2;DP=2313;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1149,102,0:0,0,24,10 chr1 22307478 . G A 1528.56 PASS AC=1;AF=0.5;AN=2;DP=627;set=variant23-variant25-variant26-variant30 GT:AD:DP:GQ:PL:SB 0/1:66,68:134:99:1557,0,1558:32,34,35,33 chr1 22307538 . C T 3489.79 PASS AC=2;AF=0.989;AN=2;DP=6013;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3340,312,0:0,0,42,62 chr1 22310139 . T G 5088.23 PASS AC=2;AF=0.966;AN=2;DP=5715;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,125:125:99:5752,391,0:0,0,97,28 chr1 22310145 . C T 5286.66 PASS AC=2;AF=0.966;AN=2;DP=6223;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,135:135:99:5883,406,0:0,0,103,32 chr1 22310262 . G C 9192.96 PASS AC=2;AF=0.966;AN=2;DP=19163;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,367:367:99:10742,1099,0:0,0,180,187 chr1 22310411 . A G 2301.01 PASS AC=1;AF=0.943;AN=2;DP=3931;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:8,74:82:99:3073,0,143:4,4,20,54 chr1 22310413 . A G 2301.01 PASS AC=1;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 0/1:8,73:81:99:3073,0,143:4,4,20,53 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 1/1:0,358:358:99:10353,1069,0:0,0,180,178 chr1 22310674 . C T 8334.33 PASS AC=2;AF=0.966;AN=2;DP=17648;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,344:344:99:9818,1024,0:0,0,163,181 chr1 22310725 . G C 5771.42 PASS AC=2;AF=0.932;AN=2;DP=11307;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,232:232:99:7124,694,0:0,0,86,146 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 1/1:0,34:34:99:1490,102,0:0,0,0,34 chr1 22313161 . T C 2287.51 PASS AC=2;AF=0.966;AN=2;DP=7176;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,139:139:99:4061,416,0:0,0,56,83 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 1/1:1,75:76:99:2335,217,0:0,1,24,51 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 1/1:0,7:7:21:283,21,0:0,0,0,7 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 1/1:0,13:13:39:342,39,0:0,0,6,7 chr1 22329062 . C G 3049.13 PASS AC=1;AF=0.5;AN=2;DP=13932;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:119,125:244:99:4945,0,6382:85,34,70,55 chr1 22329063 . C T 3049.13 PASS AC=1;AF=0.5;AN=2;DP=14150;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:121,128:249:99:4945,0,6382:87,34,71,57 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 1/1:0,82:82:99:2663,245,0:0,0,50,32 chr1 22332319 . G A 1058.79 PASS AC=1;AF=0.5;AN=2;DP=4189;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:61,17:78:99:530,0,3302:28,33,12,5 chr1 22332332 . T C 1217.72 PASS AC=1;AF=0.5;AN=2;DP=4438;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:60,24:84:99:824,0,3347:30,30,16,8 chr1 22332333 . G A 1223.74 PASS AC=1;AF=0.5;AN=2;DP=4459;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:60,25:85:99:824,0,3347:30,30,16,9 chr1 22332411 . A G 842.63 PASS AC=1;AF=0.5;AN=2;DP=4695;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:50,44:94:99:947,0,1264:21,29,23,21 chr1 22333538 . A G 1970.54 PASS AC=1;AF=0.5;AN=2;DP=1072;set=variant23-variant25-variant26-variant30-variant36 GT:AD:DP:GQ:PL:SB 0/1:110,86:196:99:1999,0,2765:39,71,35,51 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 1/1:1,58:59:99:2153,167,0:0,1,15,43 chr1 22336277 . C G 3553.56 PASS AC=2;AF=0.977;AN=2;DP=8843;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,179:179:99:5430,536,0:0,0,86,93 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 1/1:0,99:99:99:2973,296,0:0,0,36,63 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 1/1:0,19:19:60:573,60,0:0,0,6,13 chr1 22379088 . G A 1237.64 PASS AC=2;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 1/1:0,81:81:99:2222,240,0:0,0,44,37 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 1/1:0,89:89:99:2784,267,0:0,0,48,41 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 1/1:0,27:27:81:1067,81,0:0,0,4,23 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 1/1:0,22:22:69:1024,69,0:0,0,19,3 chr1 22592949 . A G 217.65 PASS AC=1;AF=0.5;AN=2;DP=52;FractionInformativeReads=1;MQ=60;set=variant6-variant23-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:112,0,150:1,4,1,3 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 1/1:0,13:13:39:423,39,0:0,0,9,4 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 1/1:0,28:28:84:1001,84,0:0,0,6,22 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 1/1:0,96:96:99:2931,288,0:0,0,38,58 chr1 22837586 . CTT CT,C,CTTT 481.62 PASS AC=2,0,0;AF=0.513,0.013,0.013;AN=2;DP=2042;MQ=60;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-variant29-variant30-variant33-variant34-filterInvariant36-variant37-variant38-variant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:DP:GQ:SB 1/1:37:99:0,0,24,13 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 1/1:0,53:53:99:1571,159,0:0,0,21,32 chr1 22849003 . A C 786.45 PASS AC=2;AF=0.625;AN=2;DP=930;MQ=60;set=variant-variant5-variant6-variant9-variant16-variant18-variant19-variant20-variant23-variant25-variant26-variant29-variant30-variant31-variant33-variant34-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1271,108,0:0,0,7,29 chr1 22852715 . G C 418.97 PASS AC=2;AF=0.625;AN=2;DP=1675;MQ=60;set=variant-variant5-variant6-variant9-variant16-variant18-variant19-variant20-variant23-variant25-variant26-variant29-variant30-variant31-variant33-variant34-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2104,210,0:0,0,38,32 chr1 22853141 . G A 413.68 PASS AC=1;AF=0.559;AN=2;DP=1067;MQ=60;set=variant-variant5-variant9-variant16-variant18-variant19-variant20-variant23-variant25-variant26-variant30-variant31-variant33-variant34-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,30:58:99:799,0,715:12,16,14,16 chr1 22855741 . G A 1314.16 PASS AC=1;AF=0.5;AN=2;DP=556;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant20-variant23-variant29-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,45:70:99:1172,0,547:11,14,23,22 chr1 22856601 . T C 437.41 PASS AC=2;AF=0.625;AN=2;DP=959;MQ=60;set=variant-variant5-variant6-variant9-variant16-variant18-variant19-variant20-variant23-variant25-variant26-variant29-variant30-variant31-variant33-variant34-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1335,132,0:0,0,21,23 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 1/1:0,17:17:51:560,51,0:0,0,9,8 chr1 22924783 . C T 600.75 PASS AC=1;AF=0.5;AN=2;DP=349;MQ=60;set=variant3-variant4-variant5-variant6-variant20-variant21-variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:18,25:43:99:538,0,464:5,13,9,16 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 1/1:0,149:149:99:4522,446,0:0,0,92,57 chr1 22965438 . A G 1508.68 PASS AC=1;AF=0.617;AN=2;DP=3519;MQ=60;set=variant3-variant5-variant7-variant8-variant11-variant12-variant13-variant14-variant16-variant17-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,41:107:99:970,0,1627:35,31,22,19 chr1 22966227 . T G 118.52 PASS AC=1;AF=0.667;AN=2;DP=234;FractionInformativeReads=1;set=variant3-variant5-variant7-variant11-variant12-variant13-variant14-variant16-variant17-variant22-variant23-variant26-variant28-variant29-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:142,0,125:1,4,1,4 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 0/1:76,57:133:99:1206,0,1938:39,37,32,25 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 0/1:37,22:59:99:432,0,891:15,22,9,13 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 0/1:18,9:27:99:271,0,444:8,10,2,7 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 0/1:48,41:89:99:821,0,1186:20,28,18,23 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 0/1:34,11:45:99:360,0,1929:14,20,4,7 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 0/2:73:99:14,11,22,26 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 0/1:14,14:28:99:389,0,338:7,7,8,6 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 0/1:5,5:10:99:155,0,159:1,4,1,4 chr1 22985785 . AGATGGATGGATGGATGGATGGATGGATGGATGGATGCAGATGGAGGAATAGAGAGATGGATG AGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGCAGATGGAGGAATAGAGAGATGGATG,AGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGCAGATGGAGGAATAGAGAGATGGATG,AGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGCAGATGGAGGAATAGAGAGATGGATG,AGATGGATGGATGGATGGATGGATGGATGGATGCAGATGGAGGAATAGAGAGATGGATG,A 223.28 PASS AC=0,1,0,0,0;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 0/2:10:99:3,1,6,0 chr1 22985839 . AGATGGATGGATGGATG AGATGGATGGATG,AGATGGATGGATGGATGGATG,A 790.53 PASS AC=2,0,0;AF=0.576,0.091,0.015;AN=2;DP=1327;set=variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:26:79:0,0,18,8 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 1/1:0,60:60:99:1966,180,0:0,0,22,38 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 1/1:0,66:66:99:1970,198,0:0,0,41,25 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 1/1:23:3:2,1,14,6 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 1/1:0,16:16:48:578,48,0:0,0,3,13 chr1 23216712 . T C 1179.27 PASS AC=1;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 0/1:20,18:38:99:531,0,488:8,12,10,8 chr1 23219187 . C T 1368.17 PASS AC=1;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 0/1:16,12:28:99:399,0,514:14,2,10,2 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 1/1:0,293:293:99:8841,877,0:0,0,142,151 chr1 23221855 . A G 839.22 PASS AC=1;AF=0.583;AN=2;DP=337;FractionInformativeReads=1;MQ=60;set=variant9-variant13-variant23-variant33-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,15:48:99:365,0,1023:22,11,11,4 chr1 23223116 . C T 827.84 PASS AC=1;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 0/1:32,23:55:99:676,0,797:10,22,4,19 chr1 23232400 . C T 827.77 PASS AC=1;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 0/1:11,11:22:99:380,0,372:10,1,10,1 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 0/1:16,27:43:99:773,0,464:11,5,18,9 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 1/1:0,3:3:9:135,9,0:0,0,0,3 chr1 23337885 . CTT C,CT,CTTT 133.09 PASS AC=0,1,0;AF=0.05,0.35,0.1;AN=2;DP=207;set=variant2-filterInvariant5-variant10-variant13-variant14-filterInvariant15-variant16-variant23-variant27-variant39 GT:DP:GQ:SB 0/2:9:50:2,3,1,3 chr1 23342362 . A G 1759.42 PASS AC=1;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 0/1:19,30:49:99:754,0,365:10,9,16,14 chr1 23356864 . G A 44.51 PASS AC=1;AF=0.692;AN=2;DP=259;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant10-variant13-variant15-variant16-variant17-variant18-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant36-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:114,0,115:3,0,3,0 chr1 23380198 . A G 1049.64 PASS AC=1;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 0/1:16,10:26:99:256,0,517:14,2,7,3 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 0/1:47,37:84:99:1391,0,2041:23,24,18,19 chr1 23399932 . C T 2627.96 PASS AC=1;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 0/1:31,27:58:99:575,0,802:12,19,12,15 chr1 23405794 . A C 1835.22 PASS AC=1;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 0/1:30,28:58:99:752,0,811:15,15,14,14 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 0/1:91,63:154:99:1173,0,4920:51,40,34,29 chr1 23410140 . G T 3821.42 PASS AC=1;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 0/1:83,81:164:99:3018,0,3794:46,37,42,39 chr1 23410721 . A T 1190.34 PASS AC=1;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 0/1:14,12:26:99:316,0,432:5,9,8,4 chr1 23410742 . A C 1124.85 PASS AC=1;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 0/1:17,16:33:99:439,0,481:7,10,9,7 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 0/1:241,236:477:99:5757,0,5850:117,124,116,120 chr1 23413027 . T C 880.17 PASS AC=1;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 0/1:23,16:39:99:353,0,583:12,11,7,9 chr1 23413458 . T G 869.67 PASS AC=1;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 0/1:18,16:34:99:407,0,419:9,9,6,10 chr1 23413707 . T C 580.87 PASS AC=1;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 0/1:5,15:20:85:377,0,85:2,3,7,8 chr1 23415102 . T C 863.91 PASS AC=1;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 0/1:21,18:39:99:467,0,531:10,11,9,9 chr1 23418153 . C T 7204.82 PASS AC=1;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 0/1:75,96:171:99:2556,0,1980:31,44,48,48 chr1 23419261 . G A 2969.66 PASS AC=1;AF=0.809;AN=2;DP=4841;MQ=60;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-variant-variant36 GT:AD:DP:GQ:PL:SB 0/1:53,49:102:99:1242,0,1397:26,27,17,32 chr1 23419283 . G A 1489.5 PASS AC=1;AF=0.5;AN=2;DP=726;MQ=60;set=variant8-variant20-variant21-variant23-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:43,52:95:99:1344,0,1215:17,26,30,22 chr1 23419374 . G T 3057.47 PASS AC=1;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 0/1:78,45:123:99:1664,0,4288:42,36,21,24 chr1 23419383 . C T 3092.39 PASS AC=1;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 0/1:78,47:125:99:1706,0,4286:40,38,23,24 chr1 23419855 . T C 4142.99 PASS AC=1;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 0/1:61,54:115:99:1372,0,1686:32,29,23,31 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 0/1:2,7:9:61:183,0,61:0,2,2,5 chr1 23504084 . G A 2251.07 PASS AC=1;AF=0.5;AN=2;DP=899;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant9-variant14-variant23-variant25-variant36-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,40:77:99:877,0,1052:20,17,19,21 chr1 23518470 . TA T 676.68 PASS AC=1;AF=0.5;AN=2;DP=540;MQ=60;set=variant3-variant8-variant9-variant14-variant23-variant25-variant36-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,24:52:99:564,0,650:15,13,10,14 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 0/1:16,27:43:99:780,0,396:7,9,17,10 chr1 23519477 . C T 38.51 PASS AC=1;AF=0.7;AN=2;DP=407;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-variant36-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:196,0,142:2,2,5,1 chr1 23519508 . T TA 193.12 PASS AC=2;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 1/1:0,22:22:66:582,66,0:0,0,14,8 chr1 23519633 . A G 846.95 PASS AC=1;AF=0.5;AN=2;DP=805;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant9-variant14-variant23-variant25-variant36-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,29:53:99:744,0,519:12,12,16,13 chr1 23632626 . G C 5920.58 PASS AC=1;AF=0.864;AN=2;DP=6704;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:69,76:145:99:1748,0,1820:36,33,41,35 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 1/1:0,92:92:99:2983,275,0:0,0,65,27 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 2/1:83:99:0,0,38,45 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 0/1:7,12:19:99:377,0,233:1,6,2,10 chr1 23686246 . C T 1413.87 PASS AC=1;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 0/1:29,29:58:99:686,0,691:16,13,16,13 chr1 23688178 . A G 469.38 PASS AC=1;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 0/1:9,15:24:99:420,0,188:3,6,8,7 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 0/1:79,102:181:99:2648,0,2050:38,41,56,46 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 0/1:25,39:64:99:1091,0,709:18,7,26,13 chr1 23696152 . G A 1910.81 PASS AC=1;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 0/1:35,32:67:99:901,0,872:12,23,10,22 chr1 23707692 . A G 845.93 PASS AC=1;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 0/1:8,10:18:99:244,0,177:5,3,6,4 chr1 23710805 . A G 2808.84 PASS AC=1;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 0/1:61,37:98:99:804,0,1479:33,28,19,18 chr1 23713952 . T G 3230.05 PASS AC=1;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 0/1:41,64:105:99:1672,0,1014:17,24,29,35 chr1 23720260 . T G 874.87 PASS AC=1;AF=0.875;AN=2;DP=1271;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:294,0,345:8,1,8,0 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 0/1:16,19:35:99:492,0,526:5,11,5,14 chr1 23735241 . G T 1693.89 PASS AC=1;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 0/1:42,36:78:99:858,0,1058:22,20,13,23 chr1 23743581 . C G 1449.24 PASS AC=1;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 0/1:22,17:39:99:462,0,577:15,7,12,5 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 0/1:216,176:392:99:3558,0,4948:91,125,76,100 chr1 23755513 . T C 2326.93 PASS AC=1;AF=0.841;AN=2;DP=3690;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:50,34:84:99:696,0,1355:19,31,16,18 chr1 23755716 . T C 1468.01 PASS AC=1;AF=0.841;AN=2;DP=2175;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:21,25:46:99:736,0,503:8,13,14,11 chr1 23756155 . T C 958.14 PASS AC=1;AF=0.841;AN=2;DP=2165;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:20,33:53:99:898,0,448:10,10,19,14 chr1 23756695 . A G 905.77 PASS AC=1;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 0/1:1,13:14:4:336,0,4:0,1,5,8 chr1 23758134 . A G 2505.25 PASS AC=1;AF=0.841;AN=2;DP=3842;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:47,44:91:99:1010,0,1193:25,22,20,24 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 0/1:11,12:23:99:242,0,291:2,9,4,8 chr1 23762679 . A G 292.45 PASS AC=1;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 0/1:6,5:11:99:151,0,171:1,5,1,4 chr1 23765472 . A G 1280.56 PASS AC=1;AF=0.841;AN=2;DP=2030;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:25,25:50:99:640,0,653:11,14,11,14 chr1 23769359 . T C 733.04 PASS AC=1;AF=0.784;AN=2;DP=1354;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:9,14:23:99:343,0,208:4,5,5,9 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 0/1:28,34:62:99:787,0,580:13,15,14,20 chr1 23835672 . C T 667.46 PASS AC=1;AF=0.5;AN=2;DP=125;FS=0;FractionInformativeReads=1;MQ=60;set=variant19-variant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:13,20:33:99:546,0,271:5,8,8,12 chr1 23885342 . C T 502.54 PASS AC=1;AF=0.5;AN=2;DP=44;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.002;QD=11.42;ReadPosRankSum=0.766;SOR=0.752;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:24,20:44:99:531,0,556:14,10,12,8 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 1/1:0,129:129:99:3729,386,0:0,0,72,57 chr1 23886073 . T C 1596.56 PASS AC=1;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 0/1:37,28:65:99:661,0,923:18,19,14,14 chr1 23908221 . CTTTTTTT CTTTTTTTTT,CTTTTTT,CTTTTTTTTTT,CTTTT,CTT,C,CTTTTTTTT,CTTTTT 113.27 PASS AC=0,0,0,0,0,0,0,1;AF=0.19,0.214,0.024,0.048,0.024,0.024,0.095,0.071;AN=2;DP=509;set=variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant17-variant18-variant19-variant22-variant23-variant24-variant25-filterInvariant27-variant28-variant36-variant41-variant44 GT:DP:GQ:SB 0/8:11:37:1,2,1,7 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 1/1:47:70:1,1,21,24 chr1 23954524 . CTT CT,C,CTTT,CTTTTT,CTTTT 81.96 PASS AC=1,0,0,0,0;AF=0.176,0.088,0.206,0.029,0.029;AN=2;DP=968;set=filterInvariant3-variant5-variant6-variant10-filterInvariant17-filterInvariant18-variant19-variant21-filterInvariant23-variant24-filterInvariant25-filterInvariant29-filterInvariant34-filterInvariant36-variant37-filterInvariant39-variant44 GT:DP:GQ:SB 0/1:22:99:2,10,0,10 chr1 23955186 . T TTTATTATTATTA,TTTATTATTATTATTATTA,TTTATTATTATTATTATTATTATTATTA,TTTATTATTATTATTA,TTTATTATTATTATTATTATTATTA,TTTATTATTATTATTATTATTA 183.39 PASS AC=2,0,0,0,0,0;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 1/1:6:16:0,0,1,5 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 1/1:1,186:187:99:5246,531,0:1,0,74,112 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 1/1:2,92:94:99:2650,235,0:0,2,41,51 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 1/1:0,25:25:74:759,74,0:0,0,9,16 chr1 24069637 . G C 211.61 PASS AC=2;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 1/1:0,26:26:78:801,78,0:0,0,15,11 chr1 24077451 . C T 511.27 PASS AC=1;AF=0.5;AN=2;DP=522;FractionInformativeReads=1;MQ=60;set=variant-variant11-variant19-variant22-variant23-variant29-variant31-variant34-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,22:37:99:613,0,511:11,4,12,10 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 0/1:27:99:10,5,9,3 chr1 24083649 . T C 887.1 PASS AC=1;AF=0.658;AN=2;DP=1436;MQ=60;set=variant-variant11-variant14-variant15-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant29-variant31-variant34-variant36-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,25:56:99:568,0,730:14,17,14,11 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 0/1:35,38:73:99:1010,0,1013:10,25,14,24 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 1/1:0,16:16:48:523,48,0:0,0,2,14 chr1 24114129 . G A 421.61 PASS AC=2;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 1/1:0,52:52:99:1545,156,0:0,0,21,31 chr1 24122986 . C T 224.06 PASS AC=2;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 1/1:0,13:13:37:418,37,0:0,0,12,1 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 1/1:0,51:51:99:1879,153,0:0,0,31,20 chr1 24133612 . G A 847.83 PASS AC=2;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 1/1:0,77:77:99:2381,231,0:0,0,37,40 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 1/1:0,6:6:18:242,18,0:0,0,6,0 chr1 24134721 . T C 4199.35 PASS AC=2;AF=0.932;AN=2;DP=5979;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:3897,389,0:0,0,66,64 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 1/1:0,41:41:99:1195,123,0:0,0,25,16 chr1 24152213 . C A 111.22 PASS AC=2;AF=1;AN=2;DP=45;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.727;ReadPosRankSum=0.727;set=variant3-variant4-variant6-variant8-variant11-variant19-variant21-variant23-variant25-variant29-variant30-variant31-variant34-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,0,3 chr1 24196957 . C G 1441.02 PASS AC=2;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 1/1:0,80:80:99:2718,239,0:0,0,58,22 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 1/1:0,9:9:27:346,27,0:0,0,1,8 chr1 24197644 . CAAAA CAAA,CA,CAA,C 439.71 PASS AC=0,0,0,1;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 0/4:36:99:8,8,15,5 chr1 24197696 . A G 2688.7 PASS AC=2;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 1/1:0,137:137:99:4551,410,0:0,0,89,48 chr1 24197898 . C G 3717.73 PASS AC=2;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 1/1:2,228:230:99:6990,639,0:1,1,95,133 chr1 24198804 . T C 1222.79 PASS AC=2;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 1/1:0,78:78:99:2514,233,0:0,0,52,26 chr1 24198840 . C G 2177.87 PASS AC=2;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 1/1:0,123:123:99:4014,369,0:0,0,81,42 chr1 24199026 . A C 5231.98 PASS AC=2;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 1/1:0,184:184:99:6022,551,0:0,0,88,96 chr1 24199041 . T C 4860.41 PASS AC=2;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 1/1:0,185:185:99:5908,554,0:0,0,91,94 chr1 24199182 . T C 4225.3 PASS AC=2;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 1/1:0,224:224:99:7062,672,0:0,0,118,106 chr1 24199290 . T C 2802.7 PASS AC=2;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 1/1:0,189:189:99:6101,567,0:0,0,83,106 chr1 24199339 . A C 2137.62 PASS AC=2;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 1/1:0,138:138:99:5797,415,0:0,0,55,83 chr1 24199363 . T C 2300.43 PASS AC=2;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 1/1:0,107:107:99:4925,331,0:0,0,39,68 chr1 24199364 . G A 2300.43 PASS AC=2;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 1/1:0,105:105:99:4855,325,0:0,0,38,67 chr1 24199642 . G A 1797.37 PASS AC=2;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 1/1:0,141:141:99:3948,421,0:0,0,68,73 chr1 24199738 . A AT 577.63 PASS AC=2;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 1/1:0,25:25:75:1030,75,0:0,0,4,21 chr1 24199750 . C CAG 581.19 PASS AC=2;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 1/1:0,19:19:66:946,66,0:0,0,1,18 chr1 24200052 . A G 157.32 PASS AC=2;AF=0.706;AN=2;DP=580;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:333,33,0:0,0,6,5 chr1 24200158 . T C 364.75 PASS AC=2;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 1/1:0,19:19:57:607,57,0:0,0,10,9 chr1 24200524 . C T 890.54 PASS AC=2;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 1/1:0,62:62:99:1874,184,0:0,0,35,27 chr1 24200606 . A G 1366.51 PASS AC=2;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 1/1:0,83:83:99:2475,249,0:0,0,49,34 chr1 24200772 . C G 680.76 PASS AC=2;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 1/1:0,75:75:99:2330,225,0:0,0,31,44 chr1 24200800 . T C 542.26 PASS AC=2;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 1/1:0,54:54:99:1806,161,0:0,0,21,33 chr1 24200903 . G C 1005.21 PASS AC=2;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 1/1:0,27:27:84:1226,84,0:0,0,16,11 chr1 24200921 . T C 942.56 PASS AC=2;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 1/1:0,32:32:96:1346,96,0:0,0,21,11 chr1 24200969 . T C 1247.54 PASS AC=2;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 1/1:0,66:66:99:2858,199,0:0,0,36,30 chr1 24200983 . C T 1268.8 PASS AC=2;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 1/1:0,74:74:99:3134,223,0:0,0,42,32 chr1 24201094 . G C 1741.11 PASS AC=2;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 1/1:0,103:103:99:3174,309,0:0,0,53,50 chr1 24201109 . C T 1618.9 PASS AC=2;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 1/1:0,104:104:99:3174,310,0:0,0,58,46 chr1 24201262 . A G 487.54 PASS AC=2;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 1/1:0,133:133:99:4019,399,0:0,0,62,71 chr1 24201357 . A G 398.49 PASS AC=2;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 1/1:1,101:102:99:3200,268,0:1,0,48,53 chr1 24201448 . C T 660.11 PASS AC=2;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 1/1:0,100:100:99:3186,300,0:0,0,50,50 chr1 24201643 . G A 549.69 PASS AC=2;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 1/1:0,76:76:99:2445,227,0:0,0,39,37 chr1 24201919 . T C 1695.89 PASS AC=2;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 1/1:0,152:152:99:6731,460,0:0,0,79,73 chr1 24201920 . T C 1695.89 PASS AC=2;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 1/1:0,151:151:99:6731,460,0:0,0,78,73 chr1 24202318 . A G 79.71 PASS AC=2;AF=0.726;AN=2;DP=298;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant9-variant11-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:402,33,0:0,0,3,8 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 1/1:0,3:3:9:135,9,0:0,0,3,0 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 1/1:0,14:14:42:505,42,0:0,0,10,4 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 1/1:0,16:16:48:585,48,0:0,0,12,4 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 1/1:0,3:3:9:94,9,0:0,0,2,1 chr1 24287780 . GCTT G 424.79 PASS AC=2;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 1/1:0,6:6:18:270,18,0:0,0,4,2 chr1 24288404 . A G 40.5 PASS AC=2;AF=0.703;AN=2;DP=218;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant36-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 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 0/1:71,33:104:99:1172,0,5452:38,33,17,16 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 1/1:0,131:131:99:4393,392,0:0,0,55,76 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 1/1:0,295:295:99:8834,883,0:0,0,139,156 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 1/1:0,95:95:99:2755,285,0:0,0,42,53 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 0/1:45,39:84:99:918,0,1075:21,24,16,23 chr1 24294249 . C T 3760.37 PASS AC=2;AF=0.989;AN=2;DP=5335;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3291,327,0:0,0,59,50 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 0/1:42,46:88:99:1325,0,1008:21,21,22,24 chr1 24294450 . CAA CA,CAAA,C 646.13 PASS AC=1,1,0;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 1/2:68:99:5,5,32,26 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 0/1:25,26:51:99:626,0,630:9,16,10,16 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 0/1:13,11:24:99:342,0,348:4,9,3,8 chr1 24296853 . G GTTT,GTTTT,GT,GTT,GTTTTT,GTTTTTT 85.54 PASS AC=2,0,0,0,0,0;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 1/1:7:10:0,1,1,5 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 0/1:17,18:35:99:524,0,378:10,7,14,4 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 0/1:14,18:32:99:482,0,339:5,9,5,13 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 1/1:0,15:15:45:574,45,0:0,0,2,13 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 0/1:15,16:31:99:393,0,324:5,10,5,11 chr1 24306894 . C A 1479.05 PASS AC=1;AF=0.5;AN=2;DP=132;FS=0.65;FractionInformativeReads=1;MQ=60;MQRankSum=-0.105;QD=11.2;ReadPosRankSum=-2.194;SOR=0.767;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:67,65:132:99:1507,0,1765:28,39,26,39 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 0/1:37,26:63:99:648,0,909:23,14,18,8 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 0/1:51,57:108:99:1637,0,1499:22,29,26,31 chr1 24388371 . T C 3011.56 PASS AC=2;AF=0.932;AN=2;DP=3846;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2664,246,0:0,0,55,27 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 0/1:11,12:23:99:471,0,388:9,2,8,4 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 0/1:9,23:32:99:611,0,291:4,5,10,13 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 0/1:51,46:97:99:1140,0,1207:25,26,16,30 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 0/1:21,26:47:99:701,0,591:6,15,6,20 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 0/1:5,7:12:99:194,0,147:1,4,2,5 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 0/1:8,7:15:99:216,0,255:7,1,5,2 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 1/1:0,152:152:99:4787,455,0:0,0,92,60 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 1/1:0,209:209:99:6203,626,0:0,0,111,98 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 0/1:102,97:199:99:2247,0,2354:55,47,57,40 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 0/1:101,89:190:99:2207,0,2504:45,56,36,53 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 0/1:33,32:65:99:777,0,867:14,19,11,21 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 0/1:13,6:19:99:132,0,401:2,11,2,4 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 0/1:43,60:103:99:1404,0,922:21,22,28,32 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 0/1:12,14:26:99:387,0,247:6,6,8,6 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 0/1:45,60:105:99:1502,0,1000:32,13,36,24 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 0/1:11,8:19:99:224,0,438:0,11,1,7 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 1/1:0,76:76:99:2424,227,0:0,0,51,25 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 0/1:38,52:90:99:1361,0,931:24,14,35,17 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 0/1:48,52:100:99:1272,0,1176:21,27,20,32 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 0/1:78,79:157:99:2036,0,1854:44,34,50,29 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 0/1:45,26:71:99:731,0,1230:30,15,19,7 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 0/1:69,80:149:99:1895,0,1736:27,42,34,46 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 0/1:10,4:14:99:135,0,386:1,9,0,4 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 0/1:22,31:53:99:785,0,464:13,9,21,10 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 0/1:53,61:114:99:1428,0,1262:28,25,35,26 chr1 24434595 . T C 1324.17 PASS AC=1;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 0/1:108,53:161:99:1283,0,2641:46,62,18,35 chr1 24434717 . T TC 832.39 PASS AC=1;AF=0.643;AN=2;DP=1082;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,16:27:99:416,0,261:3,8,4,12 chr1 24447116 . C T 1226.77 PASS AC=2;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 1/1:0,76:76:99:2387,227,0:0,0,44,32 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 1/1:0,69:69:99:2115,205,0:0,0,34,35 chr1 24447468 . G C 1721.12 PASS AC=2;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 1/1:0,118:118:99:3783,354,0:0,0,54,64 chr1 24463563 . C T 366.35 PASS AC=1;AF=0.533;AN=2;DP=552;FractionInformativeReads=1;MQ=60;set=variant4-variant8-variant12-variant16-variant17-variant18-variant23-variant26-variant31-variant32-variant33-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,11:27:99:298,0,474:12,4,9,2 chr1 24464006 . CT CTT,CTTT,C 121.01 PASS AC=1,0,0;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 0/1:8:1:0,1,0,7 chr1 24465113 . C T 1292.73 PASS AC=2;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 1/1:0,91:91:99:2933,271,0:0,0,41,50 chr1 24469675 . C G 70.19 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=76;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:34,8:42:98:98,0,886:15,19,0,8 chr1 24480612 . CA C 667.84 PASS AC=2;AF=0.909;AN=2;DP=1066;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:508,54,0:0,0,13,5 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 0/1:61,95:156:99:2424,0,1437:33,28,48,47 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 0/1:61,68:129:99:1638,0,1573:36,25,33,35 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 0/1:4,2:6:64:64,0,123:3,1,2,0 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 1/1:2,56:58:99:2098,126,0:1,1,27,29 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 0/1:43,27:70:99:668,0,1105:23,20,11,16 chr1 24481940 . G A 1132.14 PASS AC=1;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 0/1:26,19:45:99:523,0,647:10,16,12,7 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 0/1:10,28:38:99:691,0,291:4,6,12,16 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 0/1:26,44:70:99:1074,0,568:12,14,21,23 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 1/1:0,57:57:99:1605,171,0:0,0,29,28 chr1 24482992 . C G 1393.01 PASS AC=1;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 0/1:29,32:61:99:880,0,754:16,13,20,12 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 1/1:0,65:65:99:1888,193,0:0,0,34,31 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 1/1:0,66:66:99:2004,198,0:0,0,32,34 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 1/1:0,65:65:99:2141,195,0:0,0,26,39 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 1/1:0,57:57:99:1954,171,0:0,0,36,21 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 1/1:0,40:40:99:1490,120,0:0,0,19,21 chr1 24485941 . T C 2916.41 PASS AC=1;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 0/1:55,39:94:99:887,0,1403:30,25,21,18 chr1 24486216 . GT G,GTTTTTTTTTTTTTGTTTT,GTTTTGTTTTTTTTGTTTT,GTTTT 162.83 PASS AC=1,0,1,0;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 1/3:20:99:0,0,3,17 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 1/1:0,19:19:56:598,56,0:0,0,12,7 chr1 24495722 . G A 193.42 PASS AC=1;AF=0.689;AN=2;DP=484;MQ=60;set=variant-variant2-variant4-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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:201,0,240:6,2,6,0 chr1 24507162 . T C 39.46 PASS AC=1;AF=0.5;AN=2;DP=162;FractionInformativeReads=1;MQ=60;set=filterInvariant18-variant23-filterInvariant38-filterInvariant39 GT:AD:DP:GQ:PL:SB 0/1:27,14:41:99:280,0,2118:7,20,14,0 chr1 24507165 . A C 39.45 PASS AC=1;AF=0.5;AN=2;DP=178;FractionInformativeReads=1;MQ=60;set=filterInvariant18-variant23-filterInvariant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,11:37:99:280,0,2118:5,21,11,0 chr1 24507172 . A C 51.82 PASS AC=1;AF=0.5;AN=2;DP=221;MQ=60;set=filterInvariant16-variant23-filterInvariant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,11:39:99:297,0,1293:6,22,11,0 chr1 24507176 . A C 45.7 PASS AC=1;AF=0.5;AN=2;DP=277;MQ=60;set=filterInvariant15-filterInvariant16-variant23-variant31-filterInvariant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,10:42:99:231,0,2406:8,24,10,0 chr1 24507182 . T C 187.94 PASS AC=1;AF=0.5;AN=2;DP=142;MQ=60;set=variant23-filterInvariant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,10:47:99:216,0,2502:9,28,10,0 chr1 24513608 . C T 163.63 PASS AC=1;AF=0.667;AN=2;DP=306;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant21-variant23-variant28-variant30-variant32-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:114,0,105:3,1,2,3 chr1 24513768 . G A 824.25 PASS AC=2;AF=0.94;AN=2;DP=1616;MQ=60;set=variant-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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:977,111,0:0,0,17,21 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 0/1:25,9:34:99:166,0,1067:9,16,9,0 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 0/1:29,8:37:99:160,0,1106:9,20,8,0 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 0/1:66,66:132:99:1658,0,1623:32,34,35,31 chr1 24669457 . C T 2503.9 PASS AC=1;AF=0.5;AN=2;DP=435;FractionInformativeReads=1;MQ=60;set=variant12-variant23 GT:AD:DP:GQ:PL:SB 0/1:105,86:191:99:2030,0,2773:48,57,39,47 chr1 24671287 . C T 648.79 PASS AC=1;AF=0.571;AN=2;DP=1645;MQ=60;set=variant5-variant9-variant10-variant13-variant17-variant18-variant21-variant23-variant31-variant33-variant34-variant36-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:59,54:113:99:1063,0,1421:30,29,28,26 chr1 24671464 . ACCCTCCACACCTGTGCC A 232.99 PASS AC=1;AF=0.635;AN=2;DP=406;set=variant-variant3-variant5-variant6-variant9-variant13-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:145,0,515:0,3,0,4 chr1 24673866 . A G 1105.41 PASS AC=2;AF=0.708;AN=2;DP=3501;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,110:110:99:3210,329,0:0,0,69,41 chr1 24680915 . C T 1539.79 PASS AC=1;AF=0.571;AN=2;DP=2654;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant13-variant15-variant16-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant32-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:73,44:117:99:978,0,1851:37,36,21,23 chr1 24681641 . C T 583.8 PASS AC=1;AF=0.542;AN=2;DP=513;FractionInformativeReads=1;MQ=60;set=variant5-variant9-variant10-variant13-variant17-variant18-variant23-variant31-variant33-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:25,17:42:99:415,0,674:11,14,10,7 chr1 24683536 . GC G,GCCC,GCC 349.57 PASS AC=0,1,0;AF=0.344,0.063,0.281;AN=2;DP=270;set=variant-variant2-variant4-variant6-variant13-variant14-variant16-variant18-variant22-variant23-variant27-variant29-variant30-variant32-variant41-variant44 GT:DP:GQ:SB 0/2:7:82:4,0,1,2 chr1 24683547 . CA CCCAA,C 140.65 PASS AC=0,1;AF=0.125,0.5;AN=2;DP=70;MQ=60;set=variant3-variant23-variant37-variant40 GT:DP:GQ:SB 0/2:9:99:1,3,4,1 chr1 24687653 . T C 246.22 PASS AC=2;AF=0.778;AN=2;DP=664;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:495,33,0:0,0,1,10 chr1 24690414 . A G 679.36 PASS AC=2;AF=0.778;AN=2;DP=739;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:807,66,0:0,0,18,4 chr1 24690894 . C T 1368.18 PASS AC=1;AF=0.625;AN=2;DP=600;FractionInformativeReads=1;MQ=60;set=variant23-variant31-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:79,60:139:99:1396,0,2063:35,44,28,32 chr1 24695749 . C G 1359.97 PASS AC=1;AF=0.58;AN=2;DP=4062;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant32-variant33-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:87,75:162:99:2097,0,2105:44,43,42,33 chr1 24706113 . G A 414.04 PASS AC=2;AF=0.63;AN=2;DP=1094;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1401,123,0:0,0,22,19 chr1 24706269 . A G 933.35 PASS AC=2;AF=0.63;AN=2;DP=2473;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2793,270,0:0,0,46,44 chr1 24706292 . T C 970.3 PASS AC=2;AF=0.615;AN=2;DP=2405;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2804,276,0:0,0,41,51 chr1 24706410 . T C 507.24 PASS AC=2;AF=0.63;AN=2;DP=968;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1425,120,0:0,0,9,31 chr1 24706438 . A AG 232.54 PASS AC=2;AF=0.635;AN=2;DP=544;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:641,48,0:0,0,2,14 chr1 24706461 . A G 241.61 PASS AC=2;AF=0.635;AN=2;DP=343;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:270,18,0:0,0,0,6 chr1 24718075 . T C 1789.37 PASS AC=2;AF=0.609;AN=2;DP=3788;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant11-variant13-variant15-variant16-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:3547,381,0:0,0,61,67 chr1 24727678 . C T 1582 PASS AC=2;AF=0.781;AN=2;DP=1466;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant11-variant13-variant14-variant15-variant16-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1037,99,0:0,0,21,12 chr1 24746205 . C T 1627.34 PASS AC=2;AF=0.604;AN=2;DP=4103;MQ=60;set=variant-variant3-variant4-variant6-variant11-variant13-variant15-variant16-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant34-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,132:132:99:3859,395,0:0,0,59,73 chr1 24768778 . G C 570.13 PASS AC=2;AF=0.743;AN=2;DP=1166;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:71:658,71,0:0,0,13,11 chr1 24779855 . T C 835.83 PASS AC=2;AF=0.614;AN=2;DP=851;MQ=60;set=variant-variant3-variant6-variant11-variant13-variant15-variant16-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1095,93,0:0,0,21,10 chr1 24781247 . T C 1097.43 PASS AC=2;AF=0.694;AN=2;DP=1353;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant11-variant13-variant14-variant15-variant16-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:441,48,0:0,0,7,9 chr1 24784139 . A G 1192.91 PASS AC=2;AF=0.614;AN=2;DP=1316;MQ=60;set=variant-variant3-variant6-variant11-variant13-variant15-variant16-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1455,117,0:0,0,30,9 chr1 24784197 . T C 4434.29 PASS AC=2;AF=0.694;AN=2;DP=3708;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant11-variant13-variant14-variant15-variant16-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3240,309,0:0,0,66,37 chr1 24785393 . C T 2559.76 PASS AC=2;AF=0.614;AN=2;DP=3720;MQ=60;set=variant-variant3-variant6-variant11-variant13-variant15-variant16-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,154:154:99:4757,461,0:0,0,79,75 chr1 24791915 . GTA G,GTATA 42.14 PASS AC=0,1;AF=0.45,0.05;AN=2;DP=818;MQ=60;set=filterInvariant4-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-filterInvariant15-filterInvariant17-variant23-filterInvariant25-filterInvariant32 GT:DP:GQ:SB 0/2:55:99:21,15,10,9 chr1 24792617 . T A 9603.11 PASS AC=2;AF=0.721;AN=2;DP=12137;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,294:294:99:8667,879,0:0,0,132,162 chr1 24796838 . A G 321.28 PASS AC=2;AF=0.605;AN=2;DP=485;MQ=60;set=variant-variant3-variant6-variant13-variant15-variant16-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant33-variant34-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:748,75,0:0,0,14,11 chr1 24798383 . C T 600.12 PASS AC=1;AF=0.717;AN=2;DP=838;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant33-variant36-variant38-variant39-variant40-variant41-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:18,12:30:99:288,0,430:8,10,7,5 chr1 24798498 . CTTT CT,CTT,C 482.42 PASS AC=1,1,0;AF=0.525,0.125,0.013;AN=2;DP=1455;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-filterInvariant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/2:21:99:1,0,9,11 chr1 24840768 . G A 216.06 PASS AC=1;AF=0.661;AN=2;DP=760;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant10-variant11-variant13-variant15-variant16-variant18-variant21-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:263,0,326:10,2,7,3 chr1 24859617 . G A 279.6 PASS AC=1;AF=0.633;AN=2;DP=1027;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant10-variant11-variant15-variant21-variant23-variant29-variant32-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:33,35:68:99:786,0,874:23,10,21,14 chr1 24859665 . G A 789.81 PASS AC=1;AF=0.625;AN=2;DP=1580;MQ=60;set=variant-variant3-variant5-variant6-variant9-variant10-variant11-variant15-variant21-variant23-variant29-variant32-variant36-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:41,43:84:99:1050,0,976:23,18,21,22 chr1 24861704 . G A 635.24 PASS AC=1;AF=0.607;AN=2;DP=2452;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant15-variant16-variant18-variant21-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:37,42:79:99:1033,0,1038:17,20,21,21 chr1 24862643 . T G 6476.97 PASS AC=1;AF=0.638;AN=2;DP=10648;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant15-variant16-variant18-variant21-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:185,142:327:99:5369,0,9074:97,88,76,66 chr1 24862649 . A G 6662.06 PASS AC=1;AF=0.638;AN=2;DP=10801;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant15-variant16-variant18-variant21-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:185,148:333:99:5490,0,9117:96,89,78,70 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 1/1:0,39:39:99:1237,117,0:0,0,14,25 chr1 25098245 . T C 810.95 PASS AC=1;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 0/1:30,25:55:99:774,0,851:22,8,21,4 chr1 25098341 . C T 2107.84 PASS AC=1;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 0/1:68,71:139:99:1745,0,1850:37,31,43,28 chr1 25140825 . A G 617.87 PASS AC=1;AF=0.583;AN=2;DP=1271;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant11-variant12-variant13-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant30-variant31-variant32-variant33-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:33,23:56:99:662,0,814:14,19,6,17 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 1/1:0,117:117:99:3417,350,0:0,0,53,64 chr1 25168124 . G C 2181.68 PASS AC=1;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 0/1:50,39:89:99:1043,0,1355:33,17,27,12 chr1 25169634 . A G 2387.89 PASS AC=1;AF=0.583;AN=2;DP=3439;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant11-variant12-variant13-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant30-variant31-variant32-variant33-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:60,65:125:99:1908,0,1773:39,21,43,22 chr1 25169875 . C A 12039.8 PASS AC=2;AF=0.977;AN=2;DP=15793;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,291:291:99:9480,872,0:0,0,115,176 chr1 25227538 . T G 188.47 PASS AC=1;AF=0.5;AN=2;DP=46;FractionInformativeReads=1;set=variant8-variant17-variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:63:153,0,63:2,1,4,2 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 0/1:8,2:10:60:60,0,252:2,6,1,1 chr1 25254317 . C T 434.65 PASS AC=1;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 0/1:7,11:18:99:385,0,257:0,7,1,10 chr1 25256444 . G A 1345.61 PASS AC=1;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 0/1:33,45:78:99:1062,0,757:13,20,18,27 chr1 25554079 . AT A 773.62 PASS AC=1;AF=0.5;AN=2;DP=281;MQ=60;set=variant5-variant23-variant29-variant30-variant42 GT:AD:DP:GQ:PL:SB 0/1:28,37:65:99:1190,0,849:11,17,13,24 chr1 25570081 . T C 952.02 PASS AC=1;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 0/1:21,33:54:99:692,0,463:13,8,16,17 chr1 25570550 . A AT 123.85 PASS AC=2;AF=0.92;AN=2;DP=735;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:221,27,0:0,0,7,2 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 1/1:0,244:244:99:7462,731,0:0,0,145,99 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 1/1:2,17:19:3:313,3,0:1,1,13,4 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 1/1:0,71:71:99:2006,212,0:0,0,28,43 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 1/1:0,68:68:99:2061,204,0:0,0,32,36 chr1 25688146 . A C 681.36 PASS AC=1;AF=0.5;AN=2;DP=271;FractionInformativeReads=1;MQ=60;set=variant5-variant23-variant29-variant30-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,25:51:99:729,0,569:13,13,8,17 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 1/1:0,23:23:69:788,69,0:0,0,16,7 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 1/1:0,12:12:36:527,36,0:0,0,1,11 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 1/1:0,12:12:36:527,36,0:0,0,1,11 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 1/1:0,39:39:99:1395,117,0:0,0,9,30 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 1/1:0,61:61:99:1923,182,0:0,0,23,38 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 1/1:0,47:47:99:2134,153,0:0,0,28,19 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 1/1:0,55:55:99:2304,171,0:0,0,31,24 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 1/1:0,142:142:99:4325,426,0:0,0,87,55 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 1/1:2,323:325:99:9721,922,0:1,1,172,151 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 1/1:0,12:12:36:491,36,0:0,0,11,1 chr1 25889342 . CAG C 838.25 PASS AC=1;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 0/1:30,29:59:99:1127,0,1177:15,15,10,19 chr1 25889422 . C T 622.27 PASS AC=1;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 0/1:26,19:45:99:523,0,623:11,15,7,12 chr1 25889632 . T C 632.25 PASS AC=1;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 0/1:20,21:41:99:493,0,546:6,14,10,11 chr1 25889672 . G A 306.28 PASS AC=1;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 0/1:10,14:24:99:340,0,294:2,8,5,9 chr1 25890050 . A G 511.51 PASS AC=1;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 0/1:41,31:72:99:859,0,1010:26,15,22,9 chr1 25890189 . A G 1597.92 PASS AC=1;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 0/1:126,123:249:99:2840,0,2990:65,61,67,56 chr1 25890247 . C T 2691.15 PASS AC=1;AF=0.5;AN=2;DP=851;MQ=60;set=variant14-variant23-variant30 GT:AD:DP:GQ:PL:SB 0/1:153,124:277:99:2907,0,3788:74,79,63,61 chr1 25893221 . G T 480.36 PASS AC=1;AF=0.629;AN=2;DP=889;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,21:40:99:538,0,573:15,4,14,7 chr1 25893242 . T C 701.9 PASS AC=1;AF=0.618;AN=2;DP=1378;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,23:49:99:888,0,1351:18,8,15,8 chr1 25893243 . G A 701.9 PASS AC=1;AF=0.6;AN=2;DP=1199;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,23:49:99:888,0,1351:18,8,15,8 chr1 25893927 . AT A 390.39 PASS AC=1;AF=0.597;AN=2;DP=2441;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,36:65:99:965,0,705:13,16,20,16 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 1/1:0,53:53:99:2376,159,0:0,0,22,31 chr1 25894853 . G T 1262.4 PASS AC=1;AF=0.625;AN=2;DP=3432;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,40:83:99:1016,0,1171:21,22,18,22 chr1 25895238 . C T 1002.59 PASS AC=1;AF=0.641;AN=2;DP=2343;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,26:48:99:640,0,565:10,12,9,17 chr1 25895406 . C T 262.46 PASS AC=1;AF=0.63;AN=2;DP=364;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant11-variant12-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant31-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:76:76,0,115:1,2,1,2 chr1 26073300 . A G 155.65 PASS AC=1;AF=0.5;AN=2;DP=143;MQ=60;set=variant3-filterInvariant23-variant32 GT:AD:DP:GQ:PL:SB 0/1:35,11:46:64:64,0,519:21,14,0,11 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 1/1:0,54:54:99:1719,162,0:0,0,40,14 chr1 26089977 . CAAAAAA CAA,CAAAAAAA,CAAAA,CAAA,CA,CAAAAAAAA,C,CAAAAA 346.26 PASS AC=0,0,0,0,0,0,1,0;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 0/7:20:99:5,8,5,2 chr1 26090072 . A G 2651.58 PASS AC=2;AF=0.886;AN=2;DP=4375;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,87:88:99:2639,222,0:1,0,46,41 chr1 26090285 . T G 626.18 PASS AC=1;AF=0.611;AN=2;DP=547;FractionInformativeReads=1;MQ=60;set=variant-variant13-variant16-variant21-variant23-variant28-variant31-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,28:60:99:863,0,939:18,14,20,8 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 1/1:0,50:50:99:1808,150,0:0,0,9,41 chr1 26098350 . G A 882.21 PASS AC=2;AF=0.654;AN=2;DP=438;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant8-variant13-variant14-variant16-variant23-variant28-variant30-variant31-variant34-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1258,96,0:0,0,5,27 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 1/1:0,21:21:63:734,63,0:0,0,14,7 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 1/1:0,83:83:99:2584,248,0:0,0,36,47 chr1 26111715 . CTT C,CT 82.86 PASS AC=0,1;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 0/2:9:53:0,3,2,4 chr1 26111743 . G A 359.75 PASS AC=1;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 0/1:2,4:6:74:121,0,74:0,2,1,3 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 0/3:63:99:28,8,17,10 chr1 26127020 . G A 635.57 PASS AC=1;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 0/1:7,13:20:99:331,0,197:5,2,9,4 chr1 26128307 . C T 636.35 PASS AC=1;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 0/1:9,4:13:99:100,0,289:6,3,3,1 chr1 26131638 . A G 451.24 PASS AC=1;AF=0.5;AN=2;DP=51;FractionInformativeReads=1;MQ=60;set=variant23-variant30 GT:AD:DP:GQ:PL:SB 0/1:10,14:24:99:479,0,298:7,3,11,3 chr1 26131654 . G A 582.1 PASS AC=1;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 0/1:14,13:27:99:411,0,423:10,4,9,4 chr1 26135741 . C G 1796.85 PASS AC=1;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 0/1:37,29:66:99:776,0,1038:10,27,9,20 chr1 26138136 . C A 2464.28 PASS AC=1;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 0/1:98,95:193:99:2351,0,2447:53,45,51,44 chr1 26138262 . T C 4947.17 PASS AC=1;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 0/1:57,78:135:99:1902,0,1398:19,38,34,44 chr1 26139137 . C T 759.64 PASS AC=1;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 0/1:10,16:26:99:483,0,319:8,2,11,5 chr1 26139392 . A G 899.66 PASS AC=1;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 0/1:22,18:40:99:351,0,567:7,15,9,9 chr1 26139444 . G A 248.06 PASS AC=1;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 0/1:12,6:18:99:162,0,323:4,8,2,4 chr1 26139879 . C G 510.58 PASS AC=1;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 0/1:4,6:10:99:196,0,143:4,0,5,1 chr1 26139919 . C T 973.17 PASS AC=1;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 0/1:13,16:29:99:502,0,361:10,3,13,3 chr1 26140573 . C A 1896.39 PASS AC=1;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 0/1:73,49:122:99:1002,0,1724:34,39,23,26 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 0/1:43,43:86:99:1083,0,1069:20,23,23,20 chr1 26143704 . A ATTTTG 591.25 PASS AC=1;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 0/1:9,5:14:99:182,0,516:5,4,1,4 chr1 26143931 . T C 337.32 PASS AC=1;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 0/1:3,5:8:71:140,0,71:2,1,3,2 chr1 26144437 . TC T 941.05 PASS AC=1;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 0/1:21,17:38:99:404,0,486:10,11,9,8 chr1 26144674 . G A 336.08 PASS AC=1;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 0/1:18,10:28:99:204,0,431:8,10,5,5 chr1 26146392 . C G 834.75 PASS AC=1;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 0/1:13,12:25:99:262,0,306:8,5,6,6 chr1 26146449 . C T 513.86 PASS AC=1;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 0/1:22,20:42:99:387,0,483:12,10,11,9 chr1 26146539 . A C 2182.45 PASS AC=1;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 0/1:22,25:47:99:590,0,603:15,7,16,9 chr1 26146884 . C G 4132.53 PASS AC=1;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 0/1:48,36:84:99:983,0,1324:18,30,11,25 chr1 26148011 . G A 1035.48 PASS AC=1;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 0/1:26,15:41:99:409,0,718:17,9,12,3 chr1 26148821 . C T 201.1 PASS AC=1;AF=0.5;AN=2;DP=34;FractionInformativeReads=1;MQ=60;set=variant23-variant30 GT:AD:DP:GQ:PL:SB 0/1:9,9:18:99:229,0,261:4,5,5,4 chr1 26149257 . TC T 139.45 PASS AC=1;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 0/1:6,3:9:79:79,0,197:4,2,3,0 chr1 26149356 . GCT G 807.4 PASS AC=1;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 0/1:21,21:42:99:819,0,929:13,8,14,7 chr1 26150023 . C T 2652.05 PASS AC=1;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 0/1:53,32:85:99:957,0,1545:28,25,19,13 chr1 26152666 . T C 2329.75 PASS AC=1;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 0/1:19,34:53:99:996,0,457:14,5,22,12 chr1 26152758 . A G 5017.82 PASS AC=1;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 0/1:61,88:149:99:2143,0,1261:32,29,47,41 chr1 26158900 . A ACT 1379.27 PASS AC=1;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 0/1:23,25:48:99:966,0,876:13,10,14,11 chr1 26158962 . A G 1255.14 PASS AC=1;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 0/1:30,25:55:99:643,0,765:14,16,10,15 chr1 26161037 . G C 222.07 PASS AC=1;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 0/1:1,3:4:25:120,0,25:1,0,3,0 chr1 26161086 . A G 182.78 PASS AC=1;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 0/1:1,4:5:31:165,0,31:1,0,4,0 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 1/1:0,81:81:99:2396,243,0:0,0,47,34 chr1 26189169 . GCA G 1359.7 PASS AC=1;AF=0.5;AN=2;DP=157;MQ=60;set=variant23-variant30 GT:AD:DP:GQ:PL:SB 0/1:35,36:71:99:1397,0,1353:18,17,21,15 chr1 26227608 . CAAA CAA,CA,C 181.59 PASS AC=1,0,1;AF=0.18,0.2,0.14;AN=2;DP=960;set=variant-variant2-variant5-filterInvariant6-filterInvariant8-variant9-variant10-filterInvariant12-variant14-variant15-variant17-variant21-variant22-variant23-variant25-filterInvariant26-filterInvariant27-variant28-variant30-variant33-variant34-filterInvariant36-variant40-variant43-filterInvariant44 GT:DP:GQ:SB 3/1:16:99:1,1,6,8 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 0/1:9,4:13:82:82,0,956:2,7,4,0 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 0/1:10,4:14:82:82,0,956:3,7,4,0 chr1 26232906 . ACT A 2599.32 PASS AC=1;AF=0.5;AN=2;DP=246;MQ=60;set=variant23-variant30 GT:AD:DP:GQ:PL:SB 0/1:85,71:156:99:2637,0,3317:43,42,41,30 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 1/1:9:27:0,0,3,6 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 1/1:0,6:6:18:270,18,0:0,0,5,1 chr1 26310213 . T C 388.48 PASS AC=2;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 1/1:0,29:29:87:885,87,0:0,0,17,12 chr1 26310394 . A G 1793.04 PASS AC=2;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 1/1:1,67:68:99:2266,168,0:1,0,40,27 chr1 26310836 . G T 656.26 PASS AC=2;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 1/1:0,29:29:87:1034,87,0:0,0,20,9 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 1/1:0,15:15:45:529,45,0:0,0,11,4 chr1 26324520 . T C 200.02 PASS AC=2;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 1/1:0,21:21:63:621,63,0:0,0,11,10 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 1/1:0,21:21:63:690,63,0:0,0,10,11 chr1 26348423 . C T 2917.53 PASS AC=1;AF=0.615;AN=2;DP=2468;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant13-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,34:96:99:699,0,1467:32,30,18,16 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 1/1:0,104:104:99:3212,312,0:0,0,53,51 chr1 26349109 . C CT 5918.45 PASS AC=1;AF=0.615;AN=2;DP=5323;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant13-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:109,95:204:99:2772,0,3266:54,55,48,47 chr1 26349967 . C T 647.02 PASS AC=1;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 0/1:26,44:70:99:1179,0,640:9,17,15,29 chr1 26357656 . C A 2577.79 PASS AC=1;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 0/1:102,106:208:99:2431,0,2279:52,50,52,54 chr1 26357667 . G A 3942 PASS AC=1;AF=0.64;AN=2;DP=5256;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant13-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:103,102:205:99:2234,0,2446:48,55,51,51 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 1/1:0,62:62:99:2015,185,0:0,0,32,30 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 1/1:0,62:62:99:2239,189,0:0,0,45,17 chr1 26362001 . C T 3426.18 PASS AC=1;AF=0.615;AN=2;DP=2649;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant13-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,50:91:99:1328,0,1085:25,16,31,19 chr1 26362194 . T C 1135.36 PASS AC=1;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 0/1:59,57:116:99:1371,0,1590:30,29,25,32 chr1 26364249 . C T 441.26 PASS AC=1;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 0/1:31,21:52:99:504,0,683:17,14,8,13 chr1 26364371 . T C 410.54 PASS AC=1;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 0/1:23,19:42:99:481,0,644:13,10,11,8 chr1 26365374 . T G 2206.39 PASS AC=1;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 0/1:77,69:146:99:1829,0,1963:37,40,34,35 chr1 26365549 . C T 972.83 PASS AC=1;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 0/1:28,40:68:99:1144,0,825:10,18,19,21 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 1/1:0,49:49:99:1722,147,0:0,0,37,12 chr1 26372484 . C T 551.99 PASS AC=1;AF=0.5;AN=2;DP=52;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.12;QD=10.62;ReadPosRankSum=-1.713;SOR=0.866;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:30,22:52:99:580,0,885:8,22,5,17 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 1/1:0,23:23:69:697,69,0:0,0,11,12 chr1 26377880 . G A 436.85 PASS AC=1;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 0/1:27,17:44:99:380,0,700:15,12,10,7 chr1 26378002 . C T 1344.39 PASS AC=1;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 0/1:44,29:73:99:719,0,1262:24,20,19,10 chr1 26383875 . A G 850.66 PASS AC=1;AF=0.625;AN=2;DP=1142;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,10:27:99:285,0,541:3,14,4,6 chr1 26384013 . A G 749.26 PASS AC=1;AF=0.603;AN=2;DP=797;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant11-variant12-variant13-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:302,0,322:8,3,7,2 chr1 26384907 . C T 1130.73 PASS AC=1;AF=0.5;AN=2;DP=161;FractionInformativeReads=1;MQ=60;set=variant23-variant30 GT:AD:DP:GQ:PL:SB 0/1:29,39:68:99:1159,0,906:21,8,29,10 chr1 26385003 . T C 7963.82 PASS AC=1;AF=0.645;AN=2;DP=8043;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:134,123:257:99:2861,0,3033:71,63,66,57 chr1 26385150 . G C 6623.06 PASS AC=1;AF=0.65;AN=2;DP=5833;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,104:179:99:2646,0,1754:30,45,40,64 chr1 26449335 . CAA C 3255.97 PASS AC=1;AF=0.5;AN=2;DP=2479;MQ=60;set=variant-variant2-variant3-variant8-variant11-variant14-variant15-variant19-variant23-variant25-variant28-variant30-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:85,54:139:99:1976,0,3532:41,44,26,28 chr1 26485517 . G C 346.92 PASS AC=1;AF=0.563;AN=2;DP=753;MQ=60;set=variant-variant2-variant3-variant8-variant10-variant11-variant14-variant15-variant19-variant23-variant28-variant30-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,11:43:99:186,0,822:15,17,7,4 chr1 26487940 . A G 4376.75 PASS AC=1;AF=0.559;AN=2;DP=5987;MQ=60;set=variant-variant2-variant3-variant8-variant10-variant11-variant14-variant15-variant19-variant23-variant28-variant30-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:178,164:342:99:3801,0,3969:80,98,78,86 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 0/1:55,69:124:99:1639,0,1346:26,29,37,32 chr1 26496455 . C T 2298.07 PASS AC=1;AF=0.559;AN=2;DP=3074;MQ=60;set=variant-variant2-variant3-variant8-variant10-variant11-variant14-variant15-variant19-variant23-variant28-variant30-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,54:126:99:1373,0,1896:33,39,30,24 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 0/1:34,37:71:99:901,0,892:18,16,17,20 chr1 26511700 . A G 1643.18 PASS AC=1;AF=0.672;AN=2;DP=6682;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:104,93:197:99:2186,0,2511:47,57,41,52 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 1/1:0,116:116:99:3746,347,0:0,0,68,48 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 0/1:78,76:154:99:1752,0,2040:33,45,34,42 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 0/1:10,9:19:99:345,0,666:8,2,9,0 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 0/1:11,9:20:99:345,0,666:9,2,9,0 chr1 26527783 . G A 169.9 PASS AC=1;AF=0.529;AN=2;DP=350;MQ=60;set=variant-variant2-variant3-variant8-variant14-variant15-variant19-variant22-variant23-variant28-variant30-variant31-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:278,0,170:3,4,7,2 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 0/1:15,11:26:99:448,0,582:11,4,8,3 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 0/1:15,12:27:99:448,0,582:11,4,9,3 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 0/1:67,43:110:99:901,0,1787:39,28,24,19 chr1 26528181 . CTT C,CTTTT,CTTTTT,CTTT,CT,CTTTTTTT,CTTTTTTTT 148.88 PASS AC=0,0,0,2,0,0,0;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 4/4:9:26:0,0,2,7 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 0/1:36,32:68:99:764,0,937:24,12,20,12 chr1 26529121 . G C 1150.51 PASS AC=1;AF=0.55;AN=2;DP=2885;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,38:94:99:947,0,1426:25,31,21,17 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 1/1:0,22:22:66:769,66,0:0,0,7,15 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 0/1:10,10:20:99:309,0,254:3,7,4,6 chr1 26570482 . CAAAAAAAAAAA C,CA,CAA,CAAAAAAAAAAAAA 458.96 PASS AC=1,1,0,0;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 1/2:14:80:0,0,9,5 chr1 26582091 . G A 1264.65 PASS AC=1;AF=0.567;AN=2;DP=2702;MQ=60;set=variant-variant2-variant3-variant8-variant14-variant15-variant19-variant23-variant30-variant31-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:84,96:180:99:2132,0,1957:45,39,53,43 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 0/1:20,42:62:99:1113,0,473:8,12,19,23 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 1/1:0,101:101:99:2850,302,0:0,0,49,52 chr1 26597673 . G A 464.72 PASS AC=2;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 1/1:0,35:35:99:1101,105,0:0,0,13,22 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 0/1:27,30:57:99:747,0,706:17,10,16,14 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 0/1:24,23:47:99:687,0,633:10,14,7,16 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 0/1:39,36:75:99:1374,0,1718:17,22,16,20 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 1/1:0,62:62:99:1979,186,0:0,0,26,36 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 0/1:29,21:50:99:576,0,841:16,13,9,12 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 0/1:28,17:45:99:465,0,735:14,14,7,10 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 0/1:34,33:67:99:856,0,909:13,21,15,18 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 0/1:45,55:100:99:1388,0,1053:21,24,31,24 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 0/1:42,43:85:99:1128,0,1122:20,22,22,21 chr1 26608649 . G A 2068.28 PASS AC=1;AF=0.567;AN=2;DP=2225;MQ=60;set=variant-variant2-variant3-variant8-variant14-variant15-variant19-variant23-variant30-variant31-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,77:146:99:1735,0,1735:30,39,38,39 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 0/1:51,39:90:99:1234,0,1790:26,25,23,16 chr1 26608782 . C T 695.73 PASS AC=1;AF=0.567;AN=2;DP=1449;set=variant-variant2-variant3-variant8-variant14-variant15-variant19-variant23-variant30-variant31-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,37:79:99:1267,0,1651:25,17,21,16 chr1 26608814 . A G 1616 PASS AC=2;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 1/1:2,68:70:99:2845,166,0:1,1,45,23 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 0/1:49,31:80:99:1093,0,1964:32,17,20,11 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 0/1:53,29:82:99:1042,0,2135:34,19,21,8 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 0/1:29,45:74:99:1844,0,1079:21,8,28,17 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 0/1:32,45:77:99:1832,0,1247:23,9,28,17 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 0/1:48,46:94:99:1775,0,1788:24,24,30,16 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 0/1:121,134:255:99:3299,0,2913:62,59,64,70 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 1/1:1,211:212:99:6390,626,0:1,0,99,112 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 1/1:0,140:140:99:4316,420,0:0,0,69,71 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 1/1:0,52:52:99:1642,156,0:0,0,26,26 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 0/1:42,39:81:99:928,0,1153:27,15,25,14 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 0/1:87,83:170:99:1929,0,2039:44,43,39,44 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 1/1:0,56:56:99:2133,168,0:0,0,18,38 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 0/1:18,17:35:99:414,0,479:7,11,6,11 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 0/1:89,96:185:99:2349,0,2067:42,47,48,48 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 0/1:37,26:63:99:664,0,972:16,21,12,14 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 0/1:18,19:37:99:489,0,532:12,6,12,7 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 0/1:58,58:116:99:1526,0,1422:29,29,26,32 chr1 26646611 . TA TAA,T 80.65 PASS AC=0,1;AF=0.024,0.476;AN=2;DP=1590;set=filterInvariant2-variant3-filterInvariant4-filterInvariant5-filterInvariant7-filterInvariant9-filterInvariant11-filterInvariant12-filterInvariant18-variant22-filterInvariant23-filterInvariant24-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant31-variant32-variant33-variant36-filterInvariant41 GT:DP:GQ:SB 0/2:69:88:35,21,10,3 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 0/1:64,83:147:99:3317,0,2546:33,31,37,46 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 0/1:62,83:145:99:3288,0,2528:31,31,38,45 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 0/1:39,45:84:99:1118,0,947:22,17,30,15 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 0/1:98,96:194:99:2396,0,2401:52,46,59,37 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 0/1:27,18:45:99:584,0,873:6,21,3,15 chr1 26650550 . C A 281.52 PASS AC=1;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 0/1:31,36:67:99:903,0,855:22,9,23,13 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 1/1:0,54:54:99:1776,162,0:0,0,20,34 chr1 26655208 . C T 189.7 PASS AC=1;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 0/1:15,14:29:99:341,0,377:10,5,9,5 chr1 26655462 . C T 161.9 PASS AC=1;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 0/1:17,8:25:99:183,0,455:5,12,2,6 chr1 26655507 . C A 90.15 PASS AC=1;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 0/1:9,9:18:99:293,0,267:1,8,1,8 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 1/1:0,110:110:99:3294,329,0:0,0,61,49 chr1 26662904 . C T 2362.7 PASS AC=1;AF=0.567;AN=2;DP=2174;MQ=60;set=variant-variant2-variant3-variant8-variant14-variant15-variant19-variant23-variant30-variant31-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,68:142:99:1536,0,1886:41,33,34,34 chr1 26663362 . C T 1806.38 PASS AC=1;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 0/1:75,61:136:99:1499,0,1899:40,35,33,28 chr1 26664219 . T C 333.47 PASS AC=1;AF=0.567;AN=2;DP=509;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant8-variant14-variant15-variant19-variant23-variant30-variant31-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,9:23:99:276,0,347:6,8,3,6 chr1 26664968 . C T 1004.89 PASS AC=1;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 0/1:52,42:94:99:850,0,1224:28,24,21,21 chr1 26670444 . G T 1018.28 PASS AC=1;AF=0.571;AN=2;DP=1605;MQ=60;set=variant-variant2-variant3-variant8-variant15-variant19-variant23-variant30-variant31-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,53:98:99:1366,0,1084:22,23,30,23 chr1 26670609 . C T 2715.71 PASS AC=1;AF=0.571;AN=2;DP=2888;MQ=60;set=variant-variant2-variant3-variant8-variant15-variant19-variant23-variant30-variant31-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,97:183:99:2509,0,2203:50,36,50,47 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 0/1:14,78:92:46:2273,0,46:10,4,38,40 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 0/1:14,69:83:66:2246,0,66:10,4,34,35 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 0/1:14,77:91:65:2247,0,65:10,4,37,40 chr1 26689220 . A G 114.7 PASS AC=1;AF=0.654;AN=2;DP=107;FractionInformativeReads=1;MQ=60;set=variant4-variant11-variant13-variant18-variant23-variant25-variant27-variant28-variant33-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:69:149,0,69:2,0,4,0 chr1 26689659 . G A 131.85 PASS AC=1;AF=0.559;AN=2;DP=1109;MQ=60;set=variant-variant2-variant3-variant8-variant15-variant16-variant19-variant22-variant23-variant26-variant30-variant31-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,23:41:99:599,0,511:7,11,7,16 chr1 26691174 . C A 2782.3 PASS AC=1;AF=0.559;AN=2;DP=4197;MQ=60;set=variant-variant2-variant3-variant8-variant15-variant16-variant19-variant22-variant23-variant26-variant30-variant31-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:109,118:227:99:2867,0,2608:49,60,59,59 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 0/1:43,51:94:99:1895,0,1960:23,20,24,27 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 0/1:45,50:95:99:1943,0,1968:23,22,23,27 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 0/1:50,33:83:99:741,0,1152:26,24,16,17 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 0/1:76,57:133:99:1265,0,1795:43,33,29,28 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 0/1:24,47:71:99:1151,0,696:3,21,22,25 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 0/1:9,29:38:99:764,0,209:3,6,10,19 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 0/1:23,14:37:99:318,0,469:13,10,9,5 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 1/1:0,47:47:99:1398,141,0:0,0,24,23 chr1 26737143 . G A 79.46 PASS AC=1;AF=0.621;AN=2;DP=448;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:216,0,179:4,1,7,0 chr1 26752992 . T C 1120.14 PASS AC=1;AF=0.83;AN=2;DP=3614;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:30,27:57:99:599,0,722:12,18,12,15 chr1 26753942 . T C 173.13 PASS AC=1;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 0/1:10,6:16:99:100,0,322:6,4,3,3 chr1 26758748 . G A 714.49 PASS AC=1;AF=0.83;AN=2;DP=1279;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:8,12:20:99:264,0,264:6,2,8,4 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 0/1:41:99:10,17,5,9 chr1 26797654 . C T 431.59 PASS AC=1;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 0/1:17,23:40:99:595,0,434:8,9,12,11 chr1 26801229 . C A 853.87 PASS AC=1;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 0/1:54,41:95:99:797,0,1334:22,32,18,23 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 1/1:0,38:38:99:1131,114,0:0,0,17,21 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 1/1:0,10:10:30:322,30,0:0,0,3,7 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 1/1:0,84:84:99:2519,252,0:0,0,53,31 chr1 26870730 . C G 2596.91 PASS AC=1;AF=0.6;AN=2;DP=5070;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:108,66:174:99:1404,0,2747:53,55,32,34 chr1 26872346 . C T 1168 PASS AC=1;AF=0.5;AN=2;DP=346;MQ=60;set=variant11-variant19-variant23-variant30-variant33 GT:AD:DP:GQ:PL:SB 0/1:42,37:79:99:871,0,976:25,17,18,19 chr1 26872554 . A G 1143.67 PASS AC=1;AF=0.58;AN=2;DP=3131;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,39:113:99:844,0,1970:35,39,18,21 chr1 26879376 . T C 707.82 PASS AC=1;AF=0.58;AN=2;DP=1196;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,13:34:99:370,0,508:11,10,3,10 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 1/1:0,19:19:57:686,57,0:0,0,14,5 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 1/1:0,73:73:99:2239,219,0:0,0,42,31 chr1 26880288 . C T 206.15 PASS AC=1;AF=0.583;AN=2;DP=308;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:11,8:19:99:219,0,278:4,7,2,6 chr1 26880989 . T C 307.3 PASS AC=1;AF=0.56;AN=2;DP=1118;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,19:40:99:663,0,734:19,2,14,5 chr1 26881565 . AG A 202.38 PASS AC=1;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 0/1:13,12:25:99:337,0,362:10,3,9,3 chr1 26881806 . C A 502.25 PASS AC=1;AF=0.58;AN=2;DP=2201;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,42:88:99:1224,0,1151:27,19,22,20 chr1 26887150 . A G 1039.35 PASS AC=1;AF=0.58;AN=2;DP=2276;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,34:68:99:942,0,882:23,11,25,9 chr1 26887592 . T C 1174.37 PASS AC=1;AF=0.577;AN=2;DP=3314;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,52:100:99:1170,0,1138:25,23,29,23 chr1 26898142 . A G 644.05 PASS AC=1;AF=0.577;AN=2;DP=2539;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,34:59:99:1002,0,652:10,15,14,20 chr1 26898956 . T C 1144.71 PASS AC=1;AF=0.577;AN=2;DP=1883;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,30:58:99:699,0,695:13,15,12,18 chr1 26899671 . C G 978.45 PASS AC=1;AF=0.5;AN=2;DP=503;MQ=60;set=variant11-variant19-variant22-variant23-variant27-variant30-variant33-variant34-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:28,29:57:99:724,0,702:21,7,19,10 chr1 26900428 . C CA 196.8 PASS AC=1;AF=0.5;AN=2;DP=167;MQ=60;set=variant3-filterInvariant6-variant7-variant8-variant11-variant18-variant19-variant23-variant30-variant33 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:96:124,0,96:4,1,6,1 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 1/1:0,114:114:99:3589,344,0:0,0,54,60 chr1 26901090 . C T 2008.95 PASS AC=1;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 0/1:37,33:70:99:836,0,974:20,17,18,15 chr1 27057621 . A C 1963.28 PASS AC=1;AF=0.5;AN=2;DP=663;FractionInformativeReads=1;MQ=60;set=variant7-variant20-variant23-variant29-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:54,44:98:99:1145,0,1340:26,28,24,20 chr1 27089446 . G C 905.44 PASS AC=1;AF=0.5;AN=2;DP=494;MQ=60;set=variant7-variant20-variant23-variant29-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:36,41:77:99:1000,0,871:20,16,21,20 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 0/1:4,7:11:99:201,0,141:4,0,5,2 chr1 27100243 . C T 2574.62 PASS AC=1;AF=0.5;AN=2;DP=638;FractionInformativeReads=1;MQ=60;set=variant20-variant23-variant40 GT:AD:DP:GQ:PL:SB 0/1:111,107:218:99:2633,0,2794:56,55,60,47 chr1 27107263 . T TC,TCC 802.19 PASS AC=1,0;AF=0.417,0.083;AN=2;DP=693;MQ=60;set=variant7-variant20-variant23-variant29-variant38-variant40 GT:DP:GQ:SB 0/1:98:99:21,37,16,24 chr1 27107650 . TAA TA,T,TAAAA 499.27 PASS AC=0,0,1;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 0/3:43:99:20,11,6,6 chr1 27108139 . A T 687.96 PASS AC=1;AF=0.5;AN=2;DP=291;FractionInformativeReads=1;MQ=60;set=variant7-variant20-variant23-variant29-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:28,22:50:99:562,0,771:13,15,9,13 chr1 27108245 . T C 729.45 PASS AC=1;AF=0.5;AN=2;DP=313;FractionInformativeReads=1;MQ=60;set=variant7-variant20-variant23-variant29-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:25,26:51:99:736,0,799:15,10,16,10 chr1 27114447 . G A 430.52 PASS AC=1;AF=0.5;AN=2;DP=147;FractionInformativeReads=1;MQ=60;set=variant7-variant20-variant23-variant29-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:6,13:19:99:385,0,121:5,1,8,5 chr1 27124545 . A G 3230.72 PASS AC=1;AF=0.5;AN=2;DP=1303;MQ=60;set=variant7-variant20-variant23-variant29-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:106,98:204:99:2389,0,2708:62,44,57,41 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 0/1:5,9:14:99:247,0,140:4,1,8,1 chr1 27180829 . A C 1174.44 PASS AC=2;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 1/1:0,45:45:99:1526,135,0:0,0,25,20 chr1 27181067 . C T 569.81 PASS AC=1;AF=0.5;AN=2;DP=319;FractionInformativeReads=1;MQ=60;set=variant7-variant20-variant23-variant29-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:28,29:57:99:637,0,591:13,15,11,18 chr1 27181427 . G A 336.01 PASS AC=1;AF=0.583;AN=2;DP=586;set=variant3-variant8-variant11-variant13-variant14-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant33-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,24:43:99:641,0,381:9,10,10,14 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 0/1:1,3:4:30:82,0,30:1,0,1,2 chr1 27190324 . C T 1061.64 PASS AC=1;AF=0.5;AN=2;DP=406;MQ=60;set=variant20-variant23-variant29-variant40 GT:AD:DP:GQ:PL:SB 0/1:49,45:94:99:1104,0,1220:22,27,21,24 chr1 27190821 . GGTGTGTGTGT GGTGTGTGT,GGTGTGT,G,GGTGTGTGTGTGT,GGTGTGTGTGTGTGTGTGTGTGTGT,GGTGTGTGTGTGTGT,GGTGTGTGTGTGTGTGT,GGTGTGTGTGTGTGTGTGT,GGTGT 1301.51 PASS AC=0,1,0,0,0,0,0,0,0;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 0/2:28:99:7,10,6,5 chr1 27190855 . T TGTGTGTGC 396.14 PASS AC=1;AF=0.5;AN=2;DP=38;FS=1.32;FractionInformativeReads=0.947;MQ=59.74;MQRankSum=-0.016;QD=10.42;ReadPosRankSum=0.079;SOR=1.179;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:18,18:36:99:433,0,542:9,9,7,11 chr1 27210721 . T C 3406.38 PASS AC=2;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 1/1:0,55:55:99:1755,165,0:0,0,29,26 chr1 27216669 . G A 1535.12 PASS AC=1;AF=0.5;AN=2;DP=784;FractionInformativeReads=1;MQ=60;set=variant7-variant20-variant23-variant29-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:58,56:114:99:1664,0,1586:22,36,20,36 chr1 27219768 . C T 523.81 PASS AC=1;AF=0.5;AN=2;DP=21;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.285;QD=24.94;ReadPosRankSum=0.195;SOR=1.828;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:6,15:21:99:552,0,208:6,0,15,0 chr1 27220020 . CTT CTTT,CT,C,CTTTT 203.13 PASS AC=0,1,0,0;AF=0.262,0.19,0.024,0.048;AN=2;DP=1060;set=variant2-variant4-variant7-filterInvariant8-filterInvariant9-variant11-variant12-variant14-variant16-variant17-filterInvariant18-filterInvariant21-variant23-filterInvariant24-variant25-variant26-variant29-variant31-variant33-variant36-variant37 GT:DP:GQ:SB 0/2:16:34:1,4,0,11 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 1/1:0,61:61:99:1784,182,0:0,0,33,28 chr1 27239920 . C G 804.44 PASS AC=1;AF=0.5;AN=2;DP=454;FractionInformativeReads=1;MQ=60;set=variant7-variant20-variant23-variant29-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:36,40:76:99:945,0,847:22,14,21,19 chr1 27248283 . C G 1598.94 PASS AC=1;AF=0.5;AN=2;DP=559;FractionInformativeReads=1;MQ=60;set=variant7-variant20-variant23-variant29-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:35,42:77:99:1040,0,873:22,13,23,19 chr1 27248440 . C T 1969.7 PASS AC=1;AF=0.5;AN=2;DP=843;FractionInformativeReads=1;MQ=60;set=variant7-variant20-variant23-variant29-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:66,44:110:99:1051,0,1575:30,36,19,25 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 0/1:7,3:10:99:105,0,206:3,4,0,3 chr1 27260783 . C T 462.72 PASS AC=1;AF=0.5;AN=2;DP=262;FractionInformativeReads=1;MQ=60;set=variant20-variant23-variant29-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:19,20:39:99:455,0,476:11,8,11,9 chr1 27272600 . A ATCT 1463.51 PASS AC=1;AF=0.5;AN=2;DP=953;MQ=60;set=variant7-variant20-variant23-variant29-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:54,80:134:99:3148,0,2489:22,32,35,45 chr1 27278521 . G A 1161.4 PASS AC=1;AF=0.568;AN=2;DP=3330;MQ=60;set=variant-variant3-variant5-variant8-variant11-variant13-variant14-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant33-variant36-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,60:111:99:1443,0,1153:25,26,29,31 chr1 27278573 . T C 1743.24 PASS AC=1;AF=0.5;AN=2;DP=653;MQ=60;set=variant7-variant20-variant23-variant29-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:53,37:90:99:891,0,1508:25,28,16,21 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 1/1:0,82:82:99:2555,246,0:0,0,41,41 chr1 27320730 . G T 143.03 PASS AC=1;AF=0.5;AN=2;DP=166;FractionInformativeReads=1;MQ=60;set=variant11-variant18-variant19-variant23-variant33-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,17:30:99:424,0,264:6,7,6,11 chr1 27320814 . C G 253.14 PASS AC=1;AF=0.5;AN=2;DP=70;FS=0;FractionInformativeReads=1;MQ=60;set=variant7-variant20-variant23-variant29-variant40 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:201,0,106:3,3,5,3 chr1 27331765 . G T 1031.93 PASS AC=1;AF=0.5;AN=2;DP=719;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant20-variant23-variant29-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:42,60:102:99:1535,0,1029:21,21,31,29 chr1 27332465 . G A 2596.33 PASS AC=1;AF=0.5;AN=2;DP=469;FractionInformativeReads=1;MQ=60;set=variant20-variant23-variant40 GT:AD:DP:GQ:PL:SB 0/1:82,68:150:99:2525,0,4212:42,40,40,28 chr1 27332466 . T C 2424.95 PASS AC=1;AF=0.5;AN=2;DP=1222;MQ=60;set=variant4-variant7-variant20-variant23-variant29-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:83,67:150:99:2525,0,4212:42,41,40,27 chr1 27339105 . C T 1040.44 PASS AC=1;AF=0.5;AN=2;DP=374;MQ=60;set=variant4-variant7-variant20-variant23-variant29-variant40 GT:AD:DP:GQ:PL:SB 0/1:28,22:50:99:533,0,759:15,13,10,12 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 0/1:28,30:58:99:841,0,674:17,11,20,10 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 1/1:0,134:134:99:4178,402,0:0,0,68,66 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 1/1:0,122:122:99:3894,366,0:0,0,61,61 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 0/1:33,41:74:99:1159,0,760:18,15,12,29 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 0/1:23,25:48:99:611,0,516:11,12,16,9 chr1 27480227 . G A 40.73 PASS AC=2;AF=0.786;AN=2;DP=78;FS=0;FractionInformativeReads=1;MQ=60;set=variant4-variant8-variant9-variant12-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant28-variant33-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:86,6,0:0,0,2,0 chr1 27480293 . G C 115.39 PASS AC=1;AF=0.556;AN=2;DP=225;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant32-variant33-variant34-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:4,15:19:99:398,0,123:4,0,10,5 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 0/1:44,39:83:99:920,0,1182:22,22,20,19 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 1/1:0,24:24:72:671,72,0:0,0,13,11 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 1/1:0,109:109:99:3306,323,0:0,0,45,64 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 1/1:0,67:67:99:2118,200,0:0,0,25,42 chr1 27660340 . T C 351.64 PASS AC=1;AF=0.633;AN=2;DP=629;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant34-variant36-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:231,0,238:6,0,6,0 chr1 27660568 . G A 2104.43 PASS AC=1;AF=0.629;AN=2;DP=7183;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant36-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:109,104:213:99:2601,0,3041:69,40,58,46 chr1 27661037 . T C 435.02 PASS AC=1;AF=0.607;AN=2;DP=1361;MQ=60;set=variant-variant4-variant6-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:354,0,391:7,6,6,7 chr1 27661755 . T TGTA 85.69 PASS AC=1;AF=0.629;AN=2;DP=700;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant36-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,7:19:99:258,0,596:8,4,6,1 chr1 27662235 . G T 324.49 PASS AC=1;AF=0.629;AN=2;DP=1229;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant36-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,28:43:99:710,0,377:8,7,13,15 chr1 27662666 . A G 857.56 PASS AC=1;AF=0.607;AN=2;DP=3207;MQ=60;set=variant-variant4-variant6-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:54,50:104:99:1183,0,1390:21,33,27,23 chr1 27676925 . G A 2031.29 PASS AC=1;AF=0.62;AN=2;DP=5131;MQ=60;set=variant-variant6-variant8-variant9-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:87,104:191:99:2810,0,2344:33,54,42,62 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 0/1:31,23:54:99:585,0,831:22,9,16,7 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 0/1:96,101:197:99:2341,0,2329:53,43,55,46 chr1 27679954 . G A 1032.47 PASS AC=1;AF=0.62;AN=2;DP=2867;MQ=60;set=variant-variant6-variant8-variant9-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:47,48:95:99:1202,0,1364:15,32,16,32 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 0/1:41,43:84:99:1014,0,941:22,19,23,20 chr1 27681534 . A G 97.67 PASS AC=2;AF=0.76;AN=2;DP=170;FS=0;FractionInformativeReads=1;set=variant-variant2-variant4-variant6-variant8-variant10-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant34-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:230,21,0:0,0,5,2 chr1 27682126 . T C 628.36 PASS AC=1;AF=0.571;AN=2;DP=630;MQ=60;set=variant-variant6-variant8-variant16-variant17-variant18-variant20-variant21-variant23-variant28-variant31-variant34-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:23,25:48:99:681,0,642:15,8,16,9 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 0/1:17,17:34:99:457,0,514:5,12,5,12 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 1/1:0,96:96:99:2916,288,0:0,0,42,54 chr1 27687366 . C G 1453.24 PASS AC=1;AF=0.6;AN=2;DP=3440;MQ=60;set=variant-variant2-variant6-variant8-variant9-variant12-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:71,73:144:99:1699,0,1739:28,43,30,43 chr1 27688551 . T A 1511.13 PASS AC=1;AF=0.5;AN=2;DP=98;FS=3.835;FractionInformativeReads=1;MQ=60;MQRankSum=-0.706;QD=15.42;ReadPosRankSum=1.123;SOR=0.862;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:41,57:98:99:1539,0,846:19,22,32,25 chr1 27688633 . G A 758.98 PASS AC=1;AF=0.604;AN=2;DP=3124;MQ=60;set=variant-variant6-variant8-variant9-variant12-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:44,76:120:99:1873,0,1140:25,19,41,35 chr1 27692651 . C A 232.64 PASS AC=1;AF=0.5;AN=2;DP=17;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.241;QD=13.68;ReadPosRankSum=-0.914;SOR=0.859;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:8,9:17:99:261,0,245:5,3,6,3 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 1/1:0,73:73:99:2696,219,0:0,0,12,61 chr1 27720178 . T C 430.48 PASS AC=1;AF=0.646;AN=2;DP=1098;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant7-variant8-variant9-variant10-variant11-variant14-variant19-variant20-variant21-variant22-variant23-variant25-variant28-variant30-variant34-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,18:41:99:470,0,555:14,9,12,6 chr1 27731529 . C T 1159.44 PASS AC=1;AF=0.5;AN=2;DP=83;FS=1.906;FractionInformativeReads=1;MQ=60;MQRankSum=0.647;QD=13.97;ReadPosRankSum=1.019;SOR=0.466;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:33,50:83:99:1188,0,822:11,22,20,30 chr1 27731651 . C T 394.97 PASS AC=1;AF=0.533;AN=2;DP=828;MQ=60;set=variant-variant4-variant7-variant8-variant11-variant14-variant20-variant21-variant22-variant23-variant25-variant28-variant30-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:17,23:40:99:610,0,421:8,9,9,14 chr1 27732103 . CTTT C,CT,CTT 108.24 PASS AC=0,1,0;AF=0.143,0.286,0.214;AN=2;DP=81;set=variant5-variant14-variant23-variant26-variant28-variant38-variant40 GT:DP:GQ:SB 0/2:8:46:1,2,1,4 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 0/2:153:99:27,42,28,56 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 1/1:0,262:262:99:7583,784,0:0,0,134,128 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 1/1:0,135:135:99:4027,402,0:0,0,55,80 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 1/1:0,39:39:99:1438,117,0:0,0,10,29 chr1 27949773 . G A 246.85 PASS AC=1;AF=0.5;AN=2;DP=36;FractionInformativeReads=1;MQ=60;set=variant5-variant23-variant38 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:138,0,159:0,4,0,4 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 0/2:10:76:5,0,3,2 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 1/1:3,66:69:99:1946,175,0:3,0,26,40 chr1 28086955 . C A 2117.16 PASS AC=2;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 1/1:0,52:52:99:1709,156,0:0,0,28,24 chr1 28087457 . GTTT GTT,GT,G,GTTTT 35.19 PASS AC=0,0,1,0;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 0/3:5:7:1,0,3,1 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 1/1:0,206:206:99:6156,619,0:0,0,119,87 chr1 28206250 . T C 2463.02 PASS AC=1;AF=0.5;AN=2;DP=991;FractionInformativeReads=1;MQ=60;set=variant23-variant30-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:149,104:253:99:2491,0,4057:60,89,42,62 chr1 28206588 . T C 1105.36 PASS AC=2;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 1/1:0,90:90:99:3007,270,0:0,0,28,62 chr1 28209305 . A G 682.54 PASS AC=2;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 1/1:0,71:71:99:2260,213,0:0,0,37,34 chr1 28209362 . T C 837.94 PASS AC=2;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 1/1:0,75:75:99:3351,226,0:0,0,40,35 chr1 28209366 . A G 837.94 PASS AC=2;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 1/1:0,73:73:99:3315,223,0:0,0,40,33 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 0/1:19,9:28:99:318,0,725:18,1,9,0 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 0/1:27,19:46:99:579,0,723:17,10,14,5 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 0/1:23,30:53:99:870,0,743:13,10,16,14 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 0/1:47,53:100:99:1699,0,1452:26,21,32,21 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 0/1:62,41:103:99:1018,0,1520:26,36,15,26 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 0/1:30,31:61:99:764,0,724:11,19,10,21 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 0/1:85,89:174:99:2274,0,2081:51,34,56,33 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 0/1:37,28:65:99:673,0,828:18,19,18,10 chr1 28223981 . TAA TA,T 163.71 PASS AC=0,1;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 0/2:9:99:3,2,2,2 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 0/1:11,13:24:99:296,0,249:5,6,5,8 chr1 28261593 . T C 1874.84 PASS AC=1;AF=0.656;AN=2;DP=2969;MQ=60;set=variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,46:101:99:1785,0,2403:27,28,25,21 chr1 28261600 . A C 1901.59 PASS AC=1;AF=0.621;AN=2;DP=2744;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,51:108:99:1869,0,2414:28,29,27,24 chr1 28261658 . T TG 1368.62 PASS AC=1;AF=0.672;AN=2;DP=3094;MQ=60;set=variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,56:100:99:1785,0,1342:23,21,29,27 chr1 28261902 . C A 229.52 PASS AC=1;AF=0.656;AN=2;DP=615;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:183,0,243:3,5,0,5 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 0/1:17,16:33:99:398,0,498:13,4,12,4 chr1 28268685 . T C 1371.17 PASS AC=1;AF=0.5;AN=2;DP=94;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.51;QD=14.59;ReadPosRankSum=1.373;SOR=0.742;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:40,54:94:99:1399,0,934:21,19,29,25 chr1 28268706 . G A 950.48 PASS AC=1;AF=0.636;AN=2;DP=2909;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,39:99:99:989,0,1404:30,30,19,20 chr1 28268833 . C CG 604.28 PASS AC=1;AF=0.636;AN=2;DP=1708;MQ=60;set=variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,26:52:99:1013,0,1360:8,18,11,15 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 0/1:25,26:51:99:1013,0,1360:8,17,11,15 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 0/1:74,59:133:99:1284,0,1650:42,32,31,28 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 1/1:0,99:99:99:3038,297,0:0,0,47,52 chr1 28285534 . T C 4698.08 PASS AC=2;AF=0.955;AN=2;DP=8355;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,184:184:99:5779,551,0:0,0,113,71 chr1 28285632 . A T 8723.34 PASS AC=2;AF=0.955;AN=2;DP=14084;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,291:292:99:8531,865,0:1,0,135,156 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 1/1:0,50:50:99:1637,150,0:0,0,16,34 chr1 28298116 . C A 104.62 PASS AC=1;AF=0.5;AN=2;DP=14;FS=0;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:1,6:7:20:99,0,20:1,0,3,3 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 0/1:31,16:47:99:336,0,760:15,16,6,10 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 0/1:16,12:28:99:305,0,468:4,12,2,10 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 0/1:55,75:130:99:1911,0,1304:30,25,39,36 chr1 28520161 . C T 177.99 PASS AC=2;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 1/1:0,15:15:45:509,45,0:0,0,11,4 chr1 28527011 . A G 830.33 PASS AC=2;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 1/1:0,64:64:99:1728,191,0:0,0,33,31 chr1 28555426 . G A 160.39 PASS AC=2;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 1/1:0,11:11:33:393,33,0:0,0,9,2 chr1 28555579 . C A 391.27 PASS AC=2;AF=0.643;AN=2;DP=681;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant7-variant10-variant13-variant20-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1098,114,0:0,0,15,23 chr1 28559574 . C G 565.05 PASS AC=2;AF=0.658;AN=2;DP=1772;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant7-variant8-variant10-variant13-variant20-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:1850,189,0:0,0,27,36 chr1 28559694 . A G 65.21 PASS AC=2;AF=0.65;AN=2;DP=380;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant7-variant8-variant10-variant13-variant20-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:324,27,0:0,0,2,7 chr1 28562540 . C A 1075.25 PASS AC=2;AF=0.65;AN=2;DP=2426;MQ=60;set=variant-variant5-variant7-variant8-variant10-variant13-variant20-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:3972,377,0:0,0,77,49 chr1 28562676 . A G 3333.86 PASS AC=2;AF=0.65;AN=2;DP=5013;MQ=60;set=variant-variant5-variant7-variant8-variant10-variant13-variant20-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,250:250:99:8085,750,0:0,0,139,111 chr1 28563084 . C T 1042.41 PASS AC=2;AF=0.643;AN=2;DP=1459;MQ=60;set=variant-variant5-variant7-variant10-variant13-variant20-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,125:125:99:3781,372,0:0,0,63,62 chr1 28564252 . A G 978.19 PASS AC=2;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 1/1:0,65:65:99:2084,195,0:0,0,40,25 chr1 28564279 . A G 1179.56 PASS AC=2;AF=0.65;AN=2;DP=1679;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant7-variant8-variant10-variant13-variant20-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2327,239,0:0,0,45,35 chr1 28573293 . G GA 178.93 PASS AC=2;AF=0.65;AN=2;DP=1129;MQ=60;set=variant-variant5-variant7-variant8-variant10-variant13-variant20-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1093,132,0:0,0,21,23 chr1 28598020 . T C 362.45 PASS AC=2;AF=0.611;AN=2;DP=490;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant20-variant23-variant25-variant26-variant27-variant28-variant29-variant32-variant34-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:438,33,0:0,0,10,1 chr1 28824507 . CA C,CAA,CAAA 36.62 PASS AC=1,0,0;AF=0.407,0.056,0.037;AN=2;DP=971;set=filterInvariant-variant2-filterInvariant3-filterInvariant4-variant6-variant7-variant9-filterInvariant10-filterInvariant12-variant15-filterInvariant17-variant21-variant22-variant23-variant25-variant26-variant29-filterInvariant31-variant33-filterInvariant34-filterInvariant36-filterInvariant37-variant38-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:31:99:16,5,7,3 chr1 28856738 . A C 126.54 PASS AC=1;AF=0.5;AN=2;DP=9;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.666;QD=14.06;ReadPosRankSum=-0.762;SOR=0.941;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:2,7:9:22:155,0,22:1,1,4,3 chr1 28905888 . CAAA C,CAA,CA,CAAAA,CAAAAA 77.75 PASS AC=0,0,1,0,0;AF=0.021,0.229,0.188,0.042,0.042;AN=2;DP=279;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant23-variant26-variant27-variant28-variant31-variant33-variant36-variant38-variant40-variant43-variant44 GT:DP:GQ:SB 0/3:6:43:2,0,3,1 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 1/1:0,111:111:99:3533,332,0:0,0,58,53 chr1 29016716 . T G 36.84 PASS AC=1;AF=0.5;AN=2;DP=498;set=filterInvariant2-filterInvariant3-filterInvariant18-variant20-variant23-variant27-filterInvariant29-filterInvariant33-filterInvariant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,11:24:99:139,0,179:4,9,3,8 chr1 29018316 . TTTTATTTATTTATTTA TTTTATTTATTTA,T 124.34 PASS AC=2,0;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 1/1:3:10:0,0,1,2 chr1 29019724 . G A 108.64 PASS AC=2;AF=0.571;AN=2;DP=550;set=variant2-variant3-variant4-variant7-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:763,60,0:0,0,4,16 chr1 29037240 . C CT 131.39 PASS AC=2;AF=0.65;AN=2;DP=115;MQ=60;set=variant7-variant10-variant15-variant19-variant21-variant23-variant24-variant26-variant28-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:132,15,0:0,0,0,5 chr1 29042115 . CAAAA CAA,CAAAAA,CAAA,C 37.42 PASS AC=0,0,2,0;AF=0.071,0.071,0.429,0.071;AN=2;DP=83;MQ=60;set=variant2-variant8-variant16-variant18-variant21-variant23-variant38 GT:DP:GQ:SB 3/3:6:17:0,0,3,3 chr1 29043697 . G GT 39.7 PASS AC=2;AF=0.537;AN=2;DP=715;set=filterInvariant3-variant4-filterInvariant5-variant7-filterInvariant9-filterInvariant11-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant39-variant40-filterInvariant41 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:11:77,11,0:0,0,0,4 chr1 29045123 . A G 808.25 PASS AC=2;AF=0.574;AN=2;DP=1998;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2198,201,0:0,0,34,33 chr1 29063236 . G A 680.25 PASS AC=2;AF=0.58;AN=2;DP=1054;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:584,48,0:0,0,12,4 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 1/1:0,145:145:99:4407,434,0:0,0,74,71 chr1 29070609 . A AG 94.26 PASS AC=2;AF=0.591;AN=2;DP=280;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant17-variant18-variant19-variant20-variant21-variant23-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:361,27,0:0,0,4,5 chr1 29138975 . G T 1492.59 PASS AC=2;AF=0.875;AN=2;DP=5370;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:4178,396,0:0,0,89,44 chr1 29185313 . C T 1049.23 PASS AC=1;AF=0.5;AN=2;DP=317;FractionInformativeReads=1;MQ=60;set=variant21-variant23-variant24-variant31-variant36-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,23:46:99:570,0,622:14,9,14,9 chr1 29189597 . C T 3214.03 PASS AC=2;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 1/1:0,351:351:99:9991,1046,0:0,0,175,176 chr1 29190138 . G A 538.22 PASS AC=2;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 1/1:0,38:38:99:1112,114,0:0,0,17,21 chr1 29213316 . A C,T 150.89 PASS AC=2,0;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 1/1:17:51:0,0,10,7 chr1 29220178 . G A 561.61 PASS AC=2;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 1/1:0,44:44:99:1445,132,0:0,0,31,13 chr1 29220270 . A C 1485.99 PASS AC=2;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 1/1:0,106:106:99:3105,317,0:0,0,57,49 chr1 29320169 . CTT C,CTTT,CTTTT 39.84 PASS AC=0,0,1;AF=0.063,0.25,0.188;AN=2;DP=141;FS=0;set=filterInvariant7-variant19-variant21-variant22-variant23-variant27-variant31-variant38 GT:DP:GQ:SB 0/3:5:18:0,1,1,3 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 0/1:9,7:16:99:138,0,179:6,3,6,1 chr1 29345009 . C CTT 1348.62 PASS AC=2;AF=0.875;AN=2;DP=1360;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1240,84,0:0,0,7,21 chr1 29345027 . T G 349.49 PASS AC=2;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 1/1:0,16:16:48:555,48,0:0,0,4,12 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 0/1:9,7:16:99:186,0,314:2,7,2,5 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 0/1:29,33:62:99:1009,0,759:10,19,8,25 chr1 29439016 . T A 1993.81 PASS AC=1;AF=0.621;AN=2;DP=4819;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant10-variant13-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant36-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:79,77:156:99:1863,0,1853:32,47,35,42 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 0/1:39,36:75:99:980,0,1003:15,24,12,24 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 0/1:34,25:59:99:678,0,928:14,20,12,13 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 0/1:26,20:46:99:492,0,664:11,15,8,12 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 0/1:31,30:61:99:733,0,730:16,15,16,14 chr1 29446105 . A AC 115.82 PASS AC=1;AF=0.5;AN=2;DP=22;FS=0;MQ=60;set=variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:1,6:7:9:153,0,9:1,0,2,4 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 0/1:26,37:63:99:936,0,591:17,9,22,15 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 0/1:31,31:62:99:825,0,899:12,19,16,15 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 0/1:21:99:4,6,5,6 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 0/1:17,11:28:99:281,0,548:9,8,2,9 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 0/1:21,11:32:99:259,0,563:11,10,8,3 chr1 29475648 . T G 3770.6 PASS AC=2;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 1/1:0,113:113:99:3416,337,0:0,0,48,65 chr1 29519778 . T G 2197.51 PASS AC=2;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 1/1:0,73:73:99:2128,219,0:0,0,39,34 chr1 29522384 . G A 766.86 PASS AC=1;AF=0.5;AN=2;DP=302;FractionInformativeReads=1;MQ=60;set=variant21-variant23-variant24-variant34-variant36-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:17,24:41:99:625,0,503:13,4,17,7 chr1 29529699 . T C 2043.81 PASS AC=2;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 1/1:0,120:120:99:3732,360,0:0,0,65,55 chr1 29529943 . C T 88.71 PASS AC=1;AF=0.6;AN=2;DP=279;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant10-variant13-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:168,0,152:0,4,0,5 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 1/1:0,67:67:99:2302,201,0:0,0,45,22 chr1 29542637 . A G 3414.79 PASS AC=2;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 1/1:0,167:167:99:5401,501,0:0,0,69,98 chr1 29542926 . A T 372.99 PASS AC=2;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 1/1:0,14:14:42:577,42,0:0,0,12,2 chr1 29543404 . T C 438.1 PASS AC=1;AF=0.5;AN=2;DP=121;FractionInformativeReads=1;MQ=60;set=variant21-variant23-variant24-variant34-variant36-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:231,0,211:1,5,0,6 chr1 29557224 . C T 4152.55 PASS AC=2;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 1/1:0,166:166:99:4696,493,0:0,0,92,74 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 1/1:0,20:20:60:598,60,0:0,0,11,9 chr1 29563059 . C T 222.06 PASS AC=1;AF=0.596;AN=2;DP=814;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant10-variant13-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,14:25:99:389,0,266:6,5,8,6 chr1 29563411 . G A 2952.64 PASS AC=1;AF=0.5;AN=2;DP=1101;FractionInformativeReads=1;MQ=60;set=variant21-variant23-variant24-variant34-variant36-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:73,65:138:99:1612,0,2182:20,53,21,44 chr1 29581937 . G A 5576.93 PASS AC=1;AF=0.625;AN=2;DP=528;MQ=60;set=variant21-variant23-variant34-variant36 GT:AD:DP:GQ:PL:SB 0/1:85,37:122:99:737,0,2218:37,48,14,23 chr1 29602320 . G A 242.11 PASS AC=1;AF=0.571;AN=2;DP=186;FractionInformativeReads=1;MQ=60;set=variant5-variant21-variant23-variant29-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,12:29:99:373,0,459:5,12,2,10 chr1 29609502 . TG T 540.58 PASS AC=1;AF=0.579;AN=2;DP=871;MQ=60;set=variant5-variant11-variant13-variant14-variant15-variant17-variant21-variant23-variant24-variant27-variant29-variant31-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,12:30:99:292,0,482:6,12,0,12 chr1 29609536 . G A 248.04 PASS AC=1;AF=0.536;AN=2;DP=395;set=variant5-variant11-variant13-variant21-variant23-variant24-variant29-variant31-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:322,0,360:5,8,0,9 chr1 29611123 . C T 262.1 PASS AC=1;AF=0.571;AN=2;DP=401;FractionInformativeReads=1;MQ=60;set=variant5-variant11-variant13-variant21-variant23-variant24-variant29-variant31-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,9:31:99:224,0,681:17,5,7,2 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 0/1:45,43:88:99:968,0,1054:19,26,17,26 chr1 29631782 . C T 444.98 PASS AC=1;AF=0.531;AN=2;DP=597;MQ=60;set=variant4-variant9-variant15-variant17-variant20-variant21-variant23-variant27-variant28-variant30-variant31-variant34-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,19:35:99:614,0,413:11,5,15,4 chr1 29631909 . A G 6654.72 PASS AC=1;AF=0.614;AN=2;DP=4162;MQ=60;set=variant3-variant4-variant5-variant9-variant10-variant11-variant15-variant20-variant21-variant22-variant23-variant28-variant29-variant30-variant31-variant32-variant34-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,73:155:99:1874,0,2029:46,36,41,32 chr1 29633486 . G A 115.36 PASS AC=1;AF=0.583;AN=2;DP=126;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant21-variant23-variant24-variant42 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:224,0,306:6,4,6,2 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 0/1:10,10:20:99:415,0,372:7,3,6,4 chr1 29636976 . G A 287.86 PASS AC=1;AF=0.667;AN=2;DP=21;FS=0;FractionInformativeReads=1;MQ=60;set=variant21-variant23-variant24 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:33:116,0,33:0,1,3,0 chr1 29637032 . A G 132.17 PASS AC=2;AF=0.667;AN=2;DP=69;FractionInformativeReads=1;set=variant2-variant7-variant21-variant23-variant24-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:220,21,0:0,0,5,2 chr1 29637136 . T C 474.13 PASS AC=2;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 1/1:0,34:34:99:1285,101,0:0,0,29,5 chr1 29638988 . G T 873.49 PASS AC=1;AF=0.583;AN=2;DP=398;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant21-variant23-variant24-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,32:68:99:852,0,883:22,14,22,10 chr1 29641846 . C T 689.16 PASS AC=1;AF=0.583;AN=2;DP=331;MQ=60;set=variant2-variant7-variant21-variant23-variant24-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,29:49:99:1136,0,1270:16,4,23,6 chr1 29641865 . G A 981.22 PASS AC=1;AF=0.583;AN=2;DP=421;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant21-variant23-variant24-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,35:60:99:1299,0,1415:19,6,26,9 chr1 29642681 . G A 369.53 PASS AC=1;AF=0.583;AN=2;DP=274;MQ=60;set=variant2-variant7-variant21-variant23-variant24-variant42 GT:AD:DP:GQ:PL:SB 0/1:19,35:54:99:984,0,550:4,15,11,24 chr1 29644328 . C T 1145.99 PASS AC=1;AF=0.583;AN=2;DP=797;MQ=60;set=variant2-variant7-variant21-variant23-variant24-variant42 GT:AD:DP:GQ:PL:SB 0/1:61,58:119:99:1448,0,1603:35,26,36,22 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 0/1:23,26:49:99:752,0,576:15,8,17,9 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 0/1:38,49:87:99:1167,0,775:18,20,25,24 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 0/1:3,9:12:59:239,0,59:2,1,6,3 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 0/1:3,10:13:99:400,0,159:1,2,3,7 chr1 29842261 . A T 637.02 PASS AC=2;AF=0.989;AN=2;DP=1318;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:500,39,0:0,0,9,4 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 0/1:8,12:20:99:291,0,262:1,7,3,9 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 0/1:2,3:5:99:111,0,150:1,1,0,3 chr1 29863405 . G A 295.68 PASS AC=1;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 0/1:2,5:7:71:123,0,71:0,2,2,3 chr1 31186224 . GCACA GCA,G 1105.4 PASS AC=1,0;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 0/1:66:69:29,29,3,5 chr1 31196255 . G A 500.96 PASS AC=1;AF=0.648;AN=2;DP=983;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant15-variant16-variant17-variant20-variant21-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,16:32:99:393,0,468:9,7,9,7 chr1 31207781 . C T 267.74 PASS AC=2;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 1/1:0,20:20:60:672,60,0:0,0,14,6 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 1/1:0,101:101:99:3030,302,0:0,0,58,43 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 1/1:0,8:8:24:313,24,0:0,0,7,1 chr1 31342590 . G T 566.64 PASS AC=1;AF=0.567;AN=2;DP=686;MQ=60;set=variant3-variant4-variant7-variant14-variant15-variant16-variant19-variant20-variant23-variant26-variant27-variant28-variant32-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:28,15:43:99:338,0,611:14,14,10,5 chr1 31344250 . A G 949.56 PASS AC=1;AF=0.563;AN=2;DP=1325;MQ=60;set=variant3-variant4-variant7-variant14-variant15-variant16-variant19-variant20-variant23-variant26-variant27-variant28-variant32-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,33:69:99:792,0,930:17,19,16,17 chr1 31345747 . C T 1089.3 PASS AC=1;AF=0.533;AN=2;DP=1054;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant14-variant15-variant16-variant19-variant20-variant23-variant26-variant27-variant28-variant32-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:44,40:84:99:977,0,1207:24,20,23,17 chr1 31347399 . C T 1126.55 PASS AC=1;AF=0.563;AN=2;DP=1549;MQ=60;set=variant3-variant4-variant7-variant14-variant15-variant16-variant19-variant20-variant23-variant26-variant27-variant28-variant32-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,28:67:99:703,0,995:18,21,12,16 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 0/1:23,12:35:99:201,0,612:12,11,6,6 chr1 31405486 . TTATATA T 257.64 PASS AC=1;AF=0.625;AN=2;DP=31;FS=0;MQ=60;set=variant3-variant12-variant19-variant23 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:73:73,0,124:3,1,2,0 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 0/1:22:99:6,2,8,6 chr1 31405511 . TA T 204.27 PASS AC=1;AF=0.625;AN=2;DP=177;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant8-variant9-variant13-variant15-variant20-variant22-variant23-variant32-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,14:22:99:336,0,229:6,2,8,6 chr1 31405643 . G A 2480.15 PASS AC=1;AF=0.5;AN=2;DP=732;FractionInformativeReads=1;MQ=60;set=variant3-variant12-variant18-variant19-variant23 GT:AD:DP:GQ:PL:SB 0/1:66,50:116:99:1183,0,1675:40,26,31,19 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 0/1:19,23:42:99:874,0,761:6,13,10,13 chr1 31413972 . T C 801.18 PASS AC=1;AF=0.5;AN=2;DP=338;MQ=60;set=variant3-variant12-variant18-variant19-variant23 GT:AD:DP:GQ:PL:SB 0/1:31,41:72:99:934,0,725:19,12,24,17 chr1 31415040 . A T 475.42 PASS AC=2;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 1/1:0,9:9:27:337,27,0:0,0,0,9 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 0/1:13,14:27:99:393,0,388:10,3,11,3 chr1 31426815 . A G 454.72 PASS AC=2;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 1/1:0,36:36:99:1231,108,0:0,0,11,25 chr1 31439280 . G C 87.2 PASS AC=1;AF=0.5;AN=2;DP=31;FS=0;FractionInformativeReads=1;MQ=60;set=variant12-variant18-variant19-variant23 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:70:70,0,142:1,4,1,2 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 1/1:0,10:10:30:341,30,0:0,0,8,2 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 1/1:0,21:21:62:668,62,0:0,0,14,7 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 0/1:12,13:25:99:490,0,413:4,8,6,7 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 0/1:10,13:23:99:490,0,413:3,7,6,7 chr1 31478638 . AAGAGAGAGAG AAGAG,A,AAG,AAGAGAGAGAGAGAG 806.46 PASS AC=2,0,0,0;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 1/1:82:99:0,0,53,29 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 0/1:33,21:54:99:490,0,826:13,20,9,12 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 0/1:11,17:28:99:493,0,292:3,8,5,12 chr1 31653733 . T C 1357.28 PASS AC=2;AF=0.849;AN=2;DP=1895;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1137,105,0:0,0,19,16 chr1 31653988 . A G 772.88 PASS AC=2;AF=0.826;AN=2;DP=1889;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1133,96,0:0,0,18,14 chr1 31654305 . C G 1375.67 PASS AC=2;AF=0.826;AN=2;DP=2886;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1810,183,0:0,0,35,26 chr1 31654940 . C T 921.11 PASS AC=2;AF=0.833;AN=2;DP=1401;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:80:934,80,0:0,0,8,19 chr1 31712314 . C T 1529.94 PASS AC=1;AF=0.533;AN=2;DP=1369;MQ=60;set=variant3-variant10-variant13-variant18-variant19-variant21-variant22-variant23-variant27-variant28-variant30-variant32-variant34-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,39:64:99:936,0,573:11,14,18,21 chr1 31732390 . G A 6090.03 PASS AC=2;AF=0.989;AN=2;DP=7980;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:3,143:146:99:3516,348,0:2,1,90,53 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 0/2:62:99:11,22,5,24 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 0/1:8,6:14:99:182,0,300:8,0,4,2 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 0/1:27,18:45:99:412,0,712:18,9,11,7 chr1 31733926 . A G 1475.35 PASS AC=1;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 0/1:53,59:112:99:1270,0,1175:26,27,28,31 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 0/1:9,7:16:99:133,0,161:0,9,1,6 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 0/1:29,17:46:99:377,0,659:16,13,11,6 chr1 31740706 . A G 499.74 PASS AC=1;AF=0.533;AN=2;DP=1000;MQ=60;set=variant3-variant10-variant13-variant18-variant19-variant21-variant22-variant23-variant27-variant28-variant30-variant32-variant34-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,34:59:99:844,0,529:13,12,16,18 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 0/1:16,21:37:99:469,0,411:11,5,12,9 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 0/1:11,20:31:99:636,0,304:2,9,3,17 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 1/1:0,46:46:99:1537,138,0:0,0,34,12 chr1 31762374 . C T 2043.82 PASS AC=1;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 0/1:27,27:54:99:563,0,618:14,13,14,13 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 0/1:9,8:17:99:259,0,277:7,2,7,1 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 0/1:15,10:25:99:459,0,664:12,3,9,1 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 1/1:0,42:42:99:1390,126,0:0,0,11,31 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 0/1:21,33:54:99:818,0,472:13,8,18,15 chr1 31769747 . T C 1202.47 PASS AC=1;AF=0.5;AN=2;DP=179;FractionInformativeReads=1;MQ=60;set=variant3-variant23 GT:AD:DP:GQ:PL:SB 0/1:41,40:81:99:1121,0,1121:22,19,24,16 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 0/1:14,13:27:99:382,0,416:4,10,4,9 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 0/1:25,42:67:99:1310,0,645:15,10,27,15 chr1 31838551 . TAA TA,TAAA,T 121.43 PASS AC=1,0,0;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 0/1:31:99:11,3,12,5 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 0/1:19,14:33:99:489,0,547:4,15,0,14 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 1/1:0,25:25:75:902,75,0:0,0,20,5 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 0/1:51,23:74:99:845,0,3869:25,26,11,12 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 0/1:31,29:60:99:702,0,751:12,19,12,17 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 0/1:3,8:11:62:202,0,62:2,1,3,5 chr1 31886036 . G T 43.71 PASS AC=1;AF=0.5;AN=2;DP=5;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.231;QD=8.74;ReadPosRankSum=-0.358;SOR=0.061;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:72:72,0,294:3,0,1,1 chr1 31886045 . C G 40.7 PASS AC=1;AF=0.5;AN=2;DP=7;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.922;QD=5.81;ReadPosRankSum=-1.495;SOR=0.027;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:5,2:7:69:69,0,337:5,0,1,1 chr1 31886163 . C T 1399.8 PASS AC=1;AF=0.556;AN=2;DP=1883;FractionInformativeReads=1;MQ=60;set=variant3-variant10-variant12-variant13-variant18-variant19-variant21-variant22-variant23-variant24-variant27-variant28-variant30-variant32-variant34-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:47,57:104:99:1278,0,1017:27,20,33,24 chr1 31886750 . G GTCCC 2015.99 PASS AC=1;AF=0.567;AN=2;DP=1307;MQ=60;set=variant3-variant10-variant12-variant13-variant19-variant22-variant23-variant24-variant27-variant28-variant30-variant32-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,33:75:99:1207,0,1643:27,15,17,16 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 0/1:70,46:116:99:1034,0,1692:41,29,24,22 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 1/1:0,55:55:99:1926,165,0:0,0,43,12 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 1/1:0,35:35:99:1033,104,0:0,0,12,23 chr1 31899704 . C T 281.14 PASS AC=2;AF=0.864;AN=2;DP=1335;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:868,78,0:0,0,7,19 chr1 31902418 . A G 3880.27 PASS AC=2;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 1/1:0,83:83:99:2568,248,0:0,0,31,52 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 1/1:0,157:157:99:7067,480,0:0,0,101,56 chr1 31906882 . A G 2731.08 PASS AC=2;AF=0.943;AN=2;DP=5034;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3024,303,0:0,0,55,46 chr1 31907102 . A G 1558.64 PASS AC=2;AF=0.909;AN=2;DP=3034;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1829,165,0:0,0,22,33 chr1 31907457 . A C,G 1863.63 PASS AC=2,0;AF=0.67,0.273;AN=2;DP=2053;MQ=60;set=Intersection GT:DP:GQ:SB 1/1:34:99:0,0,7,27 chr1 31971684 . C G 467.98 PASS AC=2;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 1/1:0,18:18:54:764,54,0:0,0,18,0 chr1 31973122 . GTGGAGTCTGTC G 1942.9 PASS AC=2;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 1/1:0,62:62:99:2792,190,0:0,0,32,30 chr1 31973138 . T C 2026.96 PASS AC=2;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 1/1:0,64:64:99:2878,199,0:0,0,33,31 chr1 31973215 . G A 1249.58 PASS AC=2;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 1/1:0,54:54:99:1722,162,0:0,0,25,29 chr1 31973266 . G A 1337.43 PASS AC=2;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 1/1:0,52:52:99:1698,155,0:0,0,28,24 chr1 31973348 . A C 1429.07 PASS AC=2;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 1/1:0,83:83:99:2585,249,0:0,0,42,41 chr1 31973409 . G A 1766.36 PASS AC=2;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 1/1:0,88:88:99:2719,262,0:0,0,45,43 chr1 31973440 . G A 1964.47 PASS AC=2;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 1/1:0,75:75:99:2246,225,0:0,0,38,37 chr1 31973481 . C T 1548.72 PASS AC=2;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 1/1:0,70:70:99:2137,209,0:0,0,31,39 chr1 32042268 . G A 988.97 PASS AC=1;AF=0.55;AN=2;DP=473;MQ=60;set=variant5-variant11-variant15-variant19-variant22-variant23-variant29-variant33-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,31:58:99:804,0,827:10,17,19,12 chr1 32044641 . G GTTTAATTTCAGTGAGAGCTGGTGTGTCTGTGTGTGTGTGTGTGATGTCTTCAGTTATAA,GTTTAATTTCAGTGAGAGCTGGTGTGTCTATGTGTGTGTGTGTGTGATGTCTTCAGTTATAA,GTTTAATTTCAGTGAGAGCTGTTGTGTCTATGTGTGTGTGTGTGTGATGTCTTCAGTTATAA 1710.94 PASS AC=0,1,1;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 2/3:12:99:0,0,10,2 chr1 32049151 . C T 1569.38 PASS AC=1;AF=0.5;AN=2;DP=139;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.155;QD=11.29;ReadPosRankSum=-0.1;SOR=0.704;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:77,62:139:99:1598,0,1987:42,35,34,28 chr1 32051411 . C T 637.81 PASS AC=1;AF=0.5;AN=2;DP=70;FS=3.329;FractionInformativeReads=0.986;MQ=60;MQRankSum=-1.838;QD=9.11;ReadPosRankSum=0.818;SOR=0.793;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:42,27:69:99:666,0,1010:19,23,15,12 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 0/1:24:76:8,10,3,3 chr1 32092274 . T C 77.96 PASS AC=1;AF=0.5;AN=2;DP=117;FractionInformativeReads=1;set=variant3-variant10-variant13-variant22-variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:14,4:18:99:113,0,1525:5,9,4,0 chr1 32092278 . T C 77.96 PASS AC=1;AF=0.5;AN=2;DP=136;set=variant3-variant10-variant20-variant22-variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:16,4:20:99:113,0,1525:5,11,4,0 chr1 32092283 . G C 65.92 PASS AC=1;AF=0.5;AN=2;DP=177;FractionInformativeReads=1;set=variant3-variant10-variant20-variant22-variant23-variant24-variant26 GT:AD:DP:GQ:PL:SB 0/1:17,4:21:99:104,0,1633:6,11,4,0 chr1 32092289 . T C 49.83 PASS AC=1;AF=0.5;AN=2;DP=202;set=variant3-variant10-variant20-variant22-variant23-variant24-variant26 GT:AD:DP:GQ:PL:SB 0/1:24,4:28:90:90,0,1772:12,12,4,0 chr1 32122424 . TAA TA,TAAA,T 85.64 PASS AC=1,0,0;AF=0.452,0.032,0.016;AN=2;DP=664;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant37-variant39-filterInvariant41-variant42-variant43 GT:DP:GQ:SB 0/1:15:81:6,0,7,2 chr1 32127911 . C T 1176.97 PASS AC=2;AF=0.552;AN=2;DP=2085;MQ=60;set=variant3-variant5-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2161,230,0:0,0,40,37 chr1 32127953 . G A 1065.92 PASS AC=2;AF=0.552;AN=2;DP=1987;MQ=60;set=variant3-variant5-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:1976,212,0:0,0,34,37 chr1 32128283 . C G,A 264.39 PASS AC=2,0;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 1/1:16:35:1,0,1,14 chr1 32133737 . C T 361.44 PASS AC=2;AF=0.523;AN=2;DP=952;MQ=60;set=variant3-variant5-variant8-variant10-variant11-variant14-variant15-variant18-variant19-variant20-variant23-variant24-variant26-variant28-variant30-variant32-variant33-variant34-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1268,123,0:0,0,27,14 chr1 32136168 . G C,T 4014.62 PASS AC=0,2;AF=0.693,0.273;AN=2;DP=5182;MQ=60;set=Intersection GT:DP:GQ:SB 2/2:96:99:1,0,58,37 chr1 32138045 . G A 1081.36 PASS AC=1;AF=0.5;AN=2;DP=335;FractionInformativeReads=1;MQ=60;set=variant8-variant15-variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:28,31:59:99:730,0,634:16,12,19,12 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 1/1:1,66:67:99:2001,189,0:0,1,32,34 chr1 32146425 . C T 833.04 PASS AC=1;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 0/1:18,14:32:99:291,0,555:13,5,7,7 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 1/1:0,83:83:99:2689,248,0:0,0,50,33 chr1 32149982 . A T 207.09 PASS AC=1;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 0/1:13,16:29:99:386,0,309:6,7,8,8 chr1 32155284 . T C 2509.12 PASS AC=1;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 0/1:63,50:113:99:1093,0,1385:31,32,25,25 chr1 32155911 . G T 1200.06 PASS AC=1;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 0/1:19,14:33:99:366,0,542:12,7,10,4 chr1 32155929 . G A 1571.09 PASS AC=1;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 0/1:27,22:49:99:519,0,738:18,9,14,8 chr1 32156722 . G A 1723.01 PASS AC=1;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 0/1:26,32:58:99:843,0,773:17,9,23,9 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 1/1:0,218:218:99:6468,649,0:0,0,113,105 chr1 32157248 . G T,C 200.75 PASS AC=1,0;AF=0.25,0.25;AN=2;DP=68;FractionInformativeReads=1;MQ=60;set=variant23-variant41 GT:DP:GQ:SB 0/1:27:99:8,10,2,7 chr1 32157531 . T C 4876.69 PASS AC=1;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 0/1:84,68:152:99:1637,0,2046:50,34,42,26 chr1 32158374 . T C 4550.5 PASS AC=1;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 0/1:74,98:172:99:2464,0,1894:23,51,38,60 chr1 32159588 . A C 4324.85 PASS AC=1;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 0/1:71,79:150:99:1891,0,1616:37,34,42,37 chr1 32159781 . C T 1089.74 PASS AC=1;AF=0.5;AN=2;DP=172;MQ=60;set=variant19-variant23 GT:AD:DP:GQ:PL:SB 0/1:39,39:78:99:1087,0,1032:13,26,16,23 chr1 32160918 . A G 1287.35 PASS AC=1;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 0/1:43,37:80:99:910,0,1184:15,28,14,23 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 1/1:0,33:33:99:1470,102,0:0,0,20,13 chr1 32163975 . C A 547.26 PASS AC=1;AF=0.5;AN=2;DP=360;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant14-variant16-variant19-variant23-variant32-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,18:40:99:512,0,741:19,3,10,8 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 1/1:0,98:98:99:3088,294,0:0,0,40,58 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 1/1:2,78:80:99:2467,187,0:1,1,49,29 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 1/1:0,89:89:99:2664,267,0:0,0,51,38 chr1 32192779 . G A 678.59 PASS AC=1;AF=0.5;AN=2;DP=33;FS=4.263;FractionInformativeReads=1;MQ=60;MQRankSum=0.864;QD=20.56;ReadPosRankSum=2.404;SOR=0.862;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:6,27:33:99:707,0,107:2,4,16,11 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 1/1:0,93:93:99:3192,279,0:0,0,64,29 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 1/1:6:20:0,0,0,6 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 1/1:0,70:70:99:2395,210,0:0,0,47,23 chr1 32260034 . A G 145.3 PASS AC=2;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 1/1:0,2:2:6:90,6,0:0,0,0,2 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 1/1:0,201:201:99:6010,600,0:0,0,119,82 chr1 32279629 . G A 336.29 PASS AC=2;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 1/1:0,65:65:99:1908,195,0:0,0,33,32 chr1 32280610 . T C 1753.14 PASS AC=2;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 1/1:2,60:62:99:1945,136,0:1,1,22,38 chr1 32281633 . G A 494.17 PASS AC=1;AF=0.5;AN=2;DP=92;FractionInformativeReads=1;MQ=60;set=variant19-variant23 GT:AD:DP:GQ:PL:SB 0/1:17,25:42:99:677,0,355:8,9,10,15 chr1 32372356 . TACAC TAC,T 47.89 PASS AC=1,0;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 0/1:49:99:17,7,20,5 chr1 32637419 . G C 634.27 PASS AC=1;AF=0.5;AN=2;DP=115;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant17-variant23-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,13:19:99:325,0,125:3,3,8,5 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 0/1:125:99:45,38,18,24 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 0/1:25,23:48:99:865,0,947:13,12,6,17 chr1 32661781 . AGAAAG A 1856.86 PASS AC=1;AF=0.5;AN=2;DP=271;MQ=60;set=variant3-variant19-variant23 GT:AD:DP:GQ:PL:SB 0/1:29,32:61:99:1257,0,1794:14,15,16,16 chr1 32671834 . AG A 1960.25 PASS AC=1;AF=0.5;AN=2;DP=136;FS=0.647;FractionInformativeReads=0.963;MQ=60;MQRankSum=-0.062;QD=14.41;ReadPosRankSum=0.016;SOR=0.605;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:64,67:131:99:1998,0,1839:30,34,33,34 chr1 32672932 . G A 1844.26 PASS AC=1;AF=0.5;AN=2;DP=695;FractionInformativeReads=1;MQ=60;set=variant3-variant19-variant23-variant25-variant28-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,59:110:99:1441,0,1251:28,23,34,25 chr1 32682558 . T C 1685.81 PASS AC=1;AF=0.5;AN=2;DP=685;FractionInformativeReads=1;MQ=60;set=variant5-variant17-variant23-variant43 GT:AD:DP:GQ:PL:SB 0/1:83,65:148:99:1516,0,1932:41,42,33,32 chr1 32689857 . A G 590.89 PASS AC=1;AF=0.52;AN=2;DP=1329;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant10-variant11-variant13-variant14-variant15-variant19-variant20-variant23-variant24-variant25-variant28-variant29-variant31-variant33-variant34-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,48:73:99:1340,0,788:11,14,26,22 chr1 32692168 . AT A,ATT 57.97 PASS AC=1,0;AF=0.482,0.054;AN=2;DP=869;MQ=60;set=variant-filterInvariant4-variant6-filterInvariant7-variant8-variant9-variant10-filterInvariant11-variant12-variant14-variant17-variant19-variant20-variant22-variant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-variant31-filterInvariant34-filterInvariant36-variant38-variant39-variant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/1:15:99:2,6,2,5 chr1 32751510 . A G 708.46 PASS AC=1;AF=0.5;AN=2;DP=471;MQ=60;set=variant13-variant16-variant23-variant32-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:37,31:68:99:743,0,917:17,20,14,17 chr1 32831543 . C T 604.22 PASS AC=2;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 1/1:0,27:27:81:947,81,0:0,0,13,14 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 1/1:0,30:30:90:1034,90,0:0,0,8,22 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 1/1:0,159:159:99:5063,477,0:0,0,79,80 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 0/1:28:99:13,4,9,2 chr1 33087567 . GA G,GAA 45.01 PASS AC=0,1;AF=0.25,0.25;AN=2;DP=292;set=filterInvariant17-filterInvariant18-variant21-variant23-filterInvariant27-filterInvariant28-variant30-variant37-variant38-variant40 GT:DP:GQ:SB 0/2:27:99:8,7,6,6 chr1 33099798 . A G 321.04 PASS AC=1;AF=0.548;AN=2;DP=465;FractionInformativeReads=1;MQ=60;set=variant-variant10-variant13-variant14-variant15-variant16-variant18-variant20-variant23-variant25-variant26-variant27-variant30-variant32-variant33-variant34-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,8:26:99:222,0,454:7,11,1,7 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 1/1:0,9:9:27:367,27,0:0,0,9,0 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 1/1:0,107:107:99:3037,318,0:0,0,47,60 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 1/1:0,8:8:24:238,24,0:0,0,5,3 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 1/1:0,65:65:99:2063,195,0:0,0,28,37 chr1 33134774 . A C 760.02 PASS AC=1;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 0/1:39,36:75:99:910,0,944:18,21,16,20 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 1/1:0,29:29:87:914,87,0:0,0,12,17 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 1/1:0,108:108:99:3251,324,0:0,0,53,55 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 1/1:0,66:66:99:1980,197,0:0,0,23,43 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 1/1:43:99:0,0,21,22 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 1/1:0,42:42:99:1914,129,0:0,0,20,22 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 1/1:0,75:75:99:2302,225,0:0,0,44,31 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 1/1:0,71:71:99:2554,213,0:0,0,27,44 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 1/1:0,151:151:99:4635,453,0:0,0,85,66 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 1/1:0,184:184:99:5643,551,0:0,0,100,84 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 0/1:148,147:295:99:5417,0,6712:85,63,74,73 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 0/1:154,142:296:99:5163,0,6830:86,68,71,71 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 1/1:0,35:35:99:1183,105,0:0,0,25,10 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 0/1:12,7:19:99:142,0,315:7,5,5,2 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 1/1:0,22:22:66:732,66,0:0,0,13,9 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 0/1:13,12:25:99:262,0,299:8,5,7,5 chr1 33235626 . G A 2782.96 PASS AC=1;AF=0.589;AN=2;DP=5987;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant28-variant29-variant31-variant33-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:86,84:170:99:1991,0,2319:48,38,46,38 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 0/1:21,16:37:99:427,0,469:10,11,8,8 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 0/1:5,3:8:70:70,0,121:3,2,1,2 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 0/1:21,7:28:99:203,0,583:14,7,7,0 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 0/1:33,15:48:99:527,0,7209:9,24,3,12 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 0/1:47,63:110:99:1434,0,1015:20,27,26,37 chr1 33272307 . T TA 1024.82 PASS AC=1;AF=0.583;AN=2;DP=304;MQ=60;set=variant11-variant12-variant17-variant23-variant29-variant31 GT:AD:DP:GQ:PL:SB 0/1:20,16:36:99:487,0,641:8,12,5,11 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 1/1:0,90:90:99:2809,268,0:0,0,49,41 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 0/1:45,43:88:99:1054,0,1064:22,23,22,21 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 1/1:0,8:8:24:342,24,0:0,0,0,8 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 1/1:0,18:18:54:630,54,0:0,0,4,14 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 1/1:0,26:26:78:918,78,0:0,0,20,6 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 1/1:0,98:98:99:3042,294,0:0,0,59,39 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 0/1:21,24:45:99:613,0,521:13,8,12,12 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 0/1:179,195:374:99:7674,0,7070:98,81,105,90 chr1 33324091 . G A 5663.18 PASS AC=1;AF=0.583;AN=2;DP=2294;FractionInformativeReads=1;MQ=60;set=variant11-variant12-variant17-variant23-variant29-variant31 GT:AD:DP:GQ:PL:SB 0/1:187,201:388:99:7720,0,7138:104,83,108,93 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 0/1:211,229:440:99:5331,0,4750:101,110,116,113 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 0/1:26,25:51:99:543,0,691:12,14,10,15 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 1/1:1,79:80:99:2569,204,0:1,0,25,54 chr1 33361287 . G A 1726.08 PASS AC=1;AF=0.5;AN=2;DP=489;FractionInformativeReads=1;MQ=60;set=variant7-variant20-variant23 GT:AD:DP:GQ:PL:SB 0/1:77,67:144:99:1626,0,1880:30,47,32,35 chr1 33402172 . C T 583.32 PASS AC=1;AF=0.559;AN=2;DP=1091;MQ=60;set=variant5-variant8-variant11-variant15-variant17-variant18-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,32:61:99:871,0,653:15,14,15,17 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 0/1:213:99:70,63,46,34 chr1 33409551 . C T 679.86 PASS AC=1;AF=0.595;AN=2;DP=893;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant9-variant11-variant13-variant15-variant17-variant18-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,19:40:99:504,0,495:11,10,11,8 chr1 33409693 . G A 1077.34 PASS AC=1;AF=0.559;AN=2;DP=1857;MQ=60;set=variant5-variant8-variant11-variant15-variant17-variant18-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,50:91:99:1143,0,995:20,21,25,25 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 1/1:0,11:11:33:384,33,0:0,0,9,2 chr1 33475426 . C T 1937.66 PASS AC=2;AF=0.548;AN=2;DP=2359;FractionInformativeReads=1;MQ=60;set=variant7-variant9-variant11-variant12-variant15-variant17-variant18-variant20-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2735,255,0:0,0,52,33 chr1 33485789 . AACACACAC AACACACACACACACAC,AACAC,AACACACACACACAC,A,AACACAC,AACACACACAC,AAC,AACACACACACAC,AACACACACACACACACACACAC 238.02 PASS AC=0,0,0,2,0,0,0,0,0;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 4/4:10:31:0,0,1,9 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 1/1:0,51:51:99:1726,153,0:0,0,35,16 chr1 33547768 . T C 1186.8 PASS AC=2;AF=0.565;AN=2;DP=880;MQ=60;set=variant7-variant9-variant11-variant12-variant13-variant15-variant17-variant18-variant20-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:945,78,0:0,0,17,9 chr1 33559990 . G A 501.04 PASS AC=1;AF=0.5;AN=2;DP=166;FractionInformativeReads=1;MQ=60;set=variant12-variant23-variant32-variant40 GT:AD:DP:GQ:PL:SB 0/1:20,19:39:99:501,0,523:11,9,13,6 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 1/1:0,34:34:99:1073,102,0:0,0,14,20 chr1 33586199 . T G 66.22 PASS AC=2;AF=0.813;AN=2;DP=31;FS=0;FractionInformativeReads=1;MQ=60;set=variant7-variant12-variant17-variant20-variant23-variant25-variant27-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:126,9,0:0,0,1,2 chr1 33612508 . G A 1221.16 PASS AC=2;AF=0.609;AN=2;DP=2251;MQ=60;set=variant-variant3-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2391,231,0:0,0,33,44 chr1 33625275 . C T 1717.59 PASS AC=1;AF=0.5;AN=2;DP=687;MQ=60;set=variant3-variant12-variant15-variant16-variant19-variant23-variant31-variant32 GT:AD:DP:GQ:PL:SB 0/1:35,26:61:99:683,0,959:24,11,18,8 chr1 33631069 . C A 408.73 PASS AC=2;AF=0.587;AN=2;DP=1137;MQ=60;set=variant-variant3-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1403,134,0:0,0,29,16 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 1/1:1,59:60:99:1849,169,0:0,1,36,23 chr1 33722051 . C CCCGCCG 1228.44 PASS AC=1;AF=0.683;AN=2;DP=3298;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-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,36:74:99:1479,0,2609:20,18,22,14 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 0/1:106,75:181:99:1699,0,2509:52,54,35,40 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 0/1:66,60:126:99:1487,0,1786:38,28,27,33 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 1/1:0,32:32:96:1207,96,0:0,0,15,17 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 1/1:0,25:25:75:848,75,0:0,0,5,20 chr1 33760743 . T C 1421.22 PASS AC=2;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 1/1:0,126:126:99:3838,377,0:0,0,79,47 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 2/1:35:99:1,1,17,16 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 0/1:30,40:70:99:1288,0,872:23,7,28,12 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 0/1:1,4:5:69:165,0,69:0,1,0,4 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 1/1:0,17:17:51:600,51,0:0,0,12,5 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 1/1:0,31:31:93:1005,93,0:0,0,12,19 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 1/1:1,80:81:99:2234,231,0:1,0,42,38 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 1/1:0,103:103:99:3012,309,0:0,0,53,50 chr1 33789670 . G A 1306.07 PASS AC=2;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 1/1:0,98:98:99:2945,293,0:0,0,52,46 chr1 33789968 . G T 1480.17 PASS AC=2;AF=0.607;AN=2;DP=1700;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant11-variant16-variant17-variant19-variant20-variant23-variant26-variant28-variant29-variant31-variant33-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3260,324,0:0,0,56,53 chr1 33790496 . G A 616.03 PASS AC=2;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 1/1:0,66:66:99:2161,198,0:0,0,42,24 chr1 33799548 . C T 78.22 PASS AC=2;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 1/1:1,15:16:2:507,2,0:1,0,13,2 chr1 33799900 . G A 929.55 PASS AC=2;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 1/1:0,52:52:99:1833,156,0:0,0,14,38 chr1 33820134 . C T 655.38 PASS AC=2;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 1/1:0,87:87:99:2546,260,0:0,0,44,43 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 1/1:0,203:203:99:6055,607,0:0,0,96,107 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 1/1:0,11:11:33:411,33,0:0,0,2,9 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 1/1:0,48:48:99:1631,144,0:0,0,16,32 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 1/1:0,13:13:39:487,39,0:0,0,12,1 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 1/1:0,88:88:99:2760,264,0:0,0,43,45 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 1/1:0,153:153:99:4520,458,0:0,0,71,82 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 1/1:0,90:90:99:3086,269,0:0,0,44,46 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 1/1:1,72:73:99:2173,175,0:1,0,38,34 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 1/1:0,180:180:99:5945,540,0:0,0,111,69 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 1/1:0,44:44:99:1399,132,0:0,0,24,20 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 1/1:0,201:201:99:5864,603,0:0,0,95,106 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 1/1:0,63:63:99:2005,189,0:0,0,41,22 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 1/1:0,6:6:18:218,18,0:0,0,1,5 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 1/1:0,25:25:75:842,75,0:0,0,6,19 chr1 34024672 . G A 175.47 PASS AC=1;AF=0.556;AN=2;DP=56;FractionInformativeReads=1;MQ=60;set=variant8-variant18-variant23-variant26-variant28-variant31-variant33-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:72:72,0,129:3,1,2,0 chr1 34024928 . T C 724.07 PASS AC=1;AF=0.556;AN=2;DP=577;FractionInformativeReads=1;MQ=60;set=variant8-variant18-variant23-variant26-variant28-variant31-variant33-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,28:65:99:714,0,1015:16,21,15,13 chr1 34025030 . A G 905.9 PASS AC=1;AF=0.556;AN=2;DP=823;FractionInformativeReads=1;MQ=60;set=variant8-variant18-variant23-variant26-variant28-variant31-variant33-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,42:76:99:1126,0,850:19,15,25,17 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 0/1:32,29:61:99:714,0,848:18,14,18,11 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 0/1:19,14:33:99:351,0,528:6,13,4,10 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 0/1:5,6:11:99:223,0,282:0,5,1,5 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 0/1:5,7:12:99:223,0,282:0,5,1,6 chr1 34042810 . A G 2535.77 PASS AC=1;AF=0.575;AN=2;DP=1644;MQ=60;set=variant-variant5-variant8-variant10-variant15-variant16-variant18-variant20-variant23-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant36-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,25:73:99:610,0,1349:32,16,17,8 chr1 34042834 . C A 1083.5 PASS AC=1;AF=0.55;AN=2;DP=971;FractionInformativeReads=1;MQ=60;set=variant8-variant16-variant18-variant23-variant26-variant28-variant31-variant33-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:55,29:84:99:659,0,1491:34,21,17,12 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 1/1:0,38:38:99:1184,114,0:0,0,13,25 chr1 34043287 . C A 141.1 PASS AC=1;AF=0.531;AN=2;DP=429;MQ=60;set=variant8-variant10-variant15-variant16-variant18-variant23-variant26-variant27-variant28-variant29-variant31-variant33-variant36-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:132,0,251:2,7,4,4 chr1 34052305 . C T 930.57 PASS AC=1;AF=0.538;AN=2;DP=1288;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant9-variant10-variant12-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant36-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,18:31:99:437,0,340:5,8,5,13 chr1 34052605 . A G 129.16 PASS AC=2;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 1/1:0,17:17:51:624,51,0:0,0,14,3 chr1 34065436 . C T 883.3 PASS AC=1;AF=0.588;AN=2;DP=1321;MQ=60;set=variant2-variant11-variant12-variant13-variant16-variant18-variant21-variant23-variant24-variant26-variant27-variant31-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,27:67:99:751,0,1060:20,20,11,16 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 0/1:4,4:8:99:153,0,159:4,0,4,0 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 0/1:29,25:54:99:555,0,739:18,11,13,12 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 0/1:37,27:64:99:583,0,938:19,18,14,13 chr1 34098959 . C G 659 PASS AC=1;AF=0.542;AN=2;DP=340;MQ=60;set=variant2-variant11-variant13-variant16-variant21-variant23-variant24-variant27-variant29-variant31-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,13:20:99:395,0,195:5,2,10,3 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 0/1:12,5:17:99:133,0,443:9,3,4,1 chr1 34189917 . C T 783.59 PASS AC=1;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 0/1:58,33:91:99:802,0,1353:26,32,11,22 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 1/1:0,51:51:99:1756,154,0:0,0,16,35 chr1 34205134 . C T 232.71 PASS AC=2;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 1/1:0,12:12:36:499,36,0:0,0,1,11 chr1 34238146 . G A 1232.43 PASS AC=1;AF=0.5;AN=2;DP=935;MQ=60;set=variant2-variant5-variant11-variant14-variant16-variant20-variant23-variant30-variant33-variant37 GT:AD:DP:GQ:PL:SB 0/1:37,51:88:99:1225,0,1077:20,17,28,23 chr1 34238283 . T C 3879.66 PASS AC=2;AF=0.609;AN=2;DP=2794;MQ=60;set=variant2-variant5-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant27-variant29-variant30-variant33-variant34-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3312,320,0:0,0,49,58 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 0/1:28:99:11,3,10,4 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 1/1:0,75:75:99:2035,222,0:0,0,31,44 chr1 34276210 . T TA,TAA 198.52 PASS AC=1,0;AF=0.72,0.02;AN=2;DP=236;MQ=60;set=variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant27-variant28-variant29-variant30-variant32-variant34-variant36-variant40-variant41 GT:DP:GQ:SB 0/1:7:35:2,0,5,0 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 1/1:0,9:9:27:316,27,0:0,0,7,2 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 1/1:0,14:14:42:455,42,0:0,0,10,4 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 0/1:6,4:10:99:143,0,245:6,0,3,1 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 1/1:0,22:22:66:787,66,0:0,0,8,14 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 0/1:22,18:40:99:439,0,493:13,9,11,7 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 0/1:45,21:66:99:527,0,1088:28,17,14,7 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 0/1:14,19:33:99:496,0,370:9,5,13,6 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 1/1:1,26:27:70:690,70,0:1,0,10,16 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 1/1:0,23:23:69:822,69,0:0,0,18,5 chr1 34326100 . G A 417.24 PASS AC=1;AF=0.556;AN=2;DP=290;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant12-variant23-variant27-variant33-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,16:37:99:406,0,619:16,5,10,6 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 1/1:0,92:92:99:2929,276,0:0,0,35,57 chr1 34327944 . CTGTGTGTGTGTGTGTGTGTG CTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTG,C,CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTG 206.16 PASS AC=0,0,0,0,0,0,0,0,0,0,2,0,0;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 11/11:3:9:0,0,1,2 chr1 34328552 . G A 189.51 PASS AC=1;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 0/1:17,19:36:99:538,0,394:9,8,11,8 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 1/1:0,103:103:99:3083,309,0:0,0,60,43 chr1 34330067 . A C 3194.7 PASS AC=2;AF=0.818;AN=2;DP=7171;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,143:143:99:4228,428,0:0,0,66,77 chr1 34330537 . G GGGA 508.82 PASS AC=2;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 1/1:0,6:6:18:255,18,0:0,0,0,6 chr1 34330545 . G A 418.6 PASS AC=2;AF=0.561;AN=2;DP=243;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,0,2 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 0/1:18,24:42:99:762,0,437:12,6,19,5 chr1 34663208 . C G 1741.2 PASS AC=1;AF=0.529;AN=2;DP=2478;MQ=60;set=variant2-variant3-variant5-variant6-variant9-variant10-variant13-variant14-variant17-variant20-variant23-variant28-variant29-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:76,45:121:99:1048,0,1985:39,37,24,21 chr1 34663411 . C G 887.08 PASS AC=1;AF=0.528;AN=2;DP=1439;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant9-variant10-variant13-variant14-variant17-variant18-variant20-variant23-variant28-variant29-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:42,36:78:99:847,0,1147:19,23,18,18 chr1 34663618 . G A 265.54 PASS AC=1;AF=0.528;AN=2;DP=288;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant9-variant10-variant13-variant14-variant17-variant18-variant20-variant23-variant28-variant29-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:64:162,0,64:1,2,2,4 chr1 34667863 . C A 1828.85 PASS AC=1;AF=0.529;AN=2;DP=2654;MQ=60;set=variant2-variant3-variant5-variant6-variant9-variant10-variant14-variant17-variant18-variant20-variant23-variant28-variant29-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:66,99:165:99:2531,0,1557:21,45,37,62 chr1 34673701 . A C 910.92 PASS AC=1;AF=0.5;AN=2;DP=376;MQ=60;set=variant5-variant13-variant23-variant29 GT:AD:DP:GQ:PL:SB 0/1:70,44:114:99:914,0,1634:36,34,26,18 chr1 34678040 . T G 610.86 PASS AC=1;AF=0.5;AN=2;DP=82;FractionInformativeReads=1;MQ=60;set=variant5-variant23 GT:AD:DP:GQ:PL:SB 0/1:23,17:40:99:524,0,726:3,20,2,15 chr1 34684463 . G A 516.91 PASS AC=1;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 0/1:19,38:57:99:988,0,501:10,9,17,21 chr1 34684571 . CACACAT C 696.71 PASS AC=1;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 0/1:37,29:66:99:1092,0,2046:20,17,16,13 chr1 34684621 . A G 611.18 PASS AC=1;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 0/1:43,31:74:99:673,0,977:18,25,15,16 chr1 35184034 . G A 109.31 PASS AC=1;AF=0.5;AN=2;DP=337;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant9-variant17-variant19-variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:21,15:36:99:434,0,549:8,13,5,10 chr1 35220730 . A G 1078.74 PASS AC=1;AF=0.567;AN=2;DP=2905;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant9-variant11-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,45:101:99:1054,0,1372:29,27,21,24 chr1 35223913 . A C 625.33 PASS AC=1;AF=0.5;AN=2;DP=426;FractionInformativeReads=1;MQ=60;set=variant5-variant11-variant17-variant20-variant22-variant23-variant25-variant30-variant31-variant33 GT:AD:DP:GQ:PL:SB 0/1:10,14:24:99:383,0,280:4,6,7,7 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 0/1:33,29:62:99:825,0,947:13,20,10,19 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 0/1:11,9:20:99:297,0,356:10,1,8,1 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 0/1:46,44:90:99:1001,0,1109:22,24,15,29 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 0/1:27,23:50:99:705,0,737:11,16,6,17 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 0/1:114,105:219:99:2567,0,2872:54,60,51,54 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 0/1:52,58:110:99:1475,0,1387:17,35,19,39 chr1 35260929 . G A 232.42 PASS AC=1;AF=0.773;AN=2;DP=1827;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:20,17:37:99:415,0,649:9,11,7,10 chr1 35318269 . A ATT,AT,ATTT 94.03 PASS AC=1,0,0;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 0/1:29:99:8,2,12,7 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 1/1:0,78:78:99:2351,234,0:0,0,40,38 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 1/1:0,96:96:99:2897,287,0:0,0,47,49 chr1 35319323 . C T 5725.13 PASS AC=2;AF=0.966;AN=2;DP=5201;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:4346,357,0:0,0,23,96 chr1 35321684 . A AT,ATT 54.25 PASS AC=1,0;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 0/1:18:99:1,6,3,8 chr1 35323395 . T G 740.73 PASS AC=1;AF=0.667;AN=2;DP=866;FractionInformativeReads=1;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-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,15:23:99:425,0,171:3,5,5,10 chr1 35323550 . C T 61.77 PASS AC=1;AF=0.775;AN=2;DP=152;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant13-variant14-variant15-variant18-variant23-variant24-variant27-variant28-variant30-variant32-variant34-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,7:9:22:247,0,22:1,1,3,4 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 0/1:17,11:28:99:313,0,563:7,10,7,4 chr1 35455893 . A G 616.63 PASS AC=1;AF=0.5;AN=2;DP=60;FractionInformativeReads=1;MQ=60;set=variant23-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,21:31:99:645,0,322:1,9,4,17 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 1/1:0,52:52:99:2356,159,0:0,0,28,24 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 1/1:0,62:62:99:1663,185,0:0,0,30,32 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 1/1:0,105:105:99:3383,314,0:0,0,61,44 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 1/1:0,36:36:99:1320,108,0:0,0,10,26 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 1/1:0,3:3:9:94,9,0:0,0,1,2 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 1/1:0,257:257:99:9171,774,0:0,0,136,121 chr1 35648826 . CTTTTT CTTTT,C,CTTTTTT 61.39 PASS AC=1,0,0;AF=0.346,0.077,0.077;AN=2;DP=1281;MQ=60;set=filterInvariant-variant2-variant10-filterInvariant12-filterInvariant18-filterInvariant23-filterInvariant24-filterInvariant28-filterInvariant29-filterInvariant31-variant37-filterInvariant38-variant44 GT:DP:GQ:SB 0/1:41:88:4,29,4,4 chr1 35836328 . CTTT CTTTTT,CTT,CTTTT,CT,C 83.56 PASS AC=0,0,1,0,0;AF=0.111,0.056,0.222,0.056,0.056;AN=2;DP=163;set=variant3-variant10-filterInvariant12-variant15-variant23-variant32-variant38-variant39-variant43 GT:DP:GQ:SB 0/3:8:7:0,2,1,5 chr1 35899684 . CTTT CT,CTT,C,CTTTT 158.79 PASS AC=0,1,0,0;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 0/2:12:16:0,3,2,7 chr1 35925861 . C A 2372.01 PASS AC=1;AF=0.932;AN=2;DP=3065;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:44,35:79:99:833,0,1004:27,17,22,13 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 1/1:0,56:56:99:1721,167,0:0,0,21,35 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 1/1:0,20:20:60:674,60,0:0,0,5,15 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 1/1:0,106:106:99:3206,317,0:0,0,42,64 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 1/1:1,45:46:99:1456,100,0:1,0,12,33 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 1/1:0,34:34:99:1042,102,0:0,0,11,23 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 1/1:0,14:14:42:470,42,0:0,0,11,3 chr1 36227588 . G A 1387.4 PASS AC=1;AF=0.5;AN=2;DP=332;FractionInformativeReads=1;MQ=60;set=variant23-variant32 GT:AD:DP:GQ:PL:SB 0/1:105,64:169:99:1416,0,2502:53,52,31,33 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 0/1:18:91:6,6,6,0 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 1/1:36:75:0,3,22,11 chr1 36307412 . CATAT C,CAT 212.59 PASS AC=0,1;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 0/2:4:20:0,1,0,3 chr1 36316418 . C CA 1332.99 PASS AC=2;AF=1;AN=2;DP=2394;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,40:42:72:1059,72,0:1,1,27,13 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 1/1:0,148:148:99:4204,442,0:0,0,70,78 chr1 36320284 . T G 2645.79 PASS AC=1;AF=0.5;AN=2;DP=447;FractionInformativeReads=1;MQ=60;set=variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:111,95:206:99:2674,0,2988:57,54,55,40 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 1/1:0,14:14:42:460,42,0:0,0,12,2 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 0/1:29:99:16,5,6,2 chr1 36389836 . G T 449.3 PASS AC=1;AF=0.5;AN=2;DP=45;FS=1.285;FractionInformativeReads=1;MQ=60;MQRankSum=-0.597;QD=9.98;ReadPosRankSum=-2.751;SOR=0.432;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:28,17:45:99:478,0,866:20,8,11,6 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 1/1:0,22:22:66:761,66,0:0,0,10,12 chr1 36439172 . A G 264.78 PASS AC=1;AF=0.5;AN=2;DP=65;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:293,0,318:3,9,3,8 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 1/1:0,22:22:64:605,64,0:0,0,14,8 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 1/1:0,121:121:99:3544,362,0:0,0,61,60 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 1/1:0,181:181:99:5460,541,0:0,0,101,80 chr1 36557914 . G A 143.85 PASS AC=1;AF=0.5;AN=2;DP=31;FractionInformativeReads=1;MQ=60;set=variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:172,0,155:3,3,4,2 chr1 36561656 . C T 1037.83 PASS AC=1;AF=0.5;AN=2;DP=228;FractionInformativeReads=1;MQ=60;set=variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:62,40:102:99:1066,0,1618:36,26,21,19 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 1/1:0,52:52:99:1491,155,0:0,0,25,27 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 1/1:0,37:37:99:1219,111,0:0,0,24,13 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 1/1:0,45:45:99:1381,134,0:0,0,26,19 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 1/1:0,48:48:99:1570,144,0:0,0,12,36 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 1/1:0,19:19:57:646,57,0:0,0,13,6 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 1/1:0,52:52:99:1941,157,0:0,0,38,14 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 1/1:0,85:85:99:3039,255,0:0,0,57,28 chr1 36641729 . C T 96.7 PASS AC=1;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 0/1:8,8:16:99:187,0,220:6,2,5,3 chr1 36642420 . T C 298.53 PASS AC=1;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 0/1:15,12:27:99:297,0,402:5,10,4,8 chr1 36724986 . T G 765.99 PASS AC=1;AF=0.5;AN=2;DP=93;FS=4.379;FractionInformativeReads=1;MQ=60;MQRankSum=-0.924;QD=8.24;ReadPosRankSum=-1.209;SOR=0.333;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:58,35:93:99:794,0,1542:41,17,21,14 chr1 36747997 . AT A,TT 551.09 PASS AC=1,0;AF=0.603,0.034;AN=2;DP=1647;set=variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant37-filterInvariant38-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:49:99:11,7,20,11 chr1 36752152 . C T 1178.85 PASS AC=1;AF=0.66;AN=2;DP=2441;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,33:72:99:934,0,998:19,20,19,14 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 1/1:0,112:112:99:3527,335,0:0,0,50,62 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 1/1:0,26:26:78:855,78,0:0,0,20,6 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 1/1:0,50:50:99:1494,150,0:0,0,31,19 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 1/1:0,53:53:99:1600,158,0:0,0,27,26 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 1/1:0,14:14:42:509,42,0:0,0,8,6 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 1/1:0,50:50:99:1516,150,0:0,0,19,31 chr1 36770806 . C G 2595.29 PASS AC=2;AF=0.989;AN=2;DP=2225;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:2069,164,0:0,0,46,9 chr1 36773405 . T G 490.74 PASS AC=1;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 0/1:52,37:89:99:950,0,1342:23,29,17,20 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 1/1:0,74:74:99:2243,221,0:0,0,38,36 chr1 36784499 . AAATAATAATAATAATAATAAT AAATAAT,AAATAATAATAAT,AAATAATAATAATAATAATAATAAT,A,AAATAATAATAATAAT 168.54 PASS AC=0,2,0,0,0;AF=0.077,0.654,0.077,0.077,0.077;AN=2;DP=41;FS=0;MQ=60;MQRankSum=1.026;ReadPosRankSum=1.026;set=variant3-variant7-variant11-variant22-variant23-variant25-variant26-variant29-variant32-variant36-variant37-variant42-variant43 GT:DP:GQ:SB 2/2:2:6:0,0,2,0 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 0/1:42,41:83:99:1090,0,1137:24,18,18,23 chr1 36787888 . G A 1382.92 PASS AC=1;AF=0.66;AN=2;DP=3506;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,63:105:99:1625,0,1014:20,22,31,32 chr1 36788356 . A G 1917.97 PASS AC=2;AF=0.989;AN=2;DP=2857;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1846,171,0:0,0,28,29 chr1 36789546 . A G 1036.3 PASS AC=1;AF=0.66;AN=2;DP=2089;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,37:89:99:868,0,1332:28,24,19,18 chr1 36789588 . C T 1006.59 PASS AC=1;AF=0.5;AN=2;DP=90;FS=0.778;FractionInformativeReads=1;MQ=60;MQRankSum=0.627;QD=11.18;ReadPosRankSum=-0.142;SOR=0.788;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:48,42:90:99:1035,0,1206:24,24,20,22 chr1 36807481 . C T 970.3 PASS AC=1;AF=0.6;AN=2;DP=2962;MQ=60;set=variant-variant3-variant6-variant9-variant10-variant15-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant33-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,78:135:99:1701,0,1497:29,28,40,38 chr1 36809698 . A C 959.69 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=9236;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:110,69:179:99:1116,0,4030:12,98,67,2 chr1 36809705 . G C 77.77 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=4240;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:124,35:159:99:289,0,5808:21,103,35,0 chr1 36809708 . A G 226.87 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1087;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:123,23:146:99:311,0,5742:18,105,23,0 chr1 36863456 . G A 1009.06 PASS AC=2;AF=0.618;AN=2;DP=1767;MQ=60;set=variant-variant3-variant5-variant8-variant11-variant13-variant14-variant15-variant16-variant20-variant23-variant27-variant31-variant32-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:2888,284,0:0,0,50,45 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 1/1:0,85:85:99:2525,254,0:0,0,37,48 chr1 36921371 . G T 1202.27 PASS AC=2;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 1/1:0,121:121:99:3450,362,0:0,0,66,55 chr1 36926445 . C T 990.03 PASS AC=2;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 1/1:0,96:96:99:2773,287,0:0,0,47,49 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 1/1:0,79:79:99:2453,237,0:0,0,44,35 chr1 36933492 . G T 1577.4 PASS AC=1;AF=0.5;AN=2;DP=155;FS=4.727;FractionInformativeReads=1;MQ=60;MQRankSum=-0.603;QD=10.18;ReadPosRankSum=-1.008;SOR=0.577;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:80,75:155:99:1606,0,2102:45,35,36,39 chr1 36937878 . C T 3795.12 PASS AC=2;AF=0.667;AN=2;DP=811;MQ=60;set=variant16-variant23-variant32 GT:AD:DP:GQ:PL:SB 1/1:0,215:215:99:6593,644,0:0,0,100,115 chr1 37261085 . A G 244.32 PASS AC=2;AF=0.636;AN=2;DP=224;MQ=60;set=variant2-variant3-variant4-variant9-variant10-variant11-variant13-variant16-variant17-variant23-variant25-variant27-variant28-variant31-variant32-variant34-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:214,15,0:0,0,5,0 chr1 37319610 . A G 352.06 PASS AC=2;AF=0.75;AN=2;DP=30;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.306;ReadPosRankSum=2.275;set=variant23-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:380,27,0:0,0,0,9 chr1 37324683 . A C 1843.91 PASS AC=2;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 1/1:0,61:61:99:2067,183,0:0,0,45,16 chr1 37324935 . T C 1738.02 PASS AC=2;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 1/1:0,98:98:99:3203,293,0:0,0,26,72 chr1 37325477 . A C 1058.73 PASS AC=2;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 1/1:0,72:72:99:2378,215,0:0,0,49,23 chr1 37335458 . A G 2444.71 PASS AC=2;AF=0.898;AN=2;DP=4368;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,69:70:99:2275,164,0:0,1,19,50 chr1 37335485 . A G 1982.53 PASS AC=2;AF=0.898;AN=2;DP=2813;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:2092,150,0:0,0,13,37 chr1 37335494 . G T 1681.77 PASS AC=2;AF=0.898;AN=2;DP=2417;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1649,114,0:0,0,9,27 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 0/1:9,5:14:99:140,0,220:6,3,3,2 chr1 37939999 . G A 136.66 PASS AC=1;AF=0.615;AN=2;DP=107;FS=0;FractionInformativeReads=1;MQ=60;set=variant11-variant12-variant16-variant20-variant22-variant23-variant24-variant26-variant27-variant34-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:157,0,138:4,3,4,3 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 1/1:0,28:28:83:740,83,0:0,0,14,14 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 0/1:27,21:48:99:588,0,701:12,15,8,13 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 0/1:97,109:206:99:2708,0,2356:50,47,53,56 chr1 37958161 . CAA CA,C,CAAA,CAAAA,CAAAAA 607.33 PASS AC=0,1,1,0,0;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 2/3:59:99:7,2,38,12 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 1/1:0,111:111:99:3229,330,0:0,0,43,68 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 1/1:0,96:96:99:2974,288,0:0,0,37,59 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 1/1:0,23:23:78:1030,78,0:0,0,19,4 chr1 37961307 . A AC 821.31 PASS AC=1;AF=0.55;AN=2;DP=359;set=variant3-variant4-variant7-variant8-variant13-variant20-variant23-variant24-variant26-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,17:34:99:349,0,317:12,5,12,5 chr1 37961308 . A C 796.61 PASS AC=1;AF=0.611;AN=2;DP=658;set=variant5-variant6-variant7-variant9-variant11-variant12-variant15-variant16-variant20-variant23-variant27-variant28-variant30-variant31-variant32-variant36-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,16:33:99:249,0,353:12,5,12,4 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 1/1:0,11:11:39:507,39,0:0,0,1,10 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 1/1:0,9:9:27:309,27,0:0,0,1,8 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 1/1:0,41:41:99:1361,123,0:0,0,12,29 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 1/1:0,25:25:75:899,75,0:0,0,6,19 chr1 37979933 . A G 435.26 PASS AC=2;AF=0.731;AN=2;DP=398;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:488,36,0:0,0,2,10 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 1/1:0,53:53:99:1568,159,0:0,0,20,33 chr1 38019747 . C T 1000.95 PASS AC=1;AF=0.559;AN=2;DP=1676;MQ=60;set=variant6-variant9-variant11-variant12-variant15-variant17-variant22-variant23-variant27-variant28-variant30-variant31-variant32-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,51:102:99:1277,0,1213:29,22,32,19 chr1 38022452 . C A 1113.73 PASS AC=2;AF=0.704;AN=2;DP=2424;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,101:102:99:2908,295,0:1,0,58,43 chr1 38030696 . T C 1114.41 PASS AC=2;AF=0.704;AN=2;DP=1784;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1882,162,0:0,0,30,24 chr1 38033047 . T G 154.72 PASS AC=2;AF=0.704;AN=2;DP=274;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:450,30,0:0,0,9,1 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 1/1:0,53:53:99:1744,159,0:0,0,34,19 chr1 38049373 . C T 676.44 PASS AC=2;AF=0.704;AN=2;DP=2018;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1853,174,0:0,0,33,25 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 1/1:0,67:67:99:1992,200,0:0,0,26,41 chr1 38052867 . C CA,CAA 437.94 PASS AC=2,0;AF=0.648,0.019;AN=2;DP=1336;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant36-variant38-variant43-variant44 GT:DP:GQ:SB 1/1:46:99:2,0,36,8 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 1/1:0,49:49:99:1517,146,0:0,0,16,33 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 1/1:0,40:40:99:1355,120,0:0,0,28,12 chr1 38077349 . CTTATCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTA C 396.34 PASS AC=2;AF=0.864;AN=2;DP=2035;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:96:1253,96,0:0,0,12,18 chr1 38078171 . G GGT,GGTGT,GGTGTGTGT 285.14 PASS AC=2,0,0;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 1/1:29:19:1,1,15,12 chr1 38078300 . A G 1033.69 PASS AC=2;AF=0.697;AN=2;DP=3726;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2767,269,0:0,0,47,43 chr1 38097790 . C T 439.3 PASS AC=1;AF=0.58;AN=2;DP=697;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant9-variant11-variant12-variant15-variant16-variant18-variant22-variant23-variant27-variant28-variant29-variant30-variant31-variant32-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,18:31:99:592,0,414:3,10,3,15 chr1 38098036 . G A 262.62 PASS AC=1;AF=0.58;AN=2;DP=860;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant9-variant11-variant12-variant15-variant16-variant18-variant22-variant23-variant27-variant28-variant29-variant30-variant31-variant32-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,12:25:99:242,0,352:4,9,6,6 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 1/1:0,4:4:12:180,12,0:0,0,0,4 chr1 38147606 . T A 1165.44 PASS AC=1;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 0/1:22,22:44:99:627,0,538:10,12,11,11 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 1/1:0,59:59:99:1901,177,0:0,0,29,30 chr1 38155699 . T G 43.74 PASS AC=1;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 0/1:7,8:15:99:265,0,179:2,5,1,7 chr1 38158130 . G A 1055.74 PASS AC=1;AF=0.5;AN=2;DP=121;FS=1.516;FractionInformativeReads=1;MQ=60;MQRankSum=-1.194;QD=8.73;ReadPosRankSum=-1.002;SOR=0.904;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:74,47:121:99:1084,0,1955:42,32,29,18 chr1 38158211 . C T 2756.73 PASS AC=1;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 0/1:90,76:166:99:1698,0,2145:44,46,38,38 chr1 38161694 . A G 1188.44 PASS AC=1;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 0/1:40,37:77:99:883,0,973:16,24,16,21 chr1 38164724 . C G 1363.87 PASS AC=1;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 0/1:42,53:95:99:1299,0,964:17,25,19,34 chr1 38164826 . G A 137.8 PASS AC=1;AF=0.5;AN=2;DP=227;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant17-variant19-variant23-variant31-variant32-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:227,0,147:2,4,2,5 chr1 38166022 . T C 751.21 PASS AC=1;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 0/1:23,19:42:99:526,0,554:13,10,11,8 chr1 38166327 . A T 677.34 PASS AC=1;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 0/1:28,30:58:99:752,0,708:16,12,12,18 chr1 38167345 . TA TAA,T 253.3 PASS AC=1,0;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 0/1:24:99:9,5,7,3 chr1 38170989 . G A 364.04 PASS AC=1;AF=0.5;AN=2;DP=33;FS=1.414;FractionInformativeReads=1;MQ=60;MQRankSum=1.79;QD=11.03;ReadPosRankSum=-1.247;SOR=0.982;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:18,15:33:99:392,0,459:12,6,11,4 chr1 38173983 . TTTC T 1978.03 PASS AC=1;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 0/1:64,48:112:99:1823,0,3022:38,26,27,21 chr1 38174185 . G T 1987.39 PASS AC=1;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 0/1:69,69:138:99:1772,0,1850:39,30,39,30 chr1 38174366 . G T 753.23 PASS AC=1;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 0/1:30,53:83:99:1396,0,878:11,19,23,30 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 1/1:0,50:50:99:1631,150,0:0,0,25,25 chr1 38181503 . C T 153.91 PASS AC=1;AF=0.542;AN=2;DP=427;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant13-variant16-variant17-variant19-variant20-variant21-variant23-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,8:24:99:199,0,499:11,5,6,2 chr1 38182135 . C T 978.38 PASS AC=1;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 0/1:51,64:115:99:1464,0,1283:28,23,31,33 chr1 38187888 . T C 2054.27 PASS AC=1;AF=0.5;AN=2;DP=1519;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant17-variant19-variant23-variant31-variant32-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:70,64:134:99:1363,0,1699:33,37,32,32 chr1 38200246 . A G 1099.02 PASS AC=1;AF=0.5;AN=2;DP=66;FS=1.104;FractionInformativeReads=1;MQ=60;MQRankSum=0.978;QD=16.65;ReadPosRankSum=1.304;SOR=0.465;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:27,39:66:99:1127,0,753:21,6,28,11 chr1 38226760 . T TAA,TA 108.27 PASS AC=1,0;AF=0.5,0.05;AN=2;DP=269;set=variant-variant5-variant8-variant23-variant24-variant25-variant26-variant34-variant36-variant38 GT:DP:GQ:SB 0/1:31:99:9,3,12,7 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 0/1:12,21:33:99:763,0,406:9,3,12,9 chr1 38227086 . A T 1040.88 PASS AC=1;AF=0.571;AN=2;DP=1615;MQ=60;set=variant-variant4-variant5-variant8-variant16-variant22-variant23-variant24-variant25-variant26-variant33-variant34-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:76,53:129:99:1316,0,1935:39,37,26,27 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 0/1:14,8:22:99:200,0,436:3,11,2,6 chr1 38260503 . C T 103.41 PASS AC=1;AF=0.5;AN=2;DP=438;MQ=60;set=variant-variant3-variant5-variant9-variant16-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant36-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,12:28:99:441,0,558:3,13,0,12 chr1 38265653 . T C 1719.63 PASS AC=1;AF=0.5;AN=2;DP=132;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.118;QD=13.03;ReadPosRankSum=-3.3;SOR=0.689;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:65,67:132:99:1748,0,1794:30,35,31,36 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 0/1:27,38:65:99:956,0,704:13,14,15,23 chr1 38268836 . T C 572.42 PASS AC=1;AF=0.5;AN=2;DP=796;MQ=60;set=variant-variant3-variant5-variant9-variant16-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,22:45:99:633,0,558:9,14,10,12 chr1 38268918 . T C 484.69 PASS AC=1;AF=0.629;AN=2;DP=1438;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,17:31:99:411,0,358:5,9,9,8 chr1 38275802 . T C 465.94 PASS AC=2;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 1/1:0,43:43:99:1536,129,0:0,0,20,23 chr1 38275826 . C G 466.23 PASS AC=1;AF=0.5;AN=2;DP=38;FS=2.884;FractionInformativeReads=1;MQ=60;MQRankSum=-3.328;QD=12.27;ReadPosRankSum=-0.876;SOR=1.243;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:19,19:38:99:494,0,457:10,9,7,12 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 1/1:0,129:129:99:3920,386,0:0,0,70,59 chr1 38278579 . C T 225.77 PASS AC=1;AF=0.5;AN=2;DP=571;MQ=60;set=variant-variant3-variant5-variant9-variant16-variant22-variant23-filterInvariant25-variant26-variant28-variant30-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,22:37:99:499,0,365:6,9,11,11 chr1 38278923 . A T 169.46 PASS AC=1;AF=0.673;AN=2;DP=236;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant14-variant16-variant18-variant21-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:31:121,0,31:1,0,2,2 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 0/1:189:99:52,89,16,32 chr1 38289274 . T A 886.85 PASS AC=1;AF=0.5;AN=2;DP=311;MQ=60;set=variant-variant16-variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:50,40:90:99:957,0,1246:32,18,25,15 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 0/1:14,9:23:99:237,0,316:7,7,7,2 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 0/1:7,7:14:99:273,0,158:5,2,7,0 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 1/1:0,37:37:99:1346,111,0:0,0,12,25 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 0/1:15,13:28:99:376,0,435:3,12,3,10 chr1 38301220 . G A 318.59 PASS AC=1;AF=0.5;AN=2;DP=455;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant9-variant16-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant36-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:259,0,228:6,2,7,1 chr1 38301250 . A G 484.25 PASS AC=2;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 1/1:0,35:35:99:1248,105,0:0,0,28,7 chr1 38301476 . G A 607.48 PASS AC=2;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 1/1:0,45:45:99:1568,134,0:0,0,11,34 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 0/1:6,8:14:99:219,0,190:2,4,3,5 chr1 38323553 . A T 334.27 PASS AC=1;AF=0.656;AN=2;DP=404;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant14-variant16-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:142,0,116:0,3,0,4 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 0/1:6:65:1,3,1,1 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 0/1:31,33:64:99:995,0,796:9,22,7,26 chr1 38327935 . CAG C 1312.05 PASS AC=1;AF=0.5;AN=2;DP=1420;MQ=60;set=variant-variant3-variant5-variant9-variant16-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant36-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,32:75:99:1206,0,1709:19,24,13,19 chr1 38327982 . G T 1077.17 PASS AC=2;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 1/1:0,81:81:99:2604,241,0:0,0,36,45 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 0/1:8,13:21:99:492,0,277:3,5,2,11 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 0/1:43,42:85:99:980,0,1025:23,20,21,21 chr1 38332057 . TTC TTCTC,TTCTCTC,TTCTCTCTCTC,T 101.86 PASS AC=0,0,1,0;AF=0.31,0.138,0.086,0.052;AN=2;DP=1518;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant36-variant38-variant40-variant43 GT:DP:GQ:SB 0/3:25:99:10,1,10,4 chr1 38332078 . TCACA TCTCTCTCTCACACA,TCACACACACACACACACA,TCACACACACACACACACACACA,TCACACACACACACACA,TCACACACACACACACACACA,T,TCACACACACACACACACACACACA 1449.84 PASS AC=0,0,1,0,0,0,0;AF=0.091,0.045,0.227,0.091,0.045,0.045,0.045;AN=2;DP=656;set=variant3-variant5-variant16-variant22-variant23-variant25-variant28-variant30-variant34-variant36-variant44 GT:DP:GQ:SB 0/3:44:99:19,8,12,5 chr1 38334317 . T A 955.29 PASS AC=1;AF=0.5;AN=2;DP=805;MQ=60;set=variant-variant3-variant5-variant9-variant16-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant36-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,28:48:99:1116,0,1178:6,14,9,19 chr1 38334318 . C A 955.29 PASS AC=1;AF=0.5;AN=2;DP=790;MQ=60;set=variant-variant3-variant5-variant9-variant16-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant36-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,28:48:99:1116,0,1178:6,14,9,19 chr1 38338795 . A G 1733.34 PASS AC=2;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 1/1:0,107:107:99:3396,321,0:0,0,47,60 chr1 38345896 . A C 331.48 PASS AC=2;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 1/1:0,22:22:66:732,66,0:0,0,7,15 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 0/1:60,66:126:99:1409,0,1382:34,26,37,29 chr1 38352849 . G C 619.92 PASS AC=2;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 1/1:0,44:44:99:1389,132,0:0,0,18,26 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 0/1:11,9:20:99:291,0,401:1,10,1,8 chr1 38395409 . AT A 196.57 PASS AC=1;AF=0.6;AN=2;DP=128;MQ=60;set=variant3-variant10-variant20-variant23-variant27-variant28-variant29-variant30-variant32-variant40 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:53:140,0,53:1,2,1,5 chr1 38395411 . T A 205.61 PASS AC=1;AF=0.591;AN=2;DP=139;MQ=60;set=variant3-variant9-variant10-variant20-variant23-variant27-variant28-variant29-variant30-variant32-variant40 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:53:140,0,53:1,2,1,5 chr1 38395947 . A T 1574.79 PASS AC=2;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 1/1:0,102:102:99:2827,303,0:0,0,61,41 chr1 38397341 . G A 1289.55 PASS AC=2;AF=0.688;AN=2;DP=3145;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-variant29-variant31-variant32-variant33-variant34-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2869,261,0:0,0,45,43 chr1 38397369 . C T 2010.83 PASS AC=2;AF=0.688;AN=2;DP=4039;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-variant29-variant31-variant32-variant33-variant34-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,101:102:99:3288,294,0:1,0,54,47 chr1 38411350 . C T 872.95 PASS AC=1;AF=0.621;AN=2;DP=2138;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant32-variant33-variant34-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,35:56:99:1013,0,578:15,6,26,9 chr1 38411445 . G A 1991.37 PASS AC=1;AF=0.553;AN=2;DP=2850;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant11-variant12-variant14-variant16-variant18-variant23-variant24-variant25-variant26-variant33-variant34-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:48,69:117:99:1813,0,1043:24,24,31,38 chr1 38411651 . G A 731.17 PASS AC=1;AF=0.5;AN=2;DP=155;FractionInformativeReads=1;MQ=60;set=variant-variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:20,32:52:99:1049,0,581:9,11,13,19 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 1/1:0,10:10:30:320,30,0:0,0,5,5 chr1 38422950 . A T 478.43 PASS AC=1;AF=0.5;AN=2;DP=238;MQ=60;set=variant3-variant10-variant20-variant23-variant27-variant29-variant32-variant40 GT:AD:DP:GQ:PL:SB 0/1:12,14:26:99:370,0,278:5,7,6,8 chr1 38423588 . G A 587.74 PASS AC=1;AF=0.909;AN=2;DP=1296;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:15,19:34:99:469,0,328:7,8,7,12 chr1 38423853 . G C 459.74 PASS AC=1;AF=0.909;AN=2;DP=863;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:8,13:21:99:438,0,254:8,0,11,2 chr1 38425629 . CAAAA CAA,CA,CAAA,C 677 PASS AC=0,0,1,0;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 0/3:24:33:3,2,16,3 chr1 38425724 . T C 4173.76 PASS AC=1;AF=0.909;AN=2;DP=5769;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:79,52:131:99:1251,0,1787:44,35,28,24 chr1 38425895 . T C 2299.84 PASS AC=1;AF=0.909;AN=2;DP=3945;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:33,30:63:99:741,0,948:10,23,9,21 chr1 38442547 . G A 3662.97 PASS AC=1;AF=0.909;AN=2;DP=3833;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:38,45:83:99:1124,0,932:17,21,22,23 chr1 38447615 . G T 766.07 PASS AC=1;AF=0.886;AN=2;DP=854;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:175,0,154:2,4,1,5 chr1 38450367 . A G 2078.22 PASS AC=1;AF=0.909;AN=2;DP=3383;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:45,35:80:99:772,0,1005:20,25,15,20 chr1 38455389 . C T 531.12 PASS AC=1;AF=0.898;AN=2;DP=1311;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:10,14:24:99:373,0,288:3,7,6,8 chr1 38455891 . G C 1052.56 PASS AC=1;AF=0.672;AN=2;DP=3339;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-variant29-variant31-variant32-variant33-variant34-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:50,46:96:99:1182,0,1264:24,26,29,17 chr1 38462898 . T A 1165.33 PASS AC=1;AF=0.966;AN=2;DP=1648;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:11,10:21:99:387,0,598:7,4,5,5 chr1 38462905 . C G 1088.54 PASS AC=1;AF=0.966;AN=2;DP=1703;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:412,0,624:8,4,6,6 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 1/1:0,83:83:99:2680,247,0:0,0,52,31 chr1 38465191 . GC G 634.33 PASS AC=1;AF=0.5;AN=2;DP=130;MQ=60;set=variant3-variant23-variant25-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:345,0,435:5,9,3,9 chr1 38488626 . T C 690.95 PASS AC=1;AF=0.6;AN=2;DP=457;FractionInformativeReads=1;MQ=60;set=variant7-variant10-variant16-variant19-variant23-variant27-variant28-variant30-variant34-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,20:47:99:441,0,769:8,19,8,12 chr1 38490066 . CT CTT,CTTT,C 114.27 PASS AC=1,0,0;AF=0.481,0.019,0.037;AN=2;DP=762;set=variant-variant2-variant3-variant4-filterInvariant6-variant8-variant9-variant10-filterInvariant11-variant12-variant15-filterInvariant16-filterInvariant17-variant18-variant19-variant20-variant22-variant23-filterInvariant25-variant28-variant31-variant33-variant37-variant38-variant39-variant40-filterInvariant43 GT:DP:GQ:SB 0/1:13:66:0,6,0,7 chr1 38510267 . GTT GT,GTTT,G 58.56 PASS AC=1,0,0;AF=0.44,0.04,0.06;AN=2;DP=534;set=variant-variant5-variant7-variant8-filterInvariant10-filterInvariant12-variant16-variant17-variant19-variant20-variant21-filterInvariant22-variant23-variant25-variant26-variant28-filterInvariant29-variant30-variant32-variant33-variant37-variant38-variant40-variant41-variant42 GT:DP:GQ:SB 0/1:25:90:2,6,7,10 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 1/1:0,37:37:99:1406,111,0:0,0,19,18 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 1/1:0,133:133:99:3959,398,0:0,0,56,77 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 1/1:0,82:82:99:2731,245,0:0,0,55,27 chr1 39305002 . AT A,ATTT,ATT 624.88 PASS AC=0,0,1;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 0/3:84:99:19,32,13,20 chr1 39311617 . T G 886.19 PASS AC=1;AF=0.5;AN=2;DP=244;FractionInformativeReads=1;MQ=60;set=variant2-variant14-variant23-variant41 GT:AD:DP:GQ:PL:SB 0/1:29,28:57:99:784,0,845:20,9,20,8 chr1 39325063 . T C 585.12 PASS AC=1;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 0/1:28,17:45:99:389,0,624:15,13,6,11 chr1 39332322 . C T 271.67 PASS AC=1;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 0/1:5,4:9:99:150,0,160:4,1,4,0 chr1 39339449 . C T 1690.67 PASS AC=1;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 0/1:74,61:135:99:1410,0,1797:36,38,33,28 chr1 39339682 . T C 418 PASS AC=1;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 0/1:26,26:52:99:653,0,675:11,15,8,18 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 1/1:0,5:5:15:117,15,0:0,0,4,1 chr1 39340282 . C T 1527.67 PASS AC=1;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 0/1:62,64:126:99:1506,0,1525:36,26,34,30 chr1 39340504 . T G 1106.34 PASS AC=1;AF=0.5;AN=2;DP=709;MQ=60;set=variant2-variant12-variant14-variant23-variant28-variant30-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:43,43:86:99:1210,0,1059:21,22,20,23 chr1 39351659 . G A 1504.89 PASS AC=2;AF=0.955;AN=2;DP=2462;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1513,137,0:0,0,15,31 chr1 39352083 . T G 4621.13 PASS AC=1;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 0/1:130,134:264:99:3399,0,3235:66,64,64,70 chr1 39352271 . G T 2721.24 PASS AC=1;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 0/1:106,107:213:99:2624,0,2733:50,56,53,54 chr1 39352492 . G A 251.63 PASS AC=1;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 0/1:7,6:13:99:182,0,227:1,6,1,5 chr1 39361615 . G A 683.13 PASS AC=1;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 0/1:15,27:42:99:687,0,326:9,6,18,9 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 1/1:0,37:37:99:1190,111,0:0,0,13,24 chr1 39391986 . G C 1187.37 PASS AC=1;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 0/1:42,55:97:99:1495,0,1092:26,16,34,21 chr1 39392232 . G T 1206.03 PASS AC=1;AF=0.528;AN=2;DP=1097;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant8-variant9-variant12-variant14-variant15-variant16-variant20-variant21-variant23-variant24-variant26-variant33-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,26:62:99:622,0,970:13,23,8,18 chr1 39407589 . C A 406.4 PASS AC=1;AF=0.526;AN=2;DP=594;MQ=60;set=variant2-variant5-variant8-variant9-variant12-variant14-variant15-variant16-variant20-variant21-variant23-variant24-variant26-variant33-variant34-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,10:26:99:297,0,517:3,13,1,9 chr1 39457016 . C T 319.81 PASS AC=2;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 1/1:0,26:26:78:795,78,0:0,0,12,14 chr1 39457293 . T C 209.2 PASS AC=2;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 1/1:0,10:10:30:313,30,0:0,0,3,7 chr1 39466626 . A G 380.65 PASS AC=2;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 1/1:0,37:37:99:1170,111,0:0,0,24,13 chr1 39466786 . C G 580.07 PASS AC=2;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 1/1:0,75:75:99:2337,225,0:0,0,35,40 chr1 39466955 . CTTT CTT,C,CT,CTTTTT 73.48 PASS AC=0,0,1,0;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 0/3:5:42:1,1,0,3 chr1 39471706 . T A 460.53 PASS AC=2;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 1/1:0,24:24:72:769,72,0:0,0,7,17 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 1/1:0,41:41:99:1214,123,0:0,0,25,16 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 1/1:0,105:105:99:2911,313,0:0,0,47,58 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 0/1:52:99:5,13,12,22 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 1/1:0,39:39:99:1670,117,0:0,0,7,32 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 1/1:0,10:10:30:385,30,0:0,0,1,9 chr1 39500186 . G A 118.93 PASS AC=1;AF=0.5;AN=2;DP=206;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant19-variant20-variant23-variant25-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:7,14:21:99:429,0,212:0,7,4,10 chr1 39549983 . G A 4357.57 PASS AC=2;AF=0.583;AN=2;DP=9639;MQ=60;set=variant-variant4-variant6-variant10-variant11-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant26-variant27-variant32-variant33-variant37-variant38 GT:AD:DP:GQ:PL:SB 1/1:4,463:467:99:13489,1295,0:1,3,217,246 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 1/1:0,15:15:45:647,45,0:0,0,1,14 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 0/1:3,4:7:99:159,0,116:2,1,4,0 chr1 39568765 . T C 14504.3 PASS AC=1;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 0/1:181,158:339:99:3561,0,4191:98,83,86,72 chr1 39715857 . C CA 999.91 PASS AC=1;AF=0.5;AN=2;DP=64;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.298;QD=15.62;ReadPosRankSum=-0.747;SOR=0.583;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:30,34:64:99:1037,0,918:8,22,10,24 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 1/1:0,43:43:99:1339,128,0:0,0,17,26 chr1 39735094 . G A 961.61 PASS AC=1;AF=0.5;AN=2;DP=64;FS=2.073;FractionInformativeReads=1;MQ=60;MQRankSum=0.521;QD=15.03;ReadPosRankSum=0.034;SOR=0.46;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:28,36:64:99:990,0,741:12,16,18,18 chr1 39748921 . G A 746.2 PASS AC=1;AF=0.744;AN=2;DP=3198;FractionInformativeReads=1;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-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,24:68:99:578,0,1263:25,19,14,10 chr1 39751172 . CTT CT,CTTT,C 461.92 PASS AC=1,0,0;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 0/1:29:99:11,10,5,3 chr1 39758569 . A G 1740.3 PASS AC=1;AF=0.5;AN=2;DP=122;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.172;QD=14.26;ReadPosRankSum=1.838;SOR=0.683;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:49,73:122:99:1769,0,986:25,24,36,37 chr1 39758993 . C G 85.48 PASS AC=1;AF=0.778;AN=2;DP=300;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,2:7:69:69,0,199:5,0,2,0 chr1 39763242 . G A 2129.81 PASS AC=1;AF=0.744;AN=2;DP=5544;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-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,56:123:99:1200,0,1607:41,26,36,20 chr1 39766055 . C T 796.96 PASS AC=1;AF=0.744;AN=2;DP=2530;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-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,27:51:99:582,0,550:11,13,11,16 chr1 39766138 . TA T 239.66 PASS AC=1;AF=0.5;AN=2;DP=66;FS=0;MQ=60;set=variant-variant10-variant23-variant34-variant39 GT:AD:DP:GQ:PL:SB 0/1:2,8:10:37:245,0,37:0,2,2,6 chr1 39796844 . CTTTTTTTTTTTTTT CT,CTTT,CTT,C,CTTTTTTTTTTTTT,CTTTT,CTTTTTTTTTTT 141.85 PASS AC=0,1,0,0,0,0,0;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 0/2:18:99:2,2,8,6 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 1/1:0,26:26:78:806,78,0:0,0,8,18 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 1/1:0,72:72:99:2181,216,0:0,0,45,27 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 1/1:0,121:121:99:3828,361,0:0,0,57,64 chr1 39815409 . A G 203.4 PASS AC=1;AF=0.5;AN=2;DP=10;FS=3.979;FractionInformativeReads=1;MQ=60;MQRankSum=0.633;QD=20.34;ReadPosRankSum=-0.365;SOR=2.584;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:232,0,144:1,3,0,6 chr1 39816863 . G A 409.47 PASS AC=1;AF=0.5;AN=2;DP=28;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.503;QD=14.62;ReadPosRankSum=-0.887;SOR=0.622;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:10,18:28:99:438,0,227:3,7,6,12 chr1 39824718 . C G 106.42 PASS AC=1;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 0/1:4,9:13:99:322,0,144:4,0,8,1 chr1 39826391 . A ATTAT 199.07 PASS AC=1;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 0/1:5,4:9:99:153,0,240:4,1,4,0 chr1 39843958 . G A 305.06 PASS AC=1;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 0/1:7,13:20:99:352,0,152:5,2,9,4 chr1 39879366 . T C 408.98 PASS AC=1;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 0/1:16,29:45:99:896,0,395:3,13,16,13 chr1 39881040 . G C 1143.65 PASS AC=1;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 0/1:18,21:39:99:671,0,590:2,16,4,17 chr1 39882001 . C G 1331.53 PASS AC=1;AF=0.5;AN=2;DP=233;FractionInformativeReads=1;MQ=60;set=variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:63,49:112:99:1360,0,1605:21,42,12,37 chr1 39889677 . G A 698.91 PASS AC=1;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 0/1:24,24:48:99:566,0,635:13,11,14,10 chr1 39893093 . C T 567.85 PASS AC=1;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 0/1:26,28:54:99:734,0,571:14,12,19,9 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 1/1:0,18:18:54:704,54,0:0,0,16,2 chr1 39895460 . G A 631.1 PASS AC=1;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 0/1:29,28:57:99:607,0,717:17,12,15,13 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 0/1:39:71:17,12,7,3 chr1 39908506 . G A 404.72 PASS AC=1;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 0/1:42,30:72:99:748,0,1041:24,18,16,14 chr1 39908726 . A G 230.53 PASS AC=1;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 0/1:2,4:6:73:159,0,73:0,2,0,4 chr1 39914363 . G C 1108.19 PASS AC=1;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 0/1:70,35:105:99:649,0,1718:38,32,17,18 chr1 39919346 . T G 451.24 PASS AC=1;AF=0.5;AN=2;DP=92;FractionInformativeReads=1;MQ=60;set=variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:30,18:48:99:479,0,773:20,10,12,6 chr1 39927507 . G A 1786.71 PASS AC=2;AF=0.989;AN=2;DP=1503;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:913,75,0:0,0,19,6 chr1 39929240 . T C 767.23 PASS AC=1;AF=0.756;AN=2;DP=3137;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-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,34:68:99:761,0,752:19,15,21,13 chr1 39929582 . G A 117.8 PASS AC=1;AF=0.5;AN=2;DP=32;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:17,6:23:99:146,0,485:5,12,1,5 chr1 39951742 . TA T,TAA 1486.22 PASS AC=1,0;AF=0.167,0.333;AN=2;DP=586;MQ=60;set=variant23-variant26-variant27 GT:DP:GQ:SB 0/1:176:99:45,53,40,38 chr1 39952745 . G A 2090.72 PASS AC=1;AF=0.5;AN=2;DP=325;FractionInformativeReads=1;MQ=60;set=variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:73,82:155:99:2119,0,1951:26,47,28,54 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 0/1:38,35:73:99:944,0,1001:12,26,11,24 chr1 39957268 . G A 254.2 PASS AC=1;AF=0.5;AN=2;DP=28;FS=2.208;FractionInformativeReads=1;MQ=60;MQRankSum=-0.36;QD=9.08;ReadPosRankSum=-0.935;SOR=0.247;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:18,10:28:99:282,0,549:16,2,8,2 chr1 39957913 . A G 7354.32 PASS AC=1;AF=0.909;AN=2;DP=20590;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:212,220:432:99:5093,0,4818:119,93,120,100 chr1 39981462 . G T 1620.1 PASS AC=1;AF=0.5;AN=2;DP=93;FS=1.945;FractionInformativeReads=1;MQ=46.35;MQRankSum=4.484;QD=17.42;ReadPosRankSum=-0.533;SOR=1.002;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:25,68:93:99:1648,0,341:12,13,28,40 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 0/1:110,23:133:99:296,0,2546:62,48,11,12 chr1 39988913 . CAG C 1802.26 PASS AC=1;AF=0.5;AN=2;DP=134;FS=0;FractionInformativeReads=0.963;MQ=60;MQRankSum=-1.216;QD=13.45;ReadPosRankSum=0.138;SOR=0.731;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:79,50:129:99:1840,0,3172:34,45,21,29 chr1 39991474 . A C 2554.8 PASS AC=1;AF=0.5;AN=2;DP=3893;FractionInformativeReads=1;set=variant-variant4-variant9-variant11-variant12-variant15-variant17-variant22-variant23-variant24-variant26-variant29-variant32-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:111,127:238:99:4823,0,5287:57,54,63,64 chr1 39991475 . G A 2554.8 PASS AC=1;AF=0.5;AN=2;DP=3891;FractionInformativeReads=1;set=variant-variant4-variant9-variant11-variant12-variant15-variant17-variant22-variant23-variant24-variant26-variant29-variant32-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:113,125:238:99:4823,0,5287:58,55,61,64 chr1 39991588 . G T 1433.13 PASS AC=2;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 1/1:2,149:151:99:4662,402,0:1,1,52,97 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 0/1:67,57:124:99:1498,0,1644:25,42,22,35 chr1 40033651 . C T 543.59 PASS AC=1;AF=0.5;AN=2;DP=33;FS=1.624;FractionInformativeReads=1;MQ=60;MQRankSum=0.919;QD=16.47;ReadPosRankSum=0.847;SOR=1.125;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:572,0,435:4,12,3,14 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 0/1:26,22:48:99:478,0,644:9,17,12,10 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 0/1:13,13:26:99:422,0,462:12,1,7,6 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 0/1:3,13:16:89:334,0,89:1,2,6,7 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 0/1:29,24:53:99:693,0,875:26,3,20,4 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 0/1:12,7:19:99:258,0,827:5,7,3,4 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 1/1:0,64:64:99:1878,192,0:0,0,31,33 chr1 40089999 . G A 929.35 PASS AC=1;AF=0.5;AN=2;DP=69;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.078;QD=13.47;ReadPosRankSum=1.125;SOR=0.629;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:32,37:69:99:958,0,779:17,15,19,18 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 1/1:0,104:104:99:3108,311,0:0,0,59,45 chr1 40097136 . T C 1439.15 PASS AC=1;AF=0.65;AN=2;DP=489;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant14-variant19-variant22-variant23-variant30-variant34-variant40 GT:AD:DP:GQ:PL:SB 0/1:19,14:33:99:356,0,434:11,8,10,4 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 0/1:6,2:8:66:66,0,189:4,2,2,0 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 1/1:0,49:49:99:1463,147,0:0,0,24,25 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 0/1:60,42:102:99:959,0,1405:27,33,20,22 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 0/1:33,51:84:99:2119,0,1597:11,22,23,28 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 0/1:60,56:116:99:1389,0,1623:19,41,20,36 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 0/1:36,35:71:99:932,0,878:17,19,19,16 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 0/1:23,30:53:99:704,0,571:13,10,16,14 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 0/1:24,21:45:99:605,0,543:14,10,14,7 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 0/1:24,25:49:99:741,0,619:16,8,19,6 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 0/1:37,45:82:99:1261,0,913:24,13,32,13 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 0/1:99,107:206:99:2741,0,2587:63,36,62,45 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 0/1:18,30:48:99:1113,0,608:0,18,0,30 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 0/1:5,4:9:99:142,0,227:0,5,0,4 chr1 40149971 . G A 174 PASS AC=1;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 0/1:5,2:7:69:69,0,193:3,2,1,1 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 0/1:18,20:38:99:562,0,406:7,11,6,14 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 0/1:84,68:152:99:1673,0,1951:42,42,38,30 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 0/1:53,59:112:99:1332,0,1401:23,30,25,34 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 0/1:11,12:23:99:419,0,527:1,10,3,9 chr1 40207169 . T G 973.03 PASS AC=1;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 0/1:35,24:59:99:603,0,868:15,20,8,16 chr1 40219280 . T C 2099.49 PASS AC=1;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 0/1:24,34:58:99:945,0,552:10,14,16,18 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 0/1:100,84:184:99:2123,0,2594:37,63,38,46 chr1 40228185 . T C 1638.58 PASS AC=1;AF=0.5;AN=2;DP=122;FS=1.516;FractionInformativeReads=0.992;MQ=60;MQRankSum=-0.129;QD=13.43;ReadPosRankSum=1.677;SOR=0.519;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:50,71:121:99:1667,0,1202:32,18,42,29 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 0/1:128,111:239:99:2818,0,2772:68,60,72,39 chr1 40253726 . C T 1507.47 PASS AC=1;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 0/1:87,37:124:99:950,0,2332:56,31,29,8 chr1 40253768 . C CA 5320.45 PASS AC=1;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 0/1:149,94:243:99:3550,0,7103:85,64,63,31 chr1 40253770 . C T 5363.87 PASS AC=1;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 0/1:151,96:247:99:3550,0,7103:86,65,65,31 chr1 40253786 . C T 6004.05 PASS AC=1;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 0/1:173,132:305:99:2877,0,4199:97,76,80,52 chr1 40254522 . G A 417.84 PASS AC=1;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 0/1:38,41:79:99:886,0,927:14,24,19,22 chr1 40319587 . A C 2902.21 PASS AC=1;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 0/1:42,52:94:99:1313,0,1142:26,16,31,21 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 0/1:12,8:20:99:248,0,317:3,9,2,6 chr1 40349410 . T C 376.77 PASS AC=1;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 0/1:4,2:6:72:72,0,123:1,3,0,2 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 0/1:20,21:41:99:562,0,464:8,12,8,13 chr1 40363054 . G C 4297.35 PASS AC=2;AF=0.909;AN=2;DP=5869;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:2920,282,0:0,0,47,47 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 1/1:0,115:115:99:3220,343,0:0,0,59,56 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 0/1:19,8:27:99:238,0,535:9,10,5,3 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 1/1:1,73:74:99:2111,193,0:1,0,40,33 chr1 40506239 . G A 1623.78 PASS AC=1;AF=0.729;AN=2;DP=4800;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,72:143:99:1682,0,1891:36,35,36,36 chr1 40524866 . T C 1503.52 PASS AC=1;AF=0.825;AN=2;DP=3308;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-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,37:68:99:899,0,779:18,13,24,13 chr1 40526003 . T C 329.95 PASS AC=1;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 0/1:10,10:20:99:296,0,263:3,7,3,7 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 1/1:0,44:44:99:1855,135,0:0,0,24,20 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 1/1:0,46:46:99:1952,138,0:0,0,24,22 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 1/1:0,46:46:99:2105,147,0:0,0,18,28 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 1/1:0,45:45:99:2106,141,0:0,0,19,26 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 1/1:0,46:46:99:2113,141,0:0,0,18,28 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 1/1:0,47:47:99:2043,144,0:0,0,17,30 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 1/1:0,110:110:99:4520,340,0:0,0,54,56 chr1 40539076 . C T 45.01 PASS AC=1;AF=0.825;AN=2;DP=1376;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-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,20:32:99:513,0,319:5,7,10,10 chr1 40539203 . A ATGAT 184.52 PASS AC=1;AF=0.8;AN=2;DP=1119;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-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,11:32:99:431,0,1235:11,10,5,6 chr1 40539228 . G C 147.06 PASS AC=1;AF=0.825;AN=2;DP=1314;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-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,12:37:99:320,0,604:12,13,6,6 chr1 40539448 . A C 2128.31 PASS AC=1;AF=0.825;AN=2;DP=5611;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-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,49:104:99:1284,0,1357:35,20,30,19 chr1 40548094 . CA CAA,C 73.89 PASS AC=0,2;AF=0.583,0.083;AN=2;DP=103;FS=0;MQ=60;set=variant3-variant4-variant5-variant7-variant13-variant19-variant23-variant24-variant29-variant39-variant40-variant44 GT:DP:GQ:SB 2/2:5:15:0,0,2,3 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 1/1:0,90:90:99:3014,270,0:0,0,56,34 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 1/1:0,25:25:75:856,75,0:0,0,5,20 chr1 40559831 . G A 505.59 PASS AC=1;AF=0.7;AN=2;DP=171;FractionInformativeReads=1;MQ=60;set=variant14-variant23-variant27-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:13,24:37:99:589,0,260:6,7,11,13 chr1 40562993 . T C 351.79 PASS AC=1;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 0/1:18,22:40:99:629,0,532:5,13,8,14 chr1 40705726 . A T 1477.58 PASS AC=2;AF=0.625;AN=2;DP=1231;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant11-variant13-variant14-variant22-variant23-variant25-variant27-variant36-variant37 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2497,247,0:0,0,45,38 chr1 40733658 . A G 309.79 PASS AC=2;AF=0.594;AN=2;DP=412;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant11-variant13-variant14-variant19-variant22-variant23-variant25-variant27-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:80:874,80,0:0,0,8,19 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 1/1:0,27:27:81:954,81,0:0,0,21,6 chr1 40777138 . CTG C 146.08 PASS AC=1;AF=0.5;AN=2;DP=13;FS=6.368;FractionInformativeReads=1;MQ=60;MQRankSum=0.696;QD=11.24;ReadPosRankSum=2.313;SOR=2.833;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:183,0,315:3,5,0,5 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 0/2:36:99:11,15,4,6 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 0/1:53,31:84:99:528,0,878:12,41,31,0 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 0/1:61,27:88:99:196,0,1731:17,44,27,0 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 0/1:12,8:20:99:173,0,476:10,2,6,2 chr1 40840296 . T A,TGA,TGTGA 973.38 PASS AC=1,1,0;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 1/2:22:99:2,0,15,5 chr1 40879636 . T C 460.98 PASS AC=1;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 0/1:6,2:8:66:66,0,181:5,1,2,0 chr1 40879808 . G T,C 2011.23 PASS AC=1,0;AF=0.898,0.068;AN=2;DP=3576;MQ=60;set=Intersection GT:DP:GQ:SB 0/1:68:99:23,13,16,16 chr1 40881041 . C G 4550.02 PASS AC=1;AF=0.92;AN=2;DP=6688;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:84,42:126:99:854,0,2080:37,47,18,24 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 0/1:57:99:9,17,14,17 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 1/1:0,70:70:99:2148,210,0:0,0,43,27 chr1 40955156 . A T 345.04 PASS AC=1;AF=0.62;AN=2;DP=1249;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant12-variant13-variant14-variant16-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant28-variant30-variant33-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,19:36:99:541,0,442:8,9,13,6 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 1/1:0,35:35:99:1105,105,0:0,0,16,19 chr1 40980668 . T C 1476.53 PASS AC=1;AF=0.5;AN=2;DP=448;FractionInformativeReads=1;MQ=60;set=variant14-variant23-variant25-variant43 GT:AD:DP:GQ:PL:SB 0/1:60,54:114:99:1431,0,1563:29,31,27,27 chr1 41087734 . C T 671.22 PASS AC=1;AF=0.526;AN=2;DP=1049;MQ=60;set=variant2-variant3-variant5-variant10-variant11-variant13-variant16-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant31-variant32-variant37-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,23:50:99:560,0,645:13,14,9,14 chr1 41089965 . G A 477.67 PASS AC=1;AF=0.5;AN=2;DP=44;FS=4.42;FractionInformativeReads=1;MQ=60;MQRankSum=-0.9;QD=10.86;ReadPosRankSum=-3.554;SOR=0.811;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:25,19:44:99:506,0,640:10,15,11,8 chr1 41090250 . A G 438.52 PASS AC=1;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 0/1:18,14:32:99:409,0,533:10,8,5,9 chr1 41091127 . T C 328.38 PASS AC=1;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 0/1:21,25:46:99:625,0,521:11,10,15,10 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 0/1:13,12:25:99:377,0,376:9,4,10,2 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 0/1:23,13:36:99:333,0,654:12,11,5,8 chr1 41101572 . A G 523.55 PASS AC=1;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 0/1:32,21:53:99:537,0,859:21,11,10,11 chr1 41107360 . T C 2240.71 PASS AC=1;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 0/1:136,109:245:99:2456,0,3199:73,63,55,54 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 0/1:53,45:98:99:1114,0,1269:20,33,23,22 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 0/1:17,22:39:99:545,0,478:4,13,8,14 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 0/1:19,14:33:99:418,0,610:10,9,7,7 chr1 41177943 . T C 1025.65 PASS AC=1;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 0/1:24,23:47:99:723,0,758:20,4,19,4 chr1 41178228 . AT A 540.14 PASS AC=1;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 0/1:19,9:28:99:170,0,450:4,15,2,7 chr1 41188915 . A G 124.38 PASS AC=1;AF=0.529;AN=2;DP=531;MQ=60;set=variant-variant2-variant7-variant14-variant15-variant18-variant19-variant21-variant23-variant24-variant31-variant32-variant33-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,13:29:99:269,0,395:7,9,7,6 chr1 41201257 . C G 435.11 PASS AC=1;AF=0.529;AN=2;DP=920;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant7-variant14-variant15-variant18-variant19-variant21-variant23-variant24-variant31-variant32-variant33-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,20:42:99:540,0,530:11,11,12,8 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 0/1:39,35:74:99:1031,0,1027:20,19,15,20 chr1 41224008 . C T 103.93 PASS AC=1;AF=0.529;AN=2;DP=703;MQ=60;set=variant-variant2-variant7-variant14-variant15-variant18-variant19-variant21-variant23-variant24-variant31-variant32-variant33-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,22:44:99:493,0,499:10,12,10,12 chr1 41232194 . T C 135.18 PASS AC=1;AF=0.531;AN=2;DP=259;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant14-variant15-variant18-variant19-variant21-variant23-variant24-variant31-variant32-variant33-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:153,0,151:4,0,4,0 chr1 41236837 . CT C,CTT 1653.95 PASS AC=1,0;AF=0.5,0.026;AN=2;DP=3299;MQ=60;set=variant-variant2-variant7-variant9-variant14-variant15-variant18-variant19-variant20-variant21-variant23-variant24-variant31-variant32-variant33-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:160:99:48,36,40,36 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 0/1:20,14:34:99:383,0,588:6,14,3,11 chr1 41284366 . G C 980.79 PASS AC=1;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 0/1:46,39:85:99:997,0,1263:16,30,16,23 chr1 41284406 . A G 491.66 PASS AC=1;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 0/1:32,21:53:99:507,0,812:12,20,7,14 chr1 41285087 . T C 2431.51 PASS AC=1;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 0/1:180,146:326:99:3435,0,4171:88,92,68,78 chr1 41285171 . C A 1911.54 PASS AC=1;AF=0.5;AN=2;DP=3468;MQ=60;set=variant-variant2-variant3-variant10-variant13-variant14-variant15-variant16-variant18-variant23-variant29-variant30-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:75,92:167:99:2213,0,1955:28,47,39,53 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 0/1:6,14:20:99:346,0,131:4,2,8,6 chr1 41289993 . T C 1605.58 PASS AC=1;AF=0.543;AN=2;DP=2701;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant10-variant11-variant15-variant16-variant18-variant22-variant23-variant24-variant25-variant30-variant31-variant32-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,55:111:99:1199,0,1206:25,31,27,28 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 1/1:0,133:133:99:3982,398,0:0,0,78,55 chr1 41301019 . T C 125.41 PASS AC=1;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 0/1:8,3:11:61:61,0,327:3,5,1,2 chr1 41301034 . G C 74.42 PASS AC=1;AF=0.5;AN=2;DP=72;FractionInformativeReads=1;MQ=60;set=variant8-variant15-variant17-variant18-variant20-variant23-variant29-variant30 GT:AD:DP:GQ:PL:SB 0/1:3,8:11:99:243,0,102:1,2,3,5 chr1 41305217 . A T 1659.74 PASS AC=1;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 0/1:34,27:61:99:711,0,821:18,16,14,13 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 0/1:31,44:75:99:1126,0,750:14,17,23,21 chr1 41328050 . C T 768.54 PASS AC=1;AF=0.531;AN=2;DP=607;MQ=60;set=variant4-variant9-variant11-variant19-variant20-variant21-variant23-variant25-variant29-variant30-variant32-variant33-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,17:31:99:408,0,324:5,9,6,11 chr1 41449291 . CT C,CTT 265.85 PASS AC=0,1;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 0/2:13:75:1,5,0,7 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 1/1:0,43:43:99:1579,129,0:0,0,10,33 chr1 41478285 . G A 94.73 PASS AC=1;AF=0.5;AN=2;DP=9;FS=0;FractionInformativeReads=1;MQ=60;SOR=1.609;set=variant-variant23 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:75:75,0,76:1,2,0,2 chr1 41487404 . G T 621.88 PASS AC=2;AF=0.688;AN=2;DP=481;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant11-variant14-variant23-variant29-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1846,165,0:0,0,25,30 chr1 41540853 . A T 4040.78 PASS AC=2;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 1/1:0,101:101:99:4598,313,0:0,0,63,38 chr1 41540861 . T C 4235.78 PASS AC=2;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 1/1:0,111:111:99:4755,334,0:0,0,66,45 chr1 41618442 . A T 1140.11 PASS AC=2;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 1/1:0,33:33:99:958,99,0:0,0,12,21 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 1/1:0,17:17:51:515,51,0:0,0,7,10 chr1 41847881 . CCA C,CGGGACA,CGGGACGCCCGCCTACTTCGGCGGCTGCA 214.6 PASS AC=1,0,0;AF=0.3,0.1,0.1;AN=2;DP=87;set=variant14-variant23-variant28-variant33-variant37 GT:DP:GQ:SB 0/1:19:99:0,9,2,8 chr1 41847884 . G GGGAC 211.59 PASS AC=1;AF=0.5;AN=2;DP=43;FractionInformativeReads=1;set=variant14-variant23-variant37 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:348,0,1725:0,10,2,8 chr1 41847887 . C CCGCCTACTTCGGCGGCTGCAAGGG 103.6 PASS AC=1;AF=0.5;AN=2;DP=40;FractionInformativeReads=1;set=variant14-variant23-variant37 GT:AD:DP:GQ:PL:SB 0/1:10,7:17:99:264,0,1734:0,10,0,7 chr1 41848060 . C T 769.14 PASS AC=2;AF=0.643;AN=2;DP=2183;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2218,212,0:0,0,46,25 chr1 41848296 . G A 1822.14 PASS AC=2;AF=0.643;AN=2;DP=8765;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:3,233:236:99:6411,655,0:0,3,101,132 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 1/1:0,31:31:93:1122,93,0:0,0,18,13 chr1 41849340 . A C 34.68 PASS AC=2;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 1/1:0,12:12:36:366,36,0:0,0,4,8 chr1 41944690 . C T 1085.32 PASS AC=1;AF=0.538;AN=2;DP=889;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant10-variant15-variant20-variant21-variant23-variant28-variant36-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,26:59:99:642,0,926:16,17,12,14 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 1/1:0,62:62:99:1963,186,0:0,0,39,23 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 0/1:30,43:73:99:1179,0,777:14,16,26,17 chr1 41950312 . T C 4189.37 PASS AC=1;AF=0.943;AN=2;DP=5966;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:68,68:136:99:1748,0,1592:29,39,23,45 chr1 41950473 . G A 57.81 PASS AC=1;AF=0.593;AN=2;DP=356;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:100,0,119:0,3,0,3 chr1 41972198 . A T 4969.69 PASS AC=1;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 0/1:153,133:286:99:3166,0,3768:80,73,70,63 chr1 41972270 . TTTTTG T 2712.91 PASS AC=1;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 0/1:148,123:271:99:2628,0,5738:72,76,67,56 chr1 41972283 . C T 3405.85 PASS AC=1;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 0/1:140,148:288:99:5433,0,5559:66,74,80,68 chr1 41972555 . GTTTCT G 7604.85 PASS AC=1;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 0/1:162,154:316:99:5843,0,7678:66,96,68,86 chr1 41973095 . A G 1768.27 PASS AC=1;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 0/1:42,45:87:99:1083,0,893:24,18,20,25 chr1 41973908 . C T 280.37 PASS AC=1;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 0/1:10,14:24:99:375,0,219:4,6,8,6 chr1 41974258 . G A 669.6 PASS AC=1;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 0/1:24,25:49:99:665,0,633:12,12,15,10 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 1/1:0,109:109:99:3232,327,0:0,0,64,45 chr1 41975493 . CAAAA CA,CAAA,C 259.94 PASS AC=0,1,0;AF=0.286,0.214,0.071;AN=2;DP=122;set=variant4-variant5-variant20-variant23-variant29-variant32-variant43 GT:DP:GQ:SB 0/2:13:64:3,3,6,1 chr1 41976017 . C T 4322.4 PASS AC=1;AF=0.703;AN=2;DP=5886;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,70:161:99:1581,0,2142:47,44,36,34 chr1 41976217 . G A 680.84 PASS AC=1;AF=0.5;AN=2;DP=701;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant12-variant14-variant21-variant23-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:36,32:68:99:755,0,935:15,21,13,19 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 1/1:0,64:64:99:2101,192,0:0,0,34,30 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 1/1:0,9:9:27:321,27,0:0,0,7,2 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 1/1:0,102:102:99:3111,305,0:0,0,54,48 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 1/1:0,276:276:99:8516,825,0:0,0,146,130 chr1 41979156 . A G 3354.13 PASS AC=1;AF=0.613;AN=2;DP=4047;MQ=60;set=variant-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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,36:72:99:954,0,957:14,22,17,19 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 1/1:0,62:62:99:1894,184,0:0,0,42,20 chr1 42041479 . A C 1146.41 PASS AC=1;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 0/1:44,40:84:99:958,0,1017:19,25,21,19 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 1/1:0,22:22:66:756,66,0:0,0,15,7 chr1 42045770 . G A 1752.25 PASS AC=1;AF=0.5;AN=2;DP=144;FS=2.098;FractionInformativeReads=1;MQ=60;MQRankSum=0.26;QD=12.17;ReadPosRankSum=1.167;SOR=0.556;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:73,71:144:99:1780,0,1882:40,33,35,36 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 1/1:1,38:39:99:1054,104,0:1,0,18,20 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 1/1:0,129:129:99:4250,387,0:0,0,54,75 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 1/1:1,77:78:99:2612,223,0:0,1,44,33 chr1 42049140 . C G 6720.74 PASS AC=2;AF=0.977;AN=2;DP=10044;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,175:175:99:5637,525,0:0,0,105,70 chr1 42094320 . A G 276.33 PASS AC=1;AF=0.5;AN=2;DP=15;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.766;QD=18.42;ReadPosRankSum=-0.53;SOR=0.582;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:305,0,174:5,1,7,2 chr1 42094498 . A G 457.09 PASS AC=1;AF=0.611;AN=2;DP=2723;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,30:71:99:758,0,1026:20,21,12,18 chr1 42166782 . G A 258.35 PASS AC=1;AF=0.543;AN=2;DP=338;MQ=60;set=variant2-variant4-variant5-variant6-variant9-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant23-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,8:15:99:234,0,256:0,7,3,5 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 1/1:0,125:125:99:3961,374,0:0,0,63,62 chr1 42630364 . G A 1695.93 PASS AC=2;AF=0.629;AN=2;DP=2592;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2178,223,0:0,0,39,36 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 0/1:110,86:196:99:2172,0,2865:40,70,37,49 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 0/1:23,24:47:99:580,0,546:15,8,15,9 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 0/1:18,11:29:99:362,0,495:14,4,10,1 chr1 42693597 . A G 4990.59 PASS AC=1;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 0/1:70,54:124:99:1294,0,1788:32,38,23,31 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 1/1:0,114:114:99:3693,340,0:0,0,74,40 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 0/1:1,14:15:1:331,0,1:0,1,7,7 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 0/1:16,13:29:99:399,0,425:10,6,9,4 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 0/1:23,23:46:99:877,0,1205:10,13,10,13 chr1 42846365 . T C 111.22 PASS AC=1;AF=0.714;AN=2;DP=393;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,14:23:99:301,0,175:4,5,7,7 chr1 42846786 . G C 1058.07 PASS AC=1;AF=0.689;AN=2;DP=3700;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:38,53:91:99:1157,0,757:16,22,24,29 chr1 42880516 . T C 1977.74 PASS AC=1;AF=0.676;AN=2;DP=5757;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:86,64:150:99:1672,0,2274:47,39,35,29 chr1 42880841 . T TCA 6469.6 PASS AC=1;AF=0.676;AN=2;DP=12924;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-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:146,130:276:99:4982,0,5728:64,82,59,71 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 1/1:0,246:246:99:7601,736,0:0,0,104,142 chr1 42898843 . A G 3396.56 PASS AC=2;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 1/1:1,121:122:99:3449,354,0:0,1,71,50 chr1 42915727 . C G 1531.52 PASS AC=2;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 1/1:0,130:130:99:3866,389,0:0,0,66,64 chr1 42915753 . T C 1368.73 PASS AC=2;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 1/1:0,108:108:99:3437,323,0:0,0,48,60 chr1 42921211 . C G 294.08 PASS AC=2;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 1/1:0,11:11:33:355,33,0:0,0,8,3 chr1 42925688 . T G 6263.37 PASS AC=2;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 1/1:1,449:450:99:12990,1335,0:0,1,220,229 chr1 42948585 . C A 258.86 PASS AC=2;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 1/1:0,19:19:60:769,60,0:0,0,4,15 chr1 43002744 . G A 797.68 PASS AC=2;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 1/1:0,58:58:99:1805,174,0:0,0,36,22 chr1 43011030 . A G 203.25 PASS AC=2;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 1/1:0,5:5:15:173,15,0:0,0,4,1 chr1 43011389 . A G 88.71 PASS AC=2;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 1/1:0,5:5:15:217,15,0:0,0,0,5 chr1 43021698 . G T 124.71 PASS AC=2;AF=0.692;AN=2;DP=96;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant7-variant10-variant14-variant22-variant23-variant24-variant28-variant32-variant37-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,4,0 chr1 43021810 . C T 427.43 PASS AC=2;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 1/1:0,36:36:99:1147,108,0:0,0,25,11 chr1 43023713 . G GA 630.78 PASS AC=2;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 1/1:1,38:39:86:1033,86,0:1,0,22,16 chr1 43030115 . C T 180.18 PASS AC=2;AF=0.778;AN=2;DP=68;FractionInformativeReads=1;set=variant7-variant10-variant14-variant18-variant22-variant23-variant24-variant28-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:167,12,0:0,0,4,0 chr1 43030158 . G A 58.54 PASS AC=2;AF=0.69;AN=2;DP=267;FractionInformativeReads=1;set=variant4-variant7-variant10-variant12-variant14-variant15-variant18-variant19-variant22-variant23-variant24-variant28-variant30-variant33-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:285,30,0:0,0,6,4 chr1 43030190 . A ACCTCAGGTGATCCACCCACCTCGG 211.53 PASS AC=2;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 1/1:0,15:15:73:1110,73,0:0,0,11,4 chr1 43042703 . C T 952.46 PASS AC=2;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 1/1:2,96:98:99:2869,243,0:1,1,58,38 chr1 43047057 . A G 276.7 PASS AC=2;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 1/1:0,32:32:96:952,96,0:0,0,21,11 chr1 43054909 . T C 91.49 PASS AC=2;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 1/1:0,5:5:15:196,15,0:0,0,5,0 chr1 43055243 . C G 186.39 PASS AC=2;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 1/1:0,14:14:42:539,42,0:0,0,3,11 chr1 43110276 . G A 264.05 PASS AC=2;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 1/1:0,19:19:57:675,57,0:0,0,14,5 chr1 43124701 . A G 271.42 PASS AC=2;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 1/1:0,20:20:60:758,60,0:0,0,9,11 chr1 43124859 . C T 1263.74 PASS AC=2;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 1/1:0,61:61:99:2036,182,0:0,0,38,23 chr1 43126733 . G A 2423.44 PASS AC=2;AF=0.6;AN=2;DP=1614;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant8-variant11-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant29-variant30-variant31-variant32-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2188,207,0:0,0,26,43 chr1 43126766 . C A 1168.74 PASS AC=2;AF=0.6;AN=2;DP=1020;MQ=60;set=variant2-variant5-variant6-variant8-variant11-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant29-variant30-variant31-variant32-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1371,126,0:0,0,13,29 chr1 43132393 . G GA 592.5 PASS AC=2;AF=0.629;AN=2;DP=1623;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1802,153,0:0,0,12,39 chr1 43158943 . CT C 41.32 PASS AC=2;AF=0.625;AN=2;DP=110;FS=0;MQ=60;set=variant5-variant11-variant15-variant17-variant19-variant20-variant23-variant24-variant31-variant32-variant38-variant40 GT:AD:DP:GQ:PL:SB 1/1:1,6:7:2:113,2,0:1,0,5,1 chr1 43162182 . GC GCCC,G,GCC,GCCCC 258.4 PASS AC=0,0,1,0;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 0/3:9:2:2,0,3,4 chr1 43200526 . T C 995.33 PASS AC=2;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 1/1:0,64:64:99:2061,192,0:0,0,28,36 chr1 43201216 . A C 1324.27 PASS AC=2;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 1/1:0,77:77:99:2606,230,0:0,0,51,26 chr1 43212111 . C T 517.94 PASS AC=2;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 1/1:0,47:47:99:1556,140,0:0,0,33,14 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 1/1:0,120:120:99:3762,359,0:0,0,53,67 chr1 43213499 . C T 856.87 PASS AC=2;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 1/1:0,73:73:99:2203,219,0:0,0,30,43 chr1 43217458 . G A 466.35 PASS AC=1;AF=0.5;AN=2;DP=85;FractionInformativeReads=1;MQ=60;set=variant20-variant23 GT:AD:DP:GQ:PL:SB 0/1:23,17:40:99:381,0,574:15,8,12,5 chr1 43228189 . T A 2151.23 PASS AC=2;AF=0.989;AN=2;DP=3235;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:1932,193,0:0,0,24,41 chr1 43232807 . C G 393.51 PASS AC=2;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 1/1:0,62:62:99:2149,185,0:0,0,27,35 chr1 43232877 . A T 1008.75 PASS AC=2;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 1/1:0,78:78:99:2243,233,0:0,0,45,33 chr1 43239395 . G A 752.35 PASS AC=2;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 1/1:1,38:39:75:1382,75,0:0,1,5,33 chr1 43263489 . T C 759.48 PASS AC=2;AF=0.625;AN=2;DP=353;FractionInformativeReads=1;MQ=60;set=variant5-variant20-variant21-variant23 GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2333,239,0:0,0,43,37 chr1 43272824 . GT GTT,GTGTTTT,G 57.33 PASS AC=1,0,0;AF=0.344,0.063,0.094;AN=2;DP=296;MQ=60;set=variant-variant2-variant8-variant10-variant15-variant17-variant22-variant23-variant24-variant25-variant28-filterInvariant33-variant34-variant38-variant39-variant44 GT:DP:GQ:SB 0/1:8:45:2,1,4,1 chr1 43272841 . A T 321.11 PASS AC=2;AF=0.667;AN=2;DP=43;FS=0;MQ=60;set=variant5-variant20-variant23 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:35:354,35,0:0,0,6,6 chr1 43282455 . C T 537.67 PASS AC=2;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 1/1:0,54:54:99:1603,162,0:0,0,23,31 chr1 43296118 . G A 598.37 PASS AC=2;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 1/1:0,97:97:99:3086,289,0:0,0,56,41 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 0/1:4,10:14:56:152,0,56:3,1,7,3 chr1 43302971 . C G 121.44 PASS AC=2;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 1/1:0,9:9:27:344,27,0:0,0,2,7 chr1 43305753 . G A 1826.56 PASS AC=2;AF=0.567;AN=2;DP=1812;MQ=60;set=variant8-variant9-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant32-variant34-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:3576,355,0:0,0,66,53 chr1 43309383 . G GT 1235.45 PASS AC=2;AF=0.737;AN=2;DP=3574;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2529,235,0:0,0,45,32 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 1/1:0,199:199:99:6127,597,0:0,0,89,110 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 1/1:0,33:33:99:1008,99,0:0,0,19,14 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 1/1:0,18:18:54:581,54,0:0,0,11,7 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 1/1:0,89:89:99:3244,268,0:0,0,26,63 chr1 43315531 . T C 706.83 PASS AC=2;AF=0.567;AN=2;DP=436;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant32-variant34-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:1011,75,0:0,0,4,21 chr1 43391151 . A G 283.99 PASS AC=1;AF=0.5;AN=2;DP=25;FS=1.619;FractionInformativeReads=1;MQ=60;MQRankSum=-0.739;QD=11.36;ReadPosRankSum=2.108;SOR=0.33;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:11,14:25:99:312,0,224:7,4,7,7 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 0/1:3,2:5:99:117,0,182:3,0,2,0 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 0/1:29,34:63:99:891,0,877:9,20,13,21 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 0/1:5,7:12:99:230,0,109:2,3,2,5 chr1 43418026 . C T 656.13 PASS AC=2;AF=0.852;AN=2;DP=2866;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1386,120,0:0,0,16,24 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 0/1:20,16:36:99:490,0,637:10,10,5,11 chr1 43652281 . CAAAAAAA CAAAAAA,CAAAAA,C,CAAAAAAAA,CAAAA 204.12 PASS AC=1,0,0,0,0;AF=0.32,0.1,0.06,0.04,0.02;AN=2;DP=864;set=variant3-variant4-variant6-variant9-variant10-variant13-variant14-variant15-variant17-variant18-variant19-filterInvariant21-variant22-variant23-variant26-variant27-variant31-variant33-variant34-variant36-variant37-variant39-variant40-variant42-variant43 GT:DP:GQ:SB 0/1:30:99:6,5,18,1 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 1/1:0,124:124:99:3860,371,0:0,0,69,55 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 1/1:0,69:69:99:2310,207,0:0,0,22,47 chr1 43672636 . T G 631.42 PASS AC=2;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 1/1:0,29:29:87:993,87,0:0,0,7,22 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 1/1:0,162:162:99:5003,485,0:0,0,88,74 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 1/1:0,9:9:27:243,27,0:0,0,5,4 chr1 43676608 . C CA 63.08 PASS AC=1;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 0/1:2,8:10:22:177,0,22:0,2,3,5 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 1/1:0,48:48:99:1647,144,0:0,0,36,12 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 1/1:0,51:51:99:1677,152,0:0,0,15,36 chr1 43697968 . G A 447.98 PASS AC=2;AF=0.825;AN=2;DP=1827;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-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1315,108,0:0,0,14,22 chr1 43699813 . A G 268.79 PASS AC=2;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 1/1:0,13:13:39:502,39,0:0,0,11,2 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 1/1:0,91:91:99:2955,273,0:0,0,46,45 chr1 43700140 . A G 6913.96 PASS AC=2;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 1/1:0,250:250:99:7383,749,0:0,0,117,133 chr1 43747937 . G GA 121.49 PASS AC=2;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 1/1:0,15:15:48:417,48,0:0,0,10,5 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 1/1:0,60:60:99:1925,180,0:0,0,29,31 chr1 43771016 . TA T 1065.18 PASS AC=2;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 1/1:0,121:121:99:4337,364,0:0,0,48,73 chr1 43771090 . G A 415.91 PASS AC=2;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 1/1:0,58:58:99:1716,173,0:0,0,18,40 chr1 43773033 . A G 1235.57 PASS AC=2;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 1/1:0,84:84:99:2897,252,0:0,0,33,51 chr1 43774292 . C T 119.26 PASS AC=2;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 1/1:0,9:9:26:224,26,0:0,0,6,3 chr1 43774437 . G A 673.66 PASS AC=2;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 1/1:0,29:29:87:943,87,0:0,0,18,11 chr1 43774495 . G C 637.16 PASS AC=2;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 1/1:0,37:37:99:1157,111,0:0,0,24,13 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 1/1:0,121:121:99:4426,364,0:0,0,53,68 chr1 43779564 . T C 902.74 PASS AC=2;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 1/1:2,130:132:99:3832,346,0:1,1,69,61 chr1 43779869 . T G 1351.44 PASS AC=2;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 1/1:0,72:72:99:2122,216,0:0,0,39,33 chr1 43782846 . G A 102.87 PASS AC=2;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 1/1:0,15:15:45:510,45,0:0,0,11,4 chr1 43826312 . C A 4485.83 PASS AC=2;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 1/1:3,386:389:99:11040,1128,0:0,3,190,196 chr1 43851797 . G A 2052.83 PASS AC=2;AF=0.583;AN=2;DP=756;MQ=60;set=variant19-variant20-variant23-variant27-variant36-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3532,348,0:0,0,48,68 chr1 43855578 . G C 760.42 PASS AC=2;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 1/1:0,115:115:99:3268,344,0:0,0,56,59 chr1 43855626 . G C 2661.64 PASS AC=2;AF=1;AN=2;DP=99;FS=0;FractionInformativeReads=1;MQ=60;QD=26.89;SOR=0.842;set=variant23 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:2690,295,0:0,0,46,53 chr1 43907092 . G A 1602.55 PASS AC=2;AF=0.605;AN=2;DP=2540;MQ=60;set=variant4-variant6-variant7-variant9-variant12-variant15-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant31-variant33-variant34-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2931,278,0:0,0,40,53 chr1 43916642 . T C 1210.98 PASS AC=2;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 1/1:1,173:174:99:5157,476,0:1,0,82,91 chr1 43919413 . A G 386.7 PASS AC=2;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 1/1:0,58:58:99:1678,174,0:0,0,22,36 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 1/1:0,37:37:99:1144,111,0:0,0,14,23 chr1 44035352 . C T 249.13 PASS AC=2;AF=0.545;AN=2;DP=1183;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant12-variant13-variant15-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant31-variant33-variant36-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1225,128,0:0,0,22,21 chr1 44044468 . C T 500.38 PASS AC=2;AF=0.545;AN=2;DP=1649;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant12-variant13-variant15-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant31-variant33-variant36-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2221,216,0:0,0,44,28 chr1 44056462 . T C 864.66 PASS AC=2;AF=0.542;AN=2;DP=878;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant12-variant13-variant15-variant16-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant31-variant33-variant36-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1301,105,0:0,0,28,7 chr1 44057257 . A G 598.51 PASS AC=2;AF=0.543;AN=2;DP=2091;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant12-variant13-variant15-variant16-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant31-variant33-variant36-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2673,258,0:0,0,30,56 chr1 44057668 . G T 789.01 PASS AC=2;AF=0.543;AN=2;DP=2498;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant12-variant13-variant15-variant16-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant31-variant33-variant36-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2436,241,0:0,0,28,53 chr1 44057696 . A G 614.04 PASS AC=2;AF=0.543;AN=2;DP=1745;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant12-variant13-variant15-variant16-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant31-variant33-variant36-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1812,168,0:0,0,17,39 chr1 44058034 . G A 146.22 PASS AC=2;AF=0.543;AN=2;DP=1131;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant12-variant13-variant15-variant16-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant31-variant33-variant36-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1419,129,0:0,0,30,13 chr1 44058265 . C A 196.61 PASS AC=2;AF=0.611;AN=2;DP=1582;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant12-variant13-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant33-variant36-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1410,122,0:0,0,10,31 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 1/1:0,9:9:27:321,27,0:0,0,7,2 chr1 44064319 . A G 2150.35 PASS AC=2;AF=0.615;AN=2;DP=4361;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant12-variant13-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant33-variant36-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,156:156:99:4593,467,0:0,0,92,64 chr1 44067859 . A G 412.57 PASS AC=2;AF=0.615;AN=2;DP=3081;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant12-variant13-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant33-variant36-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:1,104:105:99:2982,268,0:0,1,53,51 chr1 44071221 . G A 4526.21 PASS AC=2;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 1/1:0,153:153:99:4733,456,0:0,0,62,91 chr1 44072018 . C T 825.39 PASS AC=2;AF=0.54;AN=2;DP=3822;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant12-variant13-variant15-variant16-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:3386,358,0:0,0,61,59 chr1 44072066 . C T 719.27 PASS AC=2;AF=0.54;AN=2;DP=3809;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant12-variant13-variant15-variant16-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:3602,365,0:0,0,59,63 chr1 44072420 . A G 1600.28 PASS AC=2;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 1/1:0,64:64:99:1909,191,0:0,0,39,25 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 1/1:0,29:29:87:1149,87,0:0,0,6,23 chr1 44078359 . T A 783.46 PASS AC=2;AF=0.543;AN=2;DP=1125;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant12-variant13-variant15-variant16-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant31-variant33-variant36-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:2695,184,0:0,0,39,21 chr1 44078384 . T C 3000.08 PASS AC=2;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 1/1:0,77:77:99:3143,232,0:0,0,45,32 chr1 44079411 . T C 1844.66 PASS AC=2;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 1/1:0,109:109:99:3465,327,0:0,0,40,69 chr1 44083110 . C T 2081.98 PASS AC=2;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 1/1:0,122:122:99:3906,365,0:0,0,78,44 chr1 44083507 . T C 1283.04 PASS AC=2;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 1/1:0,97:97:99:2948,290,0:0,0,39,58 chr1 44083519 . G A 1109.6 PASS AC=2;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 1/1:0,83:83:99:2510,248,0:0,0,32,51 chr1 44084739 . C T 3105.79 PASS AC=2;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 1/1:0,149:149:99:4431,446,0:0,0,76,73 chr1 44086080 . T C 1701.12 PASS AC=2;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 1/1:0,87:87:99:2579,261,0:0,0,49,38 chr1 44086831 . C T 4647.15 PASS AC=2;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 1/1:0,211:211:99:6159,629,0:0,0,86,125 chr1 44087496 . C T 3521.7 PASS AC=2;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 1/1:0,131:131:99:4237,392,0:0,0,89,42 chr1 44119038 . A AT 468.21 PASS AC=2;AF=0.545;AN=2;DP=1071;MQ=60;set=variant-variant2-variant4-variant6-variant9-variant10-variant12-variant15-variant16-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant31-variant33-variant36-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:883,87,0:0,0,5,24 chr1 44125962 . CA C 1026.11 PASS AC=2;AF=0.589;AN=2;DP=1797;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant33-variant36-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:2,44:46:73:1371,73,0:1,1,29,15 chr1 44137257 . C A 2100.26 PASS AC=2;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 1/1:0,82:82:99:2620,245,0:0,0,46,36 chr1 44171266 . G A 135.95 PASS AC=2;AF=0.667;AN=2;DP=213;MQ=60;set=variant-variant2-variant3-variant6-variant12-variant16-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant33-variant36-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:259,24,0:0,0,2,6 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 1/1:0,30:30:90:1046,90,0:0,0,22,8 chr1 44280425 . T G 2330.8 PASS AC=2;AF=0.625;AN=2;DP=1463;MQ=60;set=variant-variant2-variant4-variant6-variant9-variant12-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant33-variant36-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1730,167,0:0,0,36,20 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 1/1:17:80:0,0,16,1 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 1/1:0,55:55:99:1650,164,0:0,0,33,22 chr1 44365529 . G A 906.96 PASS AC=2;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 1/1:0,36:36:99:1141,108,0:0,0,13,23 chr1 44386305 . C T 377.45 PASS AC=2;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 1/1:0,18:18:54:651,54,0:0,0,9,9 chr1 44386445 . G A 980.35 PASS AC=2;AF=0.625;AN=2;DP=328;FractionInformativeReads=1;MQ=60;set=variant19-variant20-variant23-variant36 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2228,228,0:0,0,46,31 chr1 44386615 . A G 1628.99 PASS AC=2;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 1/1:0,70:70:99:2185,210,0:0,0,30,40 chr1 44395786 . C T 3372.24 PASS AC=2;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 1/1:0,125:125:99:4007,375,0:0,0,53,72 chr1 44396646 . C G 1969.18 PASS AC=2;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 1/1:0,53:53:99:1658,159,0:0,0,31,22 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 1/1:0,90:90:99:2725,268,0:0,0,45,45 chr1 44399942 . G A 381.35 PASS AC=2;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 1/1:0,10:10:30:366,30,0:0,0,4,6 chr1 44401384 . A G 3186.67 PASS AC=2;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 1/1:0,103:103:99:3242,309,0:0,0,46,57 chr1 44402565 . G A 1031.66 PASS AC=2;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 1/1:0,57:57:99:1963,171,0:0,0,30,27 chr1 44402785 . G A 1037.76 PASS AC=2;AF=0.667;AN=2;DP=290;FS=0;MQ=60;set=variant19-variant23-variant36 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2717,275,0:0,0,36,56 chr1 44415415 . C T 4281.95 PASS AC=2;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 1/1:0,189:189:99:5972,565,0:0,0,91,98 chr1 44426025 . G A 3003.28 PASS AC=2;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 1/1:0,92:92:99:2705,275,0:0,0,48,44 chr1 44426948 . G A 1849.08 PASS AC=2;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 1/1:0,84:84:99:2570,251,0:0,0,31,53 chr1 44431715 . T C 1171.93 PASS AC=2;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 1/1:0,51:51:99:1638,153,0:0,0,25,26 chr1 44432500 . C G 1124.74 PASS AC=2;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 1/1:0,61:61:99:2114,183,0:0,0,31,30 chr1 44438974 . C T 12015.3 PASS AC=2;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 1/1:2,285:287:99:8271,810,0:1,1,146,139 chr1 44442521 . A C 3212.21 PASS AC=2;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 1/1:0,96:96:99:3153,287,0:0,0,39,57 chr1 44446634 . A G 578.52 PASS AC=2;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 1/1:0,21:21:63:750,63,0:0,0,16,5 chr1 44457215 . G A 3216.74 PASS AC=2;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 1/1:1,67:68:99:1947,193,0:0,1,39,28 chr1 44457305 . G A 5186.13 PASS AC=2;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 1/1:0,130:130:99:3729,388,0:0,0,71,59 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 1/1:0,28:28:84:1062,84,0:0,0,8,20 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 0/1:29:99:10,5,12,2 chr1 44483040 . AACACACACAC AACACACAC,AACAC,AAC,AACACAC,A 260.83 PASS AC=0,0,1,0,1;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 5/3:28:99:0,0,5,23 chr1 44594966 . G A 1364.51 PASS AC=2;AF=0.605;AN=2;DP=2147;MQ=60;set=variant-variant6-variant9-variant11-variant14-variant15-variant17-variant21-variant23-variant24-variant26-variant27-variant29-variant30-variant33-variant34-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2828,266,0:0,0,63,26 chr1 44595113 . G C 7072.74 PASS AC=2;AF=0.743;AN=2;DP=9789;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,245:245:99:7275,734,0:0,0,121,124 chr1 44595410 . A G 3164.86 PASS AC=2;AF=0.614;AN=2;DP=3195;MQ=60;set=variant-variant4-variant6-variant9-variant10-variant11-variant14-variant15-variant17-variant21-variant23-variant24-variant26-variant27-variant29-variant30-variant33-variant34-variant36-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:4740,426,0:0,0,74,68 chr1 44595426 . G A 3082.66 PASS AC=2;AF=0.614;AN=2;DP=3213;MQ=60;set=variant-variant4-variant6-variant9-variant10-variant11-variant14-variant15-variant17-variant21-variant23-variant24-variant26-variant27-variant29-variant30-variant33-variant34-variant36-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,141:141:99:4528,421,0:0,0,75,66 chr1 44595995 . G GC 1183.83 PASS AC=2;AF=0.614;AN=2;DP=813;MQ=60;set=variant-variant4-variant6-variant9-variant10-variant11-variant14-variant15-variant17-variant21-variant23-variant24-variant26-variant27-variant29-variant30-variant33-variant34-variant36-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1117,108,0:0,0,9,26 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 1/1:0,53:53:99:1640,159,0:0,0,29,24 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 1/1:0,8:8:24:326,24,0:0,0,8,0 chr1 44878509 . C G 405.9 PASS AC=1;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 0/1:6,9:15:99:332,0,221:0,6,0,9 chr1 45088629 . G A 1224.31 PASS AC=2;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 1/1:0,28:28:83:1023,83,0:0,0,5,23 chr1 45097639 . T C 467.65 PASS AC=2;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 1/1:0,33:33:99:1073,99,0:0,0,19,14 chr1 45100903 . C G 205.86 PASS AC=2;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 1/1:0,18:18:54:601,54,0:0,0,11,7 chr1 45100927 . T C 211.38 PASS AC=2;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 1/1:0,22:22:66:735,66,0:0,0,14,8 chr1 45101478 . T C 1664 PASS AC=2;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 1/1:0,54:54:99:1695,162,0:0,0,25,29 chr1 45102355 . T C 157.66 PASS AC=2;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 1/1:0,20:20:60:616,60,0:0,0,10,10 chr1 45111294 . G A 356.63 PASS AC=2;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 1/1:0,18:18:54:723,54,0:0,0,4,14 chr1 45116935 . C T 779.22 PASS AC=2;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 1/1:0,59:59:99:1882,177,0:0,0,32,27 chr1 45116985 . C T 2301.59 PASS AC=2;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 1/1:0,68:68:99:2193,204,0:0,0,36,32 chr1 45117300 . G A 550.43 PASS AC=2;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 1/1:0,35:35:99:1091,105,0:0,0,15,20 chr1 45117492 . G A 93.19 PASS AC=1;AF=0.5;AN=2;DP=6;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.72;QD=15.53;ReadPosRankSum=0;SOR=0.105;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:73:121,0,73:0,2,2,2 chr1 45118901 . C T 165.67 PASS AC=2;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 1/1:0,12:12:36:371,36,0:0,0,8,4 chr1 45119390 . A G 1543.18 PASS AC=2;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 1/1:0,86:86:99:2795,258,0:0,0,56,30 chr1 45119965 . C T 492.49 PASS AC=2;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 1/1:0,53:53:99:1488,158,0:0,0,29,24 chr1 45120068 . A G 544.23 PASS AC=2;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 1/1:0,39:39:99:1347,117,0:0,0,14,25 chr1 45140619 . CTGGA C,CTGGATGGA 300.01 PASS AC=2,0;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 1/1:17:52:0,0,2,15 chr1 45276246 . G A 463.11 PASS AC=1;AF=0.5;AN=2;DP=37;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.594;QD=12.52;ReadPosRankSum=-2.606;SOR=0.879;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:20,17:37:99:491,0,522:8,12,6,11 chr1 45285457 . C A 1326.26 PASS AC=1;AF=0.5;AN=2;DP=173;FractionInformativeReads=1;MQ=60;set=variant11-variant23 GT:AD:DP:GQ:PL:SB 0/1:31,49:80:99:1179,0,702:18,13,27,22 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 1/1:0,51:51:99:1526,153,0:0,0,21,30 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 1/1:0,42:42:99:1434,126,0:0,0,15,27 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 1/1:0,22:22:66:918,66,0:0,0,5,17 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 3/1:26:99:0,0,14,12 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 1/1:0,104:104:99:3312,311,0:0,0,63,41 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 1/1:0,47:47:99:1565,141,0:0,0,29,18 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 1/1:0,21:21:63:737,63,0:0,0,11,10 chr1 45478560 . A C 42.34 PASS AC=1;AF=0.5;AN=2;DP=850;MQ=60;set=filterInvariant2-filterInvariant5-filterInvariant9-filterInvariant10-filterInvariant23-filterInvariant24-filterInvariant30-variant32-filterInvariant36-variant37-filterInvariant38-filterInvariant39-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:45,18:63:99:145,0,674:16,29,17,1 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 1/1:0,48:48:99:1402,143,0:0,0,21,27 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 1/1:0,43:43:99:1329,128,0:0,0,16,27 chr1 45486464 . T C 948.25 PASS AC=1;AF=0.5;AN=2;DP=75;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.814;QD=12.64;ReadPosRankSum=0.75;SOR=0.613;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:34,41:75:99:976,0,755:15,19,19,22 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 1/1:0,14:14:42:492,42,0:0,0,3,11 chr1 45504720 . G C 677.06 PASS AC=2;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 1/1:0,79:79:99:2276,236,0:0,0,43,36 chr1 45524213 . C T 998.6 PASS AC=2;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 1/1:0,102:102:99:3341,305,0:0,0,56,46 chr1 45524481 . G A 723.93 PASS AC=1;AF=0.5;AN=2;DP=110;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant23 GT:AD:DP:GQ:PL:SB 0/1:18,27:45:99:798,0,460:5,13,7,20 chr1 45794426 . T TG 56.79 PASS AC=2;AF=0.813;AN=2;DP=239;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:363,27,0:0,0,5,4 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 1/1:10:10:1,0,8,1 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 1/1:0,67:67:99:2225,201,0:0,0,26,41 chr1 45798225 . G T 1691.43 PASS AC=1;AF=0.5;AN=2;DP=288;FractionInformativeReads=1;MQ=60;set=variant5-variant23 GT:AD:DP:GQ:PL:SB 0/1:69,78:147:99:2032,0,1667:37,32,40,38 chr1 45798555 . T C 2265.91 PASS AC=2;AF=0.909;AN=2;DP=6469;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:3510,351,0:0,0,63,54 chr1 45804422 . T TTG 321.45 PASS AC=2;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 1/1:0,8:8:24:360,24,0:0,0,1,7 chr1 45804428 . TTTG T 289.62 PASS AC=2;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 1/1:0,8:8:24:360,24,0:0,0,1,7 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 1/1:0,137:137:99:4254,411,0:0,0,74,63 chr1 45809017 . G A 2031.08 PASS AC=1;AF=0.5;AN=2;DP=322;FractionInformativeReads=1;MQ=60;set=variant5-variant23 GT:AD:DP:GQ:PL:SB 0/1:70,82:152:99:2148,0,1695:31,39,39,43 chr1 45956700 . C A 1928.41 PASS AC=1;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 0/1:76,75:151:99:1719,0,1888:41,35,38,37 chr1 45960135 . CAA C,CA,CAAA 141.92 PASS AC=0,0,1;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 0/3:13:71:4,3,3,3 chr1 45961327 . CTTTTTTTTTTTTTT CTT,C,CT 200.49 PASS AC=0,0,1;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 0/3:6:72:0,1,1,4 chr1 45961955 . A G 1044.75 PASS AC=1;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 0/1:51,32:83:99:705,0,1262:31,20,18,14 chr1 45965307 . G A 2090.19 PASS AC=1;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 0/1:81,73:154:99:1857,0,2228:27,54,26,47 chr1 45965340 . T C 1055.79 PASS AC=1;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 0/1:51,54:105:99:1501,0,1446:18,33,20,34 chr1 45965703 . G T 466.43 PASS AC=1;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 0/1:30,41:71:99:1062,0,814:18,12,21,20 chr1 45973928 . G A 1429.46 PASS AC=1;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 0/1:79,57:136:99:1277,0,1854:39,40,26,31 chr1 45975088 . GT GTTTTTT,GTTTTTTT,GTTTTT,G,GTTTTTTTT,GTTTTTTTTTTTTTTTTT 859.22 PASS AC=0,1,0,0,0,0;AF=0.2,0.475,0.038,0.038,0.038,0.013;AN=2;DP=4011;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-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:71:99:19,23,13,16 chr1 45975739 . ACT A 208.69 PASS AC=1;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 0/1:2,4:6:73:162,0,73:2,0,3,1 chr1 45975856 . C G 190.38 PASS AC=1;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 0/1:12,14:26:99:350,0,309:8,4,9,5 chr1 45976147 . G A 76.26 PASS AC=1;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 0/1:6,10:16:99:262,0,185:3,3,5,5 chr1 45976263 . C CT 334.67 PASS AC=1;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 0/1:18,15:33:99:504,0,628:11,7,7,8 chr1 45976472 . G C 431.96 PASS AC=1;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 0/1:23,25:48:99:634,0,553:12,11,13,12 chr1 45976587 . A G 1266.88 PASS AC=1;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 0/1:34,45:79:99:1242,0,884:21,13,25,20 chr1 45981512 . T C 1022.57 PASS AC=1;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 0/1:47,47:94:99:1085,0,1032:22,25,23,24 chr1 45984353 . G A 149.16 PASS AC=1;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 0/1:6,7:13:99:228,0,193:5,1,6,1 chr1 46016687 . T C 1732.98 PASS AC=1;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 0/1:51,66:117:99:1786,0,1272:22,29,24,42 chr1 46027355 . T C 1728.02 PASS AC=1;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 0/1:70,50:120:99:1114,0,1548:41,29,31,19 chr1 46027851 . C A 40.73 PASS AC=1;AF=0.5;AN=2;DP=7;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.198;QD=5.82;ReadPosRankSum=-0.198;SOR=0.892;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:5,2:7:69:69,0,162:1,4,0,2 chr1 46032311 . A G 1144.49 PASS AC=1;AF=0.5;AN=2;DP=463;MQ=60;set=variant5-variant23-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,39:106:99:788,0,1568:32,35,19,20 chr1 46035760 . A T 546.26 PASS AC=1;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 0/1:22,19:41:99:545,0,655:7,15,4,15 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 1/1:0,108:108:99:4750,324,0:0,0,34,74 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 1/1:0,4:4:12:119,12,0:0,0,2,2 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 1/1:0,85:85:99:2476,254,0:0,0,49,36 chr1 46073489 . G A 1164.11 PASS AC=1;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 0/1:38,47:85:99:1193,0,925:16,22,24,23 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 1/1:0,8:8:24:308,24,0:0,0,7,1 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 1/1:0,73:73:99:2262,219,0:0,0,34,39 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 1/1:0,80:80:99:2459,240,0:0,0,41,39 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 1/1:0,37:37:99:1123,111,0:0,0,9,28 chr1 46080404 . T C 43.71 PASS AC=1;AF=0.5;AN=2;DP=6;FS=0;FractionInformativeReads=1;MQ=58.38;MQRankSum=-1.38;QD=7.28;ReadPosRankSum=1.38;SOR=0.039;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:72:72,0,638:4,0,1,1 chr1 46080413 . A C 43.71 PASS AC=1;AF=0.5;AN=2;DP=6;FS=0;FractionInformativeReads=1;MQ=58.38;MQRankSum=-1.38;QD=7.28;ReadPosRankSum=1.38;SOR=0.039;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:72:72,0,638:4,0,1,1 chr1 46080426 . G T 37.69 PASS AC=1;AF=0.5;AN=2;DP=8;FS=0;FractionInformativeReads=1;MQ=58.79;MQRankSum=-1.589;QD=4.71;ReadPosRankSum=-0.572;SOR=0.02;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:6,2:8:66:66,0,785:6,0,1,1 chr1 46080436 . C T 31.68 PASS AC=1;AF=0.5;AN=2;DP=10;FS=0;FractionInformativeReads=1;MQ=59.03;MQRankSum=-1.733;QD=3.17;ReadPosRankSum=-0.898;SOR=0.061;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:8,2:10:60:60,0,846:7,1,1,1 chr1 46080530 . T C 509.1 PASS AC=1;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 0/1:26,21:47:99:513,0,648:17,9,13,8 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 1/1:1,106:107:99:3359,310,0:0,1,57,49 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 1/1:0,65:65:99:2097,194,0:0,0,35,30 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 1/1:0,75:75:99:2420,225,0:0,0,42,33 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 1/1:1,138:139:99:4147,370,0:0,1,58,80 chr1 46083706 . C G 2196.86 PASS AC=1;AF=0.5;AN=2;DP=2117;MQ=60;set=variant3-variant5-variant9-variant12-variant15-variant16-variant18-variant20-variant23-variant24-variant28-variant30-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,50:109:99:1190,0,1361:31,28,26,24 chr1 46084383 . G T 1414.91 PASS AC=1;AF=0.5;AN=2;DP=1134;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant9-variant12-variant15-variant16-variant18-variant20-variant23-variant24-variant28-variant30-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,34:70:99:966,0,863:20,16,21,13 chr1 46084614 . C CTTT,CTTTT 2374.94 PASS AC=1,1;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 1/2:77:99:0,0,26,51 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 1/1:0,47:47:99:1468,140,0:0,0,28,19 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 1/1:0,57:57:99:1893,171,0:0,0,33,24 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 1/1:0,103:103:99:3075,307,0:0,0,54,49 chr1 46086096 . T A 1420.6 PASS AC=1;AF=0.5;AN=2;DP=105;FS=0.737;FractionInformativeReads=1;MQ=60;MQRankSum=-0.929;QD=13.53;ReadPosRankSum=0.58;SOR=0.573;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:45,60:105:99:1449,0,1110:21,24,30,30 chr1 46086329 . C T 1287.62 PASS AC=1;AF=0.5;AN=2;DP=1791;MQ=60;set=variant3-variant5-variant9-variant12-variant13-variant15-variant16-variant18-variant20-variant23-variant24-variant28-variant30-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,49:85:99:1401,0,794:15,21,28,21 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 1/1:0,45:45:99:1625,134,0:0,0,24,21 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 1/1:0,249:249:99:7719,740,0:0,0,92,157 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 1/1:0,64:64:99:1970,192,0:0,0,42,22 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 1/1:0,129:129:99:4043,387,0:0,0,66,63 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 1/1:0,13:13:39:442,39,0:0,0,4,9 chr1 46093396 . GA G 415.6 PASS AC=1;AF=0.5;AN=2;DP=528;set=variant3-variant5-variant9-variant12-variant13-variant15-variant16-variant18-variant20-filterInvariant23-variant24-variant28-variant30-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,5:24:71:71,0,467:11,8,4,1 chr1 46094236 . A G 318.53 PASS AC=1;AF=0.673;AN=2;DP=165;MQ=60;set=variant-variant2-variant3-variant8-variant10-variant11-variant14-variant15-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant30-variant33-variant34-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:94:94,0,155:1,4,0,3 chr1 46095126 . T TCCCCCCCC,TCCCCCCC,TTC,TCCCCCC,TCCCCC,TCCC,TCCCCCCCCC 79.26 PASS AC=0,0,0,0,2,0,0;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 5/5:4:5:0,0,4,0 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 0/1:5,4:9:99:153,0,135:3,2,4,0 chr1 46095989 . T C 457.08 PASS AC=1;AF=0.5;AN=2;DP=610;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant9-variant12-variant15-variant16-variant18-variant20-variant23-variant24-variant28-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,17:32:99:495,0,306:9,6,13,4 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 1/1:0,31:31:93:1058,93,0:0,0,8,23 chr1 46124663 . A G 3015.21 PASS AC=1;AF=0.629;AN=2;DP=3298;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant30-variant32-variant33-variant34-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,20:60:99:532,0,1094:26,14,15,5 chr1 46126854 . C T 3898.16 PASS AC=1;AF=0.533;AN=2;DP=4685;MQ=60;set=variant2-variant4-variant8-variant10-variant13-variant16-variant22-variant23-variant25-variant26-variant29-variant36-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:156,140:296:99:3339,0,3768:73,83,65,75 chr1 46153203 . G A 1869.55 PASS AC=1;AF=0.629;AN=2;DP=1689;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant30-variant32-variant33-variant34-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,24:44:99:702,0,474:10,10,15,9 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 1/1:0,61:61:99:1781,183,0:0,0,29,32 chr1 46347879 . T A 151.77 PASS AC=2;AF=0.926;AN=2;DP=167;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant27-variant28-variant32-variant34-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:167,15,0:0,0,5,0 chr1 46379518 . A G 3379.99 PASS AC=1;AF=0.795;AN=2;DP=5965;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:54,60:114:99:1565,0,1371:28,26,29,31 chr1 46424864 . G T 585.82 PASS AC=1;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 0/1:13,25:38:99:630,0,271:7,6,14,11 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 1/1:0,58:58:99:1742,174,0:0,0,33,25 chr1 46466721 . T C 1060.32 PASS AC=1;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 0/1:65,57:122:99:1322,0,1602:34,31,25,32 chr1 46476587 . T G 2687.02 PASS AC=1;AF=0.795;AN=2;DP=5290;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:62,56:118:99:1296,0,1413:27,35,26,30 chr1 46485548 . G T 186.17 PASS AC=1;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 0/1:9,5:14:99:142,0,319:2,7,2,3 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 1/1:0,10:10:30:384,30,0:0,0,3,7 chr1 46487552 . G A 2622.17 PASS AC=1;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 0/1:68,47:115:99:1216,0,1759:38,30,26,21 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 1/1:0,124:124:99:4379,372,0:0,0,68,56 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 1/1:2,38:40:70:1284,70,0:1,1,6,32 chr1 46493460 . T G 989.01 PASS AC=1;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 0/1:32,41:73:99:1107,0,663:16,16,22,19 chr1 46495024 . G A 1151.61 PASS AC=1;AF=0.526;AN=2;DP=1529;MQ=60;set=variant3-variant5-variant8-variant9-variant12-variant15-variant16-variant18-variant20-variant21-variant23-variant24-variant28-variant30-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,50:76:99:1053,0,655:18,8,28,22 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 1/1:0,60:60:99:1709,179,0:0,0,31,29 chr1 46497500 . T A 504.91 PASS AC=1;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 0/1:16,17:33:99:460,0,452:4,12,6,11 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 1/1:0,94:94:99:2990,282,0:0,0,36,58 chr1 46500613 . T C 2081.54 PASS AC=1;AF=0.5;AN=2;DP=2300;MQ=60;set=variant3-variant5-variant8-variant9-variant12-variant15-variant16-variant18-variant20-variant23-variant24-variant28-variant30-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,56:96:99:1502,0,997:24,16,32,24 chr1 46500993 . A G 780.46 PASS AC=1;AF=0.5;AN=2;DP=1149;MQ=60;set=variant2-variant4-variant8-variant10-variant13-variant16-variant22-variant23-variant25-variant26-variant29-variant36-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,30:69:99:812,0,1044:21,18,12,18 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 1/1:0,79:79:99:2860,237,0:0,0,24,55 chr1 46508785 . G GT 865.95 PASS AC=1;AF=0.5;AN=2;DP=1524;MQ=60;set=variant3-variant5-variant8-variant9-variant12-variant15-variant16-variant18-variant20-variant23-variant24-variant28-variant30-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,19:60:99:365,0,1026:16,25,6,13 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 1/1:0,8:8:24:350,24,0:0,0,8,0 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 1/1:0,69:69:99:2061,206,0:0,0,29,40 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 1/1:0,55:55:99:1743,165,0:0,0,20,35 chr1 46546208 . T C 195.8 PASS AC=1;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 0/1:2,8:10:61:276,0,61:2,0,7,1 chr1 46598269 . C A 6550.05 PASS AC=1;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 0/1:129,125:254:99:2744,0,2913:67,62,65,60 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 1/1:1,261:262:99:9371,758,0:1,0,134,127 chr1 46641741 . A G 64.74 PASS AC=1;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 0/1:6,8:14:99:318,0,190:4,2,8,0 chr1 46641837 . G A 627.09 PASS AC=1;AF=0.5;AN=2;DP=1344;set=variant2-variant4-variant10-variant13-variant14-variant16-variant19-variant22-variant23-variant25-variant26-variant29-variant34-variant36-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,34:65:99:1005,0,895:22,9,28,6 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 1/1:0,80:80:99:2440,240,0:0,0,40,40 chr1 46657701 . C T 432.83 PASS AC=1;AF=0.5;AN=2;DP=71;FractionInformativeReads=1;MQ=60;set=variant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:16,14:30:99:345,0,423:11,5,10,4 chr1 46686658 . G A 592.53 PASS AC=1;AF=0.5;AN=2;DP=157;FractionInformativeReads=1;MQ=60;set=variant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:38,39:77:99:1026,0,968:24,14,24,15 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 0/1:7,10:17:99:311,0,214:2,5,1,9 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 0/1:66,39:105:99:1077,0,1747:33,33,16,23 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 0/1:59,36:95:99:1334,0,2377:28,31,17,19 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 0/1:52,37:89:99:813,0,1286:24,28,17,20 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 0/1:42,40:82:99:820,0,1053:18,24,19,21 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 0/1:34,40:74:99:976,0,966:18,16,19,21 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 0/1:43,36:79:99:812,0,1026:20,23,17,19 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 0/1:31,26:57:99:631,0,841:14,17,12,14 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 0/1:2,5:7:71:134,0,71:0,2,0,5 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 0/1:34,22:56:99:550,0,939:24,10,16,6 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 0/1:76,73:149:99:1729,0,1599:38,38,37,36 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 0/1:81,70:151:99:1533,0,1701:38,43,30,40 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 0/1:13,7:20:99:166,0,350:3,10,2,5 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 0/1:2,2:4:78:78,0,78:1,1,2,0 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 0/1:4,5:9:99:198,0,153:3,1,4,1 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 0/1:7,9:16:99:350,0,245:6,1,8,1 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 0/1:33,38:71:99:913,0,743:21,12,22,16 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 0/1:57,73:130:99:1716,0,1279:31,26,38,35 chr1 46812852 . G A 407.08 PASS AC=1;AF=0.588;AN=2;DP=210;MQ=60;set=variant5-variant7-variant9-variant12-variant13-variant16-variant21-variant23-variant29-variant30-variant33-variant34-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,9:12:60:194,0,60:1,2,3,6 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 0/1:2,7:9:65:233,0,65:0,2,2,5 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 0/1:8,9:17:99:337,0,451:6,2,6,3 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 0/1:14,8:22:99:294,0,614:11,3,6,2 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 0/1:22,11:33:99:283,0,632:14,8,8,3 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 0/1:23,16:39:99:431,0,654:15,8,9,7 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 0/1:15,12:27:99:319,0,405:4,11,4,8 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 0/1:3,6:9:99:199,0,109:1,2,1,5 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 0/1:31,29:60:99:692,0,885:12,19,10,19 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 1/1:0,22:22:66:852,66,0:0,0,18,4 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 0/1:59,50:109:99:1254,0,1505:23,36,20,30 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 0/1:13,31:44:99:758,0,348:7,6,17,14 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 0/1:15,26:41:99:684,0,363:7,8,9,17 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 0/1:7,5:12:99:172,0,209:1,6,0,5 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 0/1:54,36:90:99:688,0,1395:26,28,17,19 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 1/1:0,207:207:99:6137,620,0:0,0,115,92 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 0/1:29,41:70:99:1058,0,925:18,11,26,15 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 1/1:0,50:50:99:1576,149,0:0,0,19,31 chr1 46976837 . C T 1778.25 PASS AC=1;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 0/1:80,79:159:99:1857,0,1899:40,40,33,46 chr1 46978497 . C T 91.91 PASS AC=1;AF=0.538;AN=2;DP=391;FractionInformativeReads=1;MQ=60;set=variant2-variant13-variant20-variant21-variant23-variant25-variant28-variant31-variant33-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,17:28:99:458,0,247:4,7,7,10 chr1 46978946 . C T 920.73 PASS AC=1;AF=0.538;AN=2;DP=910;FractionInformativeReads=1;MQ=60;set=variant2-variant13-variant20-variant21-variant23-variant25-variant28-variant31-variant33-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,23:39:99:584,0,439:8,8,13,10 chr1 46979222 . C T 1016.71 PASS AC=1;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 0/1:21,26:47:99:611,0,436:12,9,15,11 chr1 47013180 . A G 4737.81 PASS AC=1;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 0/1:75,107:182:99:2618,0,1687:39,36,54,53 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 1/1:0,73:73:99:2362,219,0:0,0,30,43 chr1 47014821 . A AAAAAG,AAAAAAG 3093.52 PASS AC=1,0;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 0/1:80:99:23,17,23,17 chr1 47016512 . G A 34.2 PASS AC=1;AF=0.607;AN=2;DP=103;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant8-variant13-variant20-variant21-variant23-variant25-variant31-variant32-variant33-variant36-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:62:62,0,159:3,2,2,1 chr1 47016761 . C T 1080.18 PASS AC=1;AF=0.5;AN=2;DP=447;MQ=60;set=variant2-variant20-variant23-variant33-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,24:66:99:546,0,1247:24,18,12,12 chr1 47025839 . GC G 887.77 PASS AC=1;AF=0.5;AN=2;DP=879;MQ=60;set=variant2-variant8-variant20-variant23-variant30-variant31-variant33-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,49:103:99:1290,0,1429:34,20,28,21 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 1/1:0,108:108:99:3318,324,0:0,0,49,59 chr1 47069708 . T TC 678.76 PASS AC=1;AF=0.571;AN=2;DP=376;MQ=60;set=variant2-variant8-variant11-variant12-variant18-variant19-variant20-variant23-variant30-variant31-variant33-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,10:18:99:271,0,207:7,1,8,2 chr1 47069730 . A G 1018.05 PASS AC=1;AF=0.662;AN=2;DP=1544;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,22:41:99:561,0,510:14,5,15,7 chr1 47073478 . CT C 1266 PASS AC=1;AF=0.571;AN=2;DP=425;MQ=60;set=variant2-variant8-variant11-variant12-variant18-variant19-variant20-variant23-variant30-variant31-variant33-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:376,0,372:6,5,7,4 chr1 47074462 . A G 452.12 PASS AC=1;AF=0.5;AN=2;DP=437;MQ=60;set=variant2-variant8-variant20-variant23-variant30-variant31-variant33-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,14:31:99:389,0,470:8,9,7,7 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 1/1:0,46:46:99:1430,138,0:0,0,22,24 chr1 47074774 . TCATGGTCTGATGGTCC T,ACATGGTCTGATGGTCC 1618.02 PASS AC=1,1;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 1/2:41:99:0,0,22,19 chr1 47078637 . T C 9133.26 PASS AC=1;AF=0.676;AN=2;DP=11730;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:166,159:325:99:3710,0,3820:90,76,88,71 chr1 47079420 . A G 274.24 PASS AC=1;AF=0.5;AN=2;DP=21;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.106;QD=13.06;ReadPosRankSum=0.528;SOR=1.022;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:11,10:21:99:302,0,291:3,8,2,8 chr1 47080679 . G A 3125.08 PASS AC=1;AF=0.682;AN=2;DP=3418;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,41:98:99:951,0,1354:28,29,20,21 chr1 47080983 . G A 1610.42 PASS AC=1;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 0/1:34,40:74:99:1070,0,851:16,18,19,21 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 1/1:1,244:245:99:7001,716,0:1,0,131,113 chr1 47099235 . A C 5454.23 PASS AC=1;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 0/1:157,183:340:99:4327,0,3763:70,87,83,100 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 1/1:0,98:98:99:3402,294,0:0,0,40,58 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 1/1:0,17:17:51:624,51,0:0,0,7,10 chr1 47100049 . C T 287.99 PASS AC=2;AF=0.989;AN=2;DP=590;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:247,24,0:0,0,2,6 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 1/1:0,24:24:72:793,72,0:0,0,10,14 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 1/1:0,31:31:92:1020,92,0:0,0,22,9 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 1/1:0,54:54:99:1721,162,0:0,0,18,36 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 1/1:0,20:20:60:551,60,0:0,0,10,10 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 1/1:0,24:24:72:796,72,0:0,0,14,10 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 1/1:2,47:49:98:1291,98,0:1,1,27,20 chr1 47123898 . TAA TAAA,TA,T 101.26 PASS AC=1,0,0;AF=0.389,0.111,0.056;AN=2;DP=173;MQ=60;set=variant2-filterInvariant7-variant13-variant19-variant23-filterInvariant31-filterInvariant33-variant34-variant37 GT:DP:GQ:SB 0/1:11:62:0,5,2,4 chr1 47133811 . T C 1228.86 PASS AC=1;AF=0.852;AN=2;DP=2236;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:26,19:45:99:442,0,567:15,11,12,7 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 1/1:0,27:27:79:899,79,0:0,0,21,6 chr1 47140775 . AT A 463.97 PASS AC=1;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 0/1:9,12:21:99:281,0,192:9,0,12,0 chr1 47141718 . T C 5377.31 PASS AC=1;AF=0.852;AN=2;DP=6318;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:75,86:161:99:2257,0,1833:41,34,48,38 chr1 47142543 . G GA 1489.84 PASS AC=1;AF=0.563;AN=2;DP=4353;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant17-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,68:116:99:1493,0,997:16,32,29,39 chr1 47279954 . C T 1177.92 PASS AC=1;AF=0.5;AN=2;DP=166;FractionInformativeReads=1;MQ=60;set=variant14-variant23 GT:AD:DP:GQ:PL:SB 0/1:38,27:65:99:618,0,965:17,21,11,16 chr1 47283005 . T C 49.76 PASS AC=1;AF=0.5;AN=2;DP=148;FractionInformativeReads=1;MQ=60;set=variant2-variant11-variant13-variant19-variant22-variant23-variant29-variant31-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:154,0,195:2,3,2,3 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 1/1:0,66:66:99:2146,197,0:0,0,19,47 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 1/1:0,104:104:99:3183,312,0:0,0,52,52 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 1/1:0,59:59:99:1746,177,0:0,0,36,23 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 1/1:0,76:76:99:2382,228,0:0,0,28,48 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 1/1:0,56:56:99:2030,168,0:0,0,13,43 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 2/2:100:99:0,0,45,55 chr1 47516239 . C T 5472.75 PASS AC=1;AF=0.5;AN=2;DP=1602;FractionInformativeReads=1;MQ=60;set=variant9-variant14-variant23 GT:AD:DP:GQ:PL:SB 0/1:301,201:502:99:4149,0,6948:147,154,105,96 chr1 47571943 . CTTT C,CTT,CTTTT,CTTTTT 1895.97 PASS AC=0,1,0,0;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 0/2:52:99:16,22,5,9 chr1 47582246 . C T 748.4 PASS AC=1;AF=0.5;AN=2;DP=757;set=variant-variant3-variant9-variant13-variant14-variant21-variant23-variant24-variant26-variant34-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,31:56:99:714,0,596:15,10,18,13 chr1 47607851 . A T 4923.21 PASS AC=1;AF=0.656;AN=2;DP=7259;set=variant-variant2-variant3-variant5-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,103:192:99:2591,0,2444:30,59,41,62 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 0/1:21,21:42:99:819,0,2993:17,4,18,3 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 0/1:22,21:43:99:879,0,3085:17,5,18,3 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 0/1:24,24:48:99:880,0,3085:18,6,20,4 chr1 47655816 . A G 901.09 PASS AC=1;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 0/1:29,23:52:99:744,0,954:6,23,3,20 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 0/1:16,28:44:99:679,0,385:8,8,12,16 chr1 47683607 . G C 456.74 PASS AC=2;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 1/1:0,33:33:99:1032,99,0:0,0,18,15 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 1/1:0,131:131:99:3718,392,0:0,0,56,75 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 0/1:31,11:42:99:171,0,1055:6,25,11,0 chr1 47726087 . T C 2008.35 PASS AC=2;AF=0.636;AN=2;DP=2606;MQ=60;set=variant3-variant4-variant6-variant8-variant16-variant18-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant36-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,112:114:99:3076,291,0:1,1,63,49 chr1 47765490 . T C 79.49 PASS AC=2;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 1/1:0,10:10:30:398,30,0:0,0,9,1 chr1 47767141 . C A 345.54 PASS AC=2;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 1/1:0,6:6:18:267,18,0:0,0,6,0 chr1 47767914 . G A 1294.02 PASS AC=2;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 1/1:0,83:83:99:2359,248,0:0,0,47,36 chr1 47770441 . A C 43.71 PASS AC=2;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 1/1:0,9:9:27:394,27,0:0,0,8,1 chr1 47770806 . T C 1332.29 PASS AC=2;AF=0.636;AN=2;DP=997;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant8-variant16-variant18-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant36-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1881,171,0:0,0,18,39 chr1 47778520 . T C 2625.86 PASS AC=2;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 1/1:0,125:125:99:4120,374,0:0,0,91,34 chr1 47799436 . G A 71.25 PASS AC=2;AF=0.778;AN=2;DP=48;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant18-variant23-variant25-variant27-variant36-variant39-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,1,1 chr1 47799639 . G C 271.11 PASS AC=2;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 1/1:0,33:33:99:1109,99,0:0,0,22,11 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 1/1:0,126:126:99:4330,377,0:0,0,77,49 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 1/1:0,253:253:99:7821,758,0:0,0,124,129 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 1/1:0,14:14:42:492,42,0:0,0,3,11 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 1/1:0,189:189:99:5518,566,0:0,0,109,80 chr1 47842666 . A T 10404 PASS AC=2;AF=1;AN=2;DP=13088;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,233:235:99:5984,646,0:1,1,106,127 chr1 47882497 . C T 916.28 PASS AC=2;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 1/1:0,97:97:99:3001,288,0:0,0,46,51 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 1/1:0,41:41:99:1832,126,0:0,0,19,22 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 1/1:0,43:43:99:1857,129,0:0,0,20,23 chr1 47902886 . C T 994.35 PASS AC=2;AF=0.675;AN=2;DP=1864;MQ=60;set=variant2-variant4-variant5-variant6-variant8-variant16-variant18-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant36-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:3245,304,0:0,0,60,42 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 1/1:0,49:49:99:2326,167,0:0,0,28,21 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 1/1:0,72:72:99:2414,216,0:0,0,47,25 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 1/1:0,16:16:48:543,48,0:0,0,8,8 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 1/1:0,8:8:24:319,24,0:0,0,1,7 chr1 48695081 . G A 2236.42 PASS AC=1;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 0/1:61,66:127:99:1596,0,1559:30,31,35,31 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 1/1:0,104:104:99:3112,309,0:0,0,43,61 chr1 48697751 . C T 3553.04 PASS AC=1;AF=0.536;AN=2;DP=1395;MQ=60;set=variant3-variant4-variant5-variant8-variant10-variant13-variant15-variant20-variant23-variant25-variant28-variant29-variant32-variant34 GT:AD:DP:GQ:PL:SB 0/1:55,28:83:99:691,0,1409:22,33,10,18 chr1 48701567 . C T 1171.65 PASS AC=1;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 0/1:26,40:66:99:1067,0,758:5,21,11,29 chr1 48705391 . G A 463.53 PASS AC=1;AF=0.596;AN=2;DP=355;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:187,0,281:0,7,1,5 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 1/1:0,41:41:99:1424,123,0:0,0,12,29 chr1 48708228 . G T 1212.68 PASS AC=1;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 0/1:39,45:84:99:1228,0,970:16,23,17,28 chr1 48713206 . T C 1610.73 PASS AC=1;AF=0.5;AN=2;DP=564;MQ=60;set=variant14-variant18-variant23 GT:AD:DP:GQ:PL:SB 0/1:96,73:169:99:1838,0,2320:43,53,35,38 chr1 48713394 . C T 1634.16 PASS AC=1;AF=0.845;AN=2;DP=2723;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,23:50:99:648,0,751:12,15,11,12 chr1 48761154 . T A 550.49 PASS AC=1;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 0/1:34,18:52:99:379,0,887:16,18,7,11 chr1 48762797 . GGTGTGTGT GGTGTGT,GGTGT,GGTGTGTGTGT,GGT,GGTGTGTGTGTGTGTGT,GGTGTGTGTGTGTGT,GGTGTGTGTGTGTGTGTGT,G,GGTGTGTGTGTGTGTGTGTGT,GGTGTGTGTGTGT 343.1 PASS AC=1,0,0,0,0,0,1,0,0,0;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 1/7:78:99:1,0,50,27 chr1 48764419 . C T 13369.9 PASS AC=1;AF=0.589;AN=2;DP=9510;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:143,153:296:99:3610,0,3395:58,85,68,85 chr1 48869288 . T A 499.88 PASS AC=1;AF=0.589;AN=2;DP=474;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,4:15:91:91,0,286:8,3,3,1 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 1/1:0,13:13:39:440,39,0:0,0,3,10 chr1 48937691 . A T 5527.15 PASS AC=1;AF=0.589;AN=2;DP=4404;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:65,64:129:99:1365,0,1505:34,31,26,38 chr1 48998442 . C A 167.98 PASS AC=2;AF=0.667;AN=2;DP=67;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant13-variant14-variant15-variant21-variant23-variant25-variant27-variant28-variant36-variant37 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:94,9,0:0,0,2,1 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 1/1:5:15:0,0,3,2 chr1 49049525 . G GT,GTT,GTTT 86.96 PASS AC=0,1,0;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 0/2:7:47:2,0,3,2 chr1 49051400 . C G 963.73 PASS AC=1;AF=0.5;AN=2;DP=73;FS=4.599;FractionInformativeReads=1;MQ=60;MQRankSum=-1.214;QD=13.2;ReadPosRankSum=-1.945;SOR=0.503;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:33,40:73:99:992,0,831:20,13,19,21 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 1/1:0,50:50:99:1597,150,0:0,0,20,30 chr1 49052263 . C A 228.38 PASS AC=1;AF=0.558;AN=2;DP=961;MQ=60;set=variant-variant3-variant4-variant5-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,14:30:99:348,0,457:9,7,8,6 chr1 49052933 . T C 810.3 PASS AC=1;AF=0.597;AN=2;DP=3039;MQ=60;set=variant-variant3-variant4-variant5-variant10-variant11-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:63,32:95:99:683,0,1503:30,33,13,19 chr1 49056695 . T C 577.27 PASS AC=1;AF=0.597;AN=2;DP=1972;MQ=60;set=variant-variant3-variant4-variant5-variant10-variant11-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,16:39:99:456,0,652:6,17,5,11 chr1 49056770 . C CCA,CA 100.44 PASS AC=0,2;AF=0.667,0.167;AN=2;DP=32;FS=0;MQ=60;set=variant14-variant23-variant27-variant30-variant39-variant43 GT:DP:GQ:SB 2/2:3:9:0,0,1,2 chr1 49100332 . C T 1887.17 PASS AC=1;AF=0.697;AN=2;DP=2225;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,25:53:99:622,0,651:12,16,12,13 chr1 49113319 . T C 2886.11 PASS AC=1;AF=0.737;AN=2;DP=3563;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-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,51:88:99:1188,0,868:16,21,22,29 chr1 49128720 . C T 1058.45 PASS AC=1;AF=0.721;AN=2;DP=1473;FractionInformativeReads=1;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-variant30-variant31-variant32-variant33-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,20:35:99:607,0,443:12,3,14,6 chr1 49128852 . C T 1682.94 PASS AC=1;AF=0.5;AN=2;DP=131;FS=0.65;FractionInformativeReads=1;MQ=60;MQRankSum=-0.062;QD=12.85;ReadPosRankSum=0.601;SOR=0.6;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:64,67:131:99:1711,0,1513:36,28,36,31 chr1 49193394 . G T 2981.62 PASS AC=2;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 1/1:0,101:101:99:3007,303,0:0,0,53,48 chr1 49224584 . G T 1218.4 PASS AC=1;AF=0.898;AN=2;DP=3088;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:30,27:57:99:656,0,820:17,13,14,13 chr1 49242748 . G A 89.64 PASS AC=1;AF=0.5;AN=2;DP=73;FS=0;FractionInformativeReads=1;set=variant2-variant5-variant8-variant23-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:75:75,0,92:2,2,2,2 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 1/1:0,36:36:99:1219,108,0:0,0,21,15 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 0/1:35,37:72:99:946,0,954:23,12,23,14 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 0/1:19,19:38:99:562,0,601:4,15,6,13 chr1 49511248 . G A 1083.8 PASS AC=1;AF=0.5;AN=2;DP=230;MQ=60;set=variant2-variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:27,37:64:99:1009,0,703:19,8,26,11 chr1 49711281 . C T 180.42 PASS AC=1;AF=0.823;AN=2;DP=230;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:66:160,0,66:2,0,4,1 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 1/1:0,4:4:12:156,12,0:0,0,1,3 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 1/1:0,24:24:72:757,72,0:0,0,8,16 chr1 50460995 . T C 556.91 PASS AC=1;AF=0.5;AN=2;DP=208;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:31,27:58:99:630,0,773:12,19,12,15 chr1 50513569 . T G 50.16 PASS AC=1;AF=0.5;AN=2;DP=110;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:17,12:29:99:310,0,440:11,6,7,5 chr1 50575675 . CTG C,CTGTG 106.19 PASS AC=1,0;AF=0.441,0.059;AN=2;DP=1207;set=filterInvariant-filterInvariant6-variant7-filterInvariant10-filterInvariant11-filterInvariant14-variant17-filterInvariant19-filterInvariant23-filterInvariant25-variant26-filterInvariant31-filterInvariant34-filterInvariant37-variant39-variant41-variant44 GT:DP:GQ:SB 0/1:47:67:15,26,2,4 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 1/1:0,93:93:99:2591,276,0:0,0,47,46 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 1/1:0,6:6:18:185,18,0:0,0,2,4 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 1/1:1,121:122:99:3599,353,0:0,1,78,43 chr1 50883804 . CTT C,CT 8804.82 PASS AC=1,0;AF=0.636,0.015;AN=2;DP=9741;set=variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant42-variant43 GT:DP:GQ:SB 0/1:233:99:55,55,66,57 chr1 50884230 . G C 1153.19 PASS AC=2;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 1/1:0,43:43:99:1420,129,0:0,0,19,24 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 1/1:0,72:72:99:2306,212,0:0,0,35,37 chr1 50889255 . G A 903.11 PASS AC=1;AF=0.636;AN=2;DP=802;MQ=60;set=variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,13:21:99:301,0,261:2,6,5,8 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 0/1:7,5:12:99:189,0,279:6,1,5,0 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 1/1:0,35:35:99:1754,117,0:0,0,26,9 chr1 50957509 . A T 1005.29 PASS AC=2;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 1/1:0,26:26:78:874,78,0:0,0,6,20 chr1 51078089 . G A 1610.1 PASS AC=1;AF=0.575;AN=2;DP=2008;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant10-variant13-variant14-variant17-variant18-variant22-variant23-variant25-variant26-variant27-variant28-variant32-variant33-variant34-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:44,48:92:99:1062,0,1058:22,22,26,22 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 1/1:0,91:91:99:3232,274,0:0,0,38,53 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 1/1:0,66:66:99:2350,201,0:0,0,25,41 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 1/1:0,57:57:99:2111,174,0:0,0,20,37 chr1 51435666 . C T 1570.47 PASS AC=1;AF=0.5;AN=2;DP=136;FS=0.646;FractionInformativeReads=1;MQ=60;MQRankSum=-1.247;QD=11.55;ReadPosRankSum=0.4;SOR=0.768;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:74,62:136:99:1599,0,1845:30,44,24,38 chr1 51739208 . C A 220.12 PASS AC=1;AF=0.5;AN=2;DP=26;FS=0;FractionInformativeReads=0.885;MQ=60;MQRankSum=-0.226;QD=8.47;ReadPosRankSum=3.518;SOR=0.275;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:15,8:23:99:248,0,554:0,15,0,8 chr1 51767352 . G A 6316 PASS AC=1;AF=0.542;AN=2;DP=2092;MQ=60;set=variant3-variant5-variant10-variant13-variant18-variant20-variant22-variant23-variant32-variant33-variant34-variant40 GT:AD:DP:GQ:PL:SB 0/1:80,66:146:99:1685,0,2033:34,46,29,37 chr1 51905949 . CTGTGTGTGTG CTGTGTG,CTGTGTGTGTGTG,CTGTGTGTG,CTGTGTGTGTGTGTG,CTGTG,C 2181.46 PASS AC=0,0,1,0,0,0;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 0/3:59:99:28,20,6,5 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 0/1:40,21:61:99:342,0,908:21,19,11,10 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 0/1:9,4:13:60:60,0,246:6,3,2,2 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 0/1:3,5:8:99:160,0,109:3,0,4,1 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 0/1:90,87:177:99:1976,0,2451:33,57,39,48 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 0/1:33,27:60:99:810,0,974:10,23,7,20 chr1 52264064 . A G 1084.39 PASS AC=1;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 0/1:45,36:81:99:788,0,947:23,22,13,23 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 0/1:33,35:68:99:954,0,866:20,13,24,11 chr1 52279650 . T G 1391.65 PASS AC=1;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 0/1:56,37:93:99:812,0,1331:30,26,18,19 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 0/1:18,15:33:99:330,0,468:6,12,6,9 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 1/1:0,7:7:21:312,21,0:0,0,0,7 chr1 52303005 . G A 560.5 PASS AC=1;AF=0.524;AN=2;DP=495;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant23-variant25-variant26-variant30-variant31-variant34-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,11:21:99:341,0,279:8,2,9,2 chr1 52379183 . G A 99.98 PASS AC=1;AF=0.5;AN=2;DP=9;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.307;QD=11.11;ReadPosRankSum=0.729;SOR=0.527;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:128,0,197:0,5,0,4 chr1 52384643 . CTTTTTTTTTTTTT C,CTTTTTTTTTTTT,CTTTTTTTTTT,CTTTTTTTTTTT,CTTTTTTTTT 937.68 PASS AC=0,1,0,0,0;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 0/2:20:79:3,10,1,6 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 1/1:0,42:42:99:1341,126,0:0,0,28,14 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 1/1:0,95:95:99:2805,284,0:0,0,51,44 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 1/1:0,74:74:99:2324,219,0:0,0,24,50 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 1/1:0,27:27:81:975,81,0:0,0,5,22 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 1/1:0,120:120:99:3647,360,0:0,0,63,57 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 1/1:0,86:86:99:2623,257,0:0,0,39,47 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 1/1:0,43:43:99:1350,129,0:0,0,23,20 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 1/1:0,43:43:99:1253,128,0:0,0,24,19 chr1 52555388 . C T 8798.47 PASS AC=2;AF=0.943;AN=2;DP=9418;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,158:158:99:4762,467,0:0,0,87,71 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 1/1:0,227:227:99:7097,679,0:0,0,110,117 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 1/1:0,79:79:99:2319,236,0:0,0,34,45 chr1 52817834 . CA C 1318.44 PASS AC=1;AF=0.5;AN=2;DP=126;FS=2.381;FractionInformativeReads=0.937;MQ=60;MQRankSum=-1.304;QD=10.46;ReadPosRankSum=-0.254;SOR=0.962;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:65,53:118:99:1356,0,1677:31,34,22,31 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 1/1:0,15:15:45:493,45,0:0,0,8,7 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 1/1:0,12:12:36:459,36,0:0,0,10,2 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 1/1:0,124:124:99:3941,371,0:0,0,61,63 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 1/1:0,32:32:96:1035,96,0:0,0,10,22 chr1 52878300 . T A 745.01 PASS AC=1;AF=0.5;AN=2;DP=1068;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant9-variant11-variant17-variant20-variant23-variant31-variant33-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,35:67:99:797,0,759:15,17,16,19 chr1 52882406 . A G 1172.09 PASS AC=1;AF=0.5;AN=2;DP=1543;MQ=60;set=variant-variant2-variant9-variant11-variant17-variant20-variant23-variant31-variant33-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,36:91:99:867,0,1427:31,24,22,14 chr1 52882970 . A G 1677.68 PASS AC=1;AF=0.5;AN=2;DP=663;FractionInformativeReads=1;MQ=60;set=variant-variant17-variant20-variant23-variant31-variant33-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,45:83:99:1049,0,1101:10,28,18,27 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 1/1:0,17:17:51:522,51,0:0,0,10,7 chr1 52947711 . T C 49.73 PASS AC=1;AF=0.5;AN=2;DP=75;FractionInformativeReads=1;MQ=60;set=variant-variant17-variant20-variant23-variant31-variant33-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:308,0,259:0,7,1,8 chr1 52961339 . C T 46.75 PASS AC=1;AF=0.5;AN=2;DP=52;FractionInformativeReads=1;MQ=60;set=variant-variant17-variant20-variant23-variant31-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:53:233,0,53:0,2,1,5 chr1 52981087 . G A 4223.82 PASS AC=1;AF=0.5;AN=2;DP=2147;FractionInformativeReads=1;MQ=60;set=variant-variant17-variant20-variant23-variant31-variant33-variant44 GT:AD:DP:GQ:PL:SB 0/1:139,121:260:99:3157,0,3862:62,77,49,72 chr1 53067914 . T G 36.65 PASS AC=1;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 0/1:7,3:10:91:91,0,222:6,1,3,0 chr1 53072454 . T C 884.59 PASS AC=1;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 0/1:50,56:106:99:1463,0,1266:23,27,25,31 chr1 53074532 . C A 3801.54 PASS AC=1;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 0/1:180,126:306:99:2996,0,4661:105,75,72,54 chr1 53153044 . T C 2116.39 PASS AC=2;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 1/1:0,176:176:99:5658,528,0:0,0,93,83 chr1 53153432 . T C 2716.49 PASS AC=2;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 1/1:0,202:202:99:6290,605,0:0,0,119,83 chr1 53164220 . C T 106.77 PASS AC=2;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 1/1:0,7:7:21:231,21,0:0,0,2,5 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 1/1:0,99:99:99:2785,296,0:0,0,59,40 chr1 53291325 . TAAAA TA,TAA,TAAA,T 2024.96 PASS AC=1,1,0,0;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 1/2:73:99:0,1,26,46 chr1 53291550 . A G 2541.41 PASS AC=2;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 1/1:0,164:164:99:4969,492,0:0,0,90,74 chr1 53292607 . T A 6546.51 PASS AC=2;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 1/1:0,344:344:99:10339,1031,0:0,0,182,162 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 0/1:13,10:23:99:225,0,361:9,4,7,3 chr1 53308275 . CTGGGGA C 689.26 PASS AC=1;AF=0.5;AN=2;DP=110;FS=0;MQ=60;set=variant9-variant11-variant23-variant36 GT:AD:DP:GQ:PL:SB 0/1:12,13:25:99:355,0,319:9,3,9,4 chr1 53308284 . CGGG C 757.23 PASS AC=1;AF=0.5;AN=2;DP=109;MQ=60;set=variant9-variant11-variant23-variant36 GT:AD:DP:GQ:PL:SB 0/1:12,13:25:99:355,0,319:9,3,9,4 chr1 53308665 . C G 2012.19 PASS AC=2;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 1/1:0,191:191:99:5624,570,0:0,0,78,113 chr1 53320274 . G T 1956.35 PASS AC=2;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 1/1:0,139:139:99:4337,417,0:0,0,63,76 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 1/1:0,14:14:42:603,42,0:0,0,0,14 chr1 53333116 . A G 188.41 PASS AC=2;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 1/1:0,11:11:33:436,33,0:0,0,10,1 chr1 53364976 . A G 943.52 PASS AC=2;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 1/1:0,74:74:99:2231,222,0:0,0,32,42 chr1 53365235 . G C 115.2 PASS AC=2;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 1/1:0,19:19:57:535,57,0:0,0,10,9 chr1 53387379 . G C 983.98 PASS AC=2;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 1/1:1,92:93:99:2900,233,0:0,1,33,59 chr1 53392908 . A G 302.38 PASS AC=2;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 1/1:0,12:12:34:293,34,0:0,0,6,6 chr1 53453640 . A G 606.22 PASS AC=1;AF=0.6;AN=2;DP=179;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant9-variant11-variant23-variant36-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,5:14:99:180,0,318:8,1,5,0 chr1 53453683 . C T 775.56 PASS AC=1;AF=0.6;AN=2;DP=403;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant9-variant11-variant23-variant36-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,8:27:99:198,0,450:11,8,6,2 chr1 53459461 . G A 1235.01 PASS AC=1;AF=0.5;AN=2;DP=185;set=variant-variant9-variant23 GT:AD:DP:GQ:PL:SB 0/1:25,22:47:99:706,0,854:11,14,10,12 chr1 53459591 . A G 4453.63 PASS AC=1;AF=0.5;AN=2;DP=556;set=variant-variant23 GT:AD:DP:GQ:PL:SB 0/1:125,114:239:99:2870,0,3170:78,47,73,41 chr1 53480745 . G A 616.5 PASS AC=1;AF=0.5;AN=2;DP=143;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant23 GT:AD:DP:GQ:PL:SB 0/1:23,27:50:99:560,0,599:9,14,13,14 chr1 53493540 . T C 73.71 PASS AC=1;AF=0.5;AN=2;DP=36;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant23 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:182,0,234:6,1,5,0 chr1 53493625 . A G 521.67 PASS AC=1;AF=0.5;AN=2;DP=159;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant23 GT:AD:DP:GQ:PL:SB 0/1:26,33:59:99:724,0,626:15,11,19,14 chr1 53493822 . G T 320.52 PASS AC=1;AF=0.5;AN=2;DP=99;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant23 GT:AD:DP:GQ:PL:SB 0/1:18,20:38:99:459,0,419:7,11,7,13 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 0/1:7,6:13:99:219,0,239:6,1,6,0 chr1 53514516 . T C 2705.17 PASS AC=1;AF=0.5;AN=2;DP=277;FractionInformativeReads=1;MQ=60;set=variant-variant23 GT:AD:DP:GQ:PL:SB 0/1:73,48:121:99:1319,0,2033:45,28,32,16 chr1 53514728 . A G 9902.35 PASS AC=1;AF=0.6;AN=2;DP=3068;MQ=60;set=variant-variant5-variant9-variant11-variant23-variant36-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:151,131:282:99:3251,0,3991:63,88,51,80 chr1 53515305 . G A 2321.3 PASS AC=1;AF=0.55;AN=2;DP=644;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant9-variant11-variant23-variant36-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,26:52:99:622,0,609:11,15,14,12 chr1 53516742 . G A 2974.46 PASS AC=1;AF=0.5;AN=2;DP=678;MQ=60;set=variant-variant9-variant23 GT:AD:DP:GQ:PL:SB 0/1:101,101:202:99:2751,0,2448:50,51,44,57 chr1 53516762 . A T 2362.42 PASS AC=1;AF=0.5;AN=2;DP=203;FS=1.084;FractionInformativeReads=1;MQ=60;MQRankSum=3.643;QD=11.64;ReadPosRankSum=0.56;SOR=0.605;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:103,100:203:99:2391,0,2632:46,57,47,53 chr1 53516999 . A C 731.5 PASS AC=1;AF=0.5;AN=2;DP=228;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant23 GT:AD:DP:GQ:PL:SB 0/1:53,39:92:99:918,0,1351:31,22,23,16 chr1 53517283 . C G,A 2238.9 PASS AC=1,0;AF=0.333,0.167;AN=2;DP=518;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant23 GT:DP:GQ:SB 0/1:154:99:55,43,35,21 chr1 53517305 . G GTTC 3650.83 PASS AC=1;AF=0.5;AN=2;DP=583;MQ=60;set=variant-variant9-variant23 GT:AD:DP:GQ:PL:SB 0/1:112,66:178:99:2427,0,4478:61,51,38,28 chr1 53517349 . G A 2694.28 PASS AC=1;AF=0.5;AN=2;DP=629;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant23 GT:AD:DP:GQ:PL:SB 0/1:101,82:183:99:1733,0,2483:48,53,39,43 chr1 53527948 . T G 2683.12 PASS AC=1;AF=0.6;AN=2;DP=978;MQ=60;set=variant-variant5-variant9-variant11-variant23-variant36-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,28:58:99:640,0,663:16,14,15,13 chr1 53527996 . A G 1905.27 PASS AC=1;AF=0.6;AN=2;DP=613;MQ=60;set=variant-variant5-variant9-variant11-variant23-variant36-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,30:52:99:667,0,488:11,11,14,16 chr1 53535443 . G A 261.77 PASS AC=1;AF=0.5;AN=2;DP=108;FractionInformativeReads=1;MQ=60;set=variant-variant23 GT:AD:DP:GQ:PL:SB 0/1:28,26:54:99:506,0,630:16,12,12,14 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 0/1:25,33:58:99:797,0,512:11,14,20,13 chr1 53535859 . T C 3142.56 PASS AC=1;AF=0.5;AN=2;DP=289;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant23 GT:AD:DP:GQ:PL:SB 0/1:63,80:143:99:3059,0,2634:27,36,35,45 chr1 53535860 . G A 3142.56 PASS AC=1;AF=0.5;AN=2;DP=283;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant23 GT:AD:DP:GQ:PL:SB 0/1:61,78:139:99:3059,0,2634:27,34,34,44 chr1 53535876 . T C 1472.18 PASS AC=1;AF=0.5;AN=2;DP=230;MQ=60;set=variant-variant23 GT:AD:DP:GQ:PL:SB 0/1:55,62:117:99:1567,0,1209:24,31,25,37 chr1 53535918 . A C 1048.64 PASS AC=1;AF=0.5;AN=2;DP=126;MQ=60;set=variant-variant23 GT:AD:DP:GQ:PL:SB 0/1:32,41:73:99:1572,0,1480:12,20,13,28 chr1 53535924 . A C 1026.91 PASS AC=1;AF=0.5;AN=2;DP=117;FractionInformativeReads=1;MQ=60;set=variant-variant23 GT:AD:DP:GQ:PL:SB 0/1:29,38:67:99:1508,0,1412:10,19,12,26 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 0/1:149,144:293:99:3432,0,3586:70,79,70,74 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 1/1:0,38:38:99:1519,113,0:0,0,1,37 chr1 53544439 . G A 10011 PASS AC=1;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 0/1:187,198:385:99:4852,0,4624:87,100,80,118 chr1 53544597 . T C 1118.32 PASS AC=1;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 0/1:71,63:134:99:1570,0,1828:27,44,26,37 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 1/1:0,43:43:99:1313,128,0:0,0,28,15 chr1 53551065 . G A 814.86 PASS AC=1;AF=0.5;AN=2;DP=144;FractionInformativeReads=1;MQ=60;set=variant-variant23 GT:AD:DP:GQ:PL:SB 0/1:45,22:67:99:504,0,1122:19,26,8,14 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 1/1:0,100:100:99:3036,300,0:0,0,49,51 chr1 53553657 . G A 983.3 PASS AC=1;AF=0.5;AN=2;DP=144;FractionInformativeReads=1;MQ=60;set=variant-variant23 GT:AD:DP:GQ:PL:SB 0/1:35,38:73:99:1037,0,892:19,16,20,18 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 1/1:1,79:80:99:2693,230,0:1,0,42,37 chr1 53553754 . T C 3027.88 PASS AC=1;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 0/1:61,37:98:99:962,0,1596:31,30,20,17 chr1 53555783 . A C 781.59 PASS AC=1;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 0/1:43,58:101:99:1435,0,875:18,25,22,36 chr1 53556695 . A C 360.58 PASS AC=1;AF=0.5;AN=2;DP=60;FractionInformativeReads=1;MQ=60;set=variant-variant23 GT:AD:DP:GQ:PL:SB 0/1:24,20:44:99:578,0,522:10,14,7,13 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 1/1:0,116:116:99:3816,347,0:0,0,78,38 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 1/1:0,24:24:72:904,72,0:0,0,4,20 chr1 53568980 . G A 242.44 PASS AC=1;AF=0.542;AN=2;DP=549;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant18-variant20-variant23-variant26-variant32-variant33-variant34-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:103,0,199:5,3,5,1 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 1/1:0,12:12:36:456,36,0:0,0,2,10 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 1/1:0,17:17:51:640,51,0:0,0,14,3 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 1/1:0,53:53:99:1794,159,0:0,0,33,20 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 1/1:0,65:65:99:2265,195,0:0,0,42,23 chr1 53580727 . C A 31.67 PASS AC=1;AF=0.5;AN=2;DP=10;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.898;QD=3.17;ReadPosRankSum=0.48;SOR=0.061;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:8,2:10:60:60,0,537:1,7,1,1 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 1/1:0,9:9:27:297,27,0:0,0,3,6 chr1 53662823 . C A 3362.04 PASS AC=2;AF=0.588;AN=2;DP=1978;set=variant-variant6-variant8-variant10-variant13-variant15-variant20-variant21-variant22-variant23-variant24-variant28-variant29-variant33-variant34-variant36-variant40 GT:AD:DP:GQ:PL:SB 1/1:1,113:114:99:2976,327,0:0,1,53,60 chr1 53676448 . G A 2675.13 PASS AC=2;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 1/1:0,95:95:99:3132,283,0:0,0,47,48 chr1 53679229 . A G 2164.73 PASS AC=2;AF=0.588;AN=2;DP=1274;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant8-variant10-variant13-variant15-variant20-variant21-variant22-variant23-variant24-variant28-variant29-variant33-variant34-variant36-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2818,264,0:0,0,30,58 chr1 53681699 . T G 1826.25 PASS AC=2;AF=0.588;AN=2;DP=1718;MQ=60;set=variant-variant6-variant8-variant10-variant13-variant15-variant20-variant21-variant22-variant23-variant24-variant28-variant29-variant33-variant34-variant36-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3238,309,0:0,0,41,62 chr1 53684525 . C G 3093.41 PASS AC=2;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 1/1:0,44:44:99:1475,132,0:0,0,24,20 chr1 53686383 . C G 400.06 PASS AC=2;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 1/1:0,18:18:54:578,54,0:0,0,5,13 chr1 53692689 . A C 57.18 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1181;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:69,22:91:99:202,0,1411:6,63,20,2 chr1 53699360 . T C 626.34 PASS AC=1;AF=0.5;AN=2;DP=56;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.895;QD=11.18;ReadPosRankSum=1.52;SOR=0.773;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:30,26:56:99:655,0,713:11,19,9,17 chr1 53755117 . G A 829.41 PASS AC=2;AF=0.636;AN=2;DP=653;MQ=60;set=variant5-variant6-variant13-variant15-variant21-variant23-variant29-variant36-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1178,114,0:0,0,26,12 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 0/1:20,34:54:99:952,0,494:13,7,22,12 chr1 53792651 . A C 1511.81 PASS AC=1;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 0/1:51,83:134:99:2106,0,1343:14,37,34,49 chr1 53793170 . C T 82.67 PASS AC=1;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 0/1:7,8:15:99:190,0,230:2,5,4,4 chr1 53793248 . T G 40.7 PASS AC=1;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 0/1:6,6:12:99:193,0,140:3,3,3,3 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 0/1:11,26:37:99:573,0,174:4,7,13,13 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 0/1:15,21:36:99:556,0,360:10,5,13,8 chr1 53930672 . T TC 261.68 PASS AC=1;AF=0.5;AN=2;DP=21;FS=0;FractionInformativeReads=0.905;MQ=60;MQRankSum=1.184;QD=12.46;ReadPosRankSum=-2.572;SOR=0.836;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:299,0,264:3,6,3,7 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 0/1:2,3:5:72:120,0,72:0,2,0,3 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 0/1:48,38:86:99:944,0,1383:25,23,20,18 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 1/1:0,62:62:99:1973,184,0:0,0,27,35 chr1 53980389 . C T 1530.55 PASS AC=1;AF=0.625;AN=2;DP=672;FractionInformativeReads=1;MQ=60;set=variant-variant23-variant27-variant34 GT:AD:DP:GQ:PL:SB 0/1:100,71:171:99:1487,0,2536:57,43,40,31 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 1/1:0,43:43:99:1589,128,0:0,0,37,6 chr1 54060342 . G A 1066.23 PASS AC=1;AF=0.5;AN=2;DP=114;FS=4.684;FractionInformativeReads=0.991;MQ=60;MQRankSum=-0.282;QD=9.35;ReadPosRankSum=-0.682;SOR=0.375;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:65,48:113:99:1094,0,1819:39,26,24,24 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 1/1:0,2:2:6:84,6,0:0,0,2,0 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 1/1:0,30:30:89:794,89,0:0,0,16,14 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 1/1:0,44:44:99:1497,131,0:0,0,27,17 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 1/1:0,71:71:99:2019,212,0:0,0,38,33 chr1 54065997 . A T 1146.95 PASS AC=2;AF=0.932;AN=2;DP=1846;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:2490,172,0:0,0,21,36 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 1/1:0,56:56:99:2465,169,0:0,0,20,36 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 1/1:0,36:36:99:1214,107,0:0,0,9,27 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 1/1:0,52:52:99:1610,156,0:0,0,25,27 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 0/1:10,8:18:99:268,0,358:9,1,8,0 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 0/1:27,20:47:99:541,0,747:17,10,14,6 chr1 54344282 . C A 1103.92 PASS AC=1;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 0/1:40,39:79:99:976,0,905:24,16,25,14 chr1 54356113 . C T 1363.01 PASS AC=2;AF=0.63;AN=2;DP=2201;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant7-variant12-variant14-variant15-variant19-variant20-variant22-variant23-variant24-variant25-variant29-variant31-variant32-variant33-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:2873,284,0:0,0,59,36 chr1 54370264 . A T 1048.42 PASS AC=2;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 1/1:1,95:96:99:2957,246,0:1,0,59,36 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 1/1:0,133:133:99:3828,397,0:0,0,65,68 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 1/1:0,91:91:99:2786,272,0:0,0,45,46 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 1/1:0,6:6:18:257,18,0:0,0,0,6 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 0/1:45,24:69:99:236,0,746:21,24,15,9 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 1/1:0,220:220:99:6638,659,0:0,0,100,120 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 0/1:37:99:7,16,5,9 chr1 54561916 . C T 804.87 PASS AC=2;AF=0.771;AN=2;DP=1168;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant23-variant27-variant29-variant30-variant34-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1086,102,0:0,0,22,12 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 1/1:0,193:193:99:5785,576,0:0,0,98,95 chr1 54563156 . A G 2263.2 PASS AC=2;AF=0.771;AN=2;DP=3810;MQ=60;set=variant2-variant3-variant4-variant5-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant23-variant27-variant29-variant30-variant34-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,149:151:99:4810,403,0:1,1,73,76 chr1 54563239 . A T 2227.21 PASS AC=2;AF=0.614;AN=2;DP=4325;MQ=60;set=variant2-variant3-variant4-variant5-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant23-variant27-variant29-variant30-variant34-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,163:163:99:4902,488,0:0,0,86,77 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 1/1:0,10:10:30:354,30,0:0,0,7,3 chr1 54605319 . G GC 315.63 PASS AC=2;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 1/1:0,56:56:99:2202,171,0:0,0,30,26 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 1/1:0,95:95:99:3047,283,0:0,0,61,34 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 1/1:0,178:178:99:5649,534,0:0,0,69,109 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 1/1:0,60:60:99:1886,179,0:0,0,17,43 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 0/1:86,94:180:99:2308,0,1909:43,43,54,40 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 1/1:0,42:42:99:1346,126,0:0,0,18,24 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 0/1:21,14:35:99:373,0,594:10,11,5,9 chr1 54619477 . T G 206.75 PASS AC=1;AF=0.5;AN=2;DP=53;FractionInformativeReads=1;MQ=60;set=variant6-variant23 GT:AD:DP:GQ:PL:SB 0/1:15,5:20:81:81,0,394:5,10,2,3 chr1 54636782 . T A 883.22 PASS AC=1;AF=0.5;AN=2;DP=288;MQ=60;set=variant6-variant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:38,40:78:99:901,0,883:21,17,20,20 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 0/1:26,37:63:99:800,0,633:13,13,18,19 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 0/1:2,5:7:70:192,0,70:0,2,0,5 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 1/1:0,133:133:99:3957,397,0:0,0,57,76 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 0/1:45,77:122:99:1976,0,1031:25,20,45,32 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 0/1:58,83:141:99:1924,0,1402:30,28,40,43 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 0/1:63,84:147:99:2335,0,1543:40,23,45,39 chr1 54692854 . A AG,AGG 152.99 PASS AC=0,1;AF=0.286,0.333;AN=2;DP=673;MQ=60;set=variant-variant8-variant10-variant11-variant12-variant14-variant16-filterInvariant18-variant19-variant20-variant21-variant23-variant24-variant27-variant29-variant32-variant34-variant37-variant38-variant43-variant44 GT:DP:GQ:SB 0/2:20:99:11,4,5,0 chr1 54692865 . T G 779.34 PASS AC=1;AF=0.536;AN=2;DP=468;MQ=60;set=variant8-filterInvariant10-variant11-variant12-variant14-variant18-filterInvariant19-variant23-filterInvariant24-variant26-variant29-variant32-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,7:26:99:134,0,536:11,8,6,1 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 0/1:9,3:12:87:87,0,317:2,7,0,3 chr1 54704462 . C CCAG 519.76 PASS AC=2;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 1/1:0,46:46:99:2194,147,0:0,0,21,25 chr1 54704510 . A C 684.15 PASS AC=2;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 1/1:0,48:48:99:1319,144,0:0,0,24,24 chr1 54704567 . A G 1203.72 PASS AC=2;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 1/1:0,34:34:99:1040,102,0:0,0,13,21 chr1 54704629 . C T 211.72 PASS AC=2;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 1/1:0,27:27:78:789,78,0:0,0,8,19 chr1 54706733 . A G 629.55 PASS AC=2;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 1/1:0,72:72:99:2159,216,0:0,0,32,40 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 0/2:28:99:8,0,18,2 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 0/1:31,15:46:99:100,0,503:18,13,12,3 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 0/1:43,28:71:99:498,0,1031:27,16,16,12 chr1 54871469 . G A 55.47 PASS AC=2;AF=0.857;AN=2;DP=25;FS=0;FractionInformativeReads=1;MQ=60;set=variant19-variant23-variant25-variant26-variant33-variant38-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:128,12,0:0,0,1,3 chr1 54871566 . ACCGC A 97.85 PASS AC=1;AF=0.821;AN=2;DP=56;FS=0;MQ=60;set=variant4-variant5-variant6-variant8-variant10-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant36 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:49:81,0,49:1,0,2,0 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 0/1:43:99:12,10,12,9 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 1/1:52:99:0,0,33,19 chr1 55014099 . C T 1466.01 PASS AC=1;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 0/1:64,67:131:99:1818,0,1557:32,32,26,41 chr1 55014160 . C T 888.54 PASS AC=1;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 0/1:50,37:87:99:859,0,1255:20,30,15,22 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 0/1:48,37:85:99:894,0,988:31,17,22,15 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 0/1:17,13:30:99:418,0,495:15,2,12,1 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 0/1:60,47:107:99:1253,0,1725:29,31,19,28 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 0/1:58,67:125:99:1711,0,1455:36,22,40,27 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 0/1:56,56:112:99:1442,0,1371:28,28,26,30 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 1/1:0,20:20:60:877,60,0:0,0,20,0 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 1/2:77:99:4,3,26,44 chr1 55080629 . A G 2467.89 PASS AC=1;AF=0.739;AN=2;DP=3722;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:7,68:75:4:2637,0,4:4,3,27,41 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 0/1:72:99:14,23,15,20 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 0/1:11,9:20:99:345,0,436:3,8,2,7 chr1 55080844 . C G 250.2 PASS AC=1;AF=0.667;AN=2;DP=66;FS=0;FractionInformativeReads=1;MQ=60;set=variant7-variant8-variant15-variant17-variant23-variant24-variant25-variant31-variant33-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:65:72,0,65:1,2,0,2 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 1/1:0,20:20:60:585,60,0:0,0,10,10 chr1 55117460 . A ACTCTCT,ACTCT,ACTCTGT,ACTCTCTCTCTCT,ACTCTCTCT 52.73 PASS AC=2,0,0,0,0;AF=0.478,0.37,0.022,0.043,0.043;AN=2;DP=94;FS=0;MQRankSum=0.731;set=variant-variant2-variant4-variant5-variant8-variant11-variant14-variant15-variant16-variant19-variant22-variant23-variant24-variant25-variant28-variant30-variant31-variant33-variant34-variant37-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:4:12:0,0,2,2 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 1/1:0,8:8:24:255,24,0:0,0,5,3 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 1/1:0,98:98:99:2836,293,0:0,0,53,45 chr1 55119144 . A G 1695.21 PASS AC=1;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 0/1:64,69:133:99:1719,0,1618:32,32,35,34 chr1 55119289 . G C 5352.67 PASS AC=1;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 0/1:59,82:141:99:2201,0,1462:29,30,43,39 chr1 55119515 . T G 2807.71 PASS AC=1;AF=0.568;AN=2;DP=4538;MQ=60;set=variant2-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant17-variant23-variant24-variant25-variant26-variant28-variant31-variant34-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:101,82:183:99:2076,0,2438:50,51,37,45 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 1/1:0,174:174:99:5273,521,0:0,0,83,91 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 0/1:9,4:13:66:66,0,377:8,1,3,1 chr1 55129564 . T C 684.31 PASS AC=1;AF=0.5;AN=2;DP=179;FractionInformativeReads=1;MQ=60;set=variant12-variant13-variant23-variant30-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,14:26:99:369,0,296:3,9,4,10 chr1 55130931 . C T 731.34 PASS AC=1;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 0/1:39,22:61:99:584,0,1040:14,25,5,17 chr1 55130946 . G C 644.13 PASS AC=1;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 0/1:32,16:48:99:484,0,830:11,21,2,14 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 1/1:0,34:34:99:1060,101,0:0,0,9,25 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 1/1:0,21:21:63:765,63,0:0,0,18,3 chr1 55134487 . G A 918.35 PASS AC=1;AF=0.6;AN=2;DP=2179;MQ=60;set=variant5-variant8-variant9-variant11-variant12-variant13-variant15-variant17-variant23-variant24-variant25-variant26-variant28-variant31-variant34-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,57:95:99:1398,0,792:21,17,31,26 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 1/1:0,23:23:69:814,69,0:0,0,17,6 chr1 55136356 . C T 301.72 PASS AC=1;AF=0.5;AN=2;DP=132;MQ=60;set=variant2-variant10-variant15-variant23-variant30-variant36-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,13:24:99:433,0,325:3,8,1,12 chr1 55136529 . T C 1047.48 PASS AC=1;AF=0.619;AN=2;DP=2552;MQ=60;set=variant5-variant8-variant9-variant11-variant12-variant13-variant15-variant17-variant23-variant24-variant25-variant26-variant28-variant31-variant34-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,57:114:99:1293,0,1350:33,24,29,28 chr1 55138673 . C T 157.76 PASS AC=1;AF=0.611;AN=2;DP=236;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant9-variant12-variant13-variant17-variant23-variant24-variant25-variant26-variant28-variant31-variant34-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,8:19:99:141,0,217:6,5,4,4 chr1 55139741 . A G 1115.68 PASS AC=1;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 0/1:37,39:76:99:939,0,825:20,17,17,22 chr1 55167773 . T A 2209.81 PASS AC=1;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 0/1:32,31:63:99:772,0,791:14,18,14,17 chr1 55174631 . T TG 66.65 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=74;FractionInformativeReads=1;MQ=60;SOR=3.584;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:29,5:34:67:67,0,1452:28,1,0,5 chr1 55174636 . T G 63.6 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=203;FractionInformativeReads=1;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:30,10:40:67:67,0,1452:28,2,0,10 chr1 55223262 . T C 390.69 PASS AC=1;AF=0.5;AN=2;DP=64;FractionInformativeReads=1;MQ=60;set=variant11-variant23 GT:AD:DP:GQ:PL:SB 0/1:14,15:29:99:336,0,409:7,7,9,6 chr1 55230233 . T C 1938.96 PASS AC=1;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 0/1:37,39:76:99:855,0,919:15,22,17,22 chr1 55246522 . T C 491.35 PASS AC=1;AF=0.536;AN=2;DP=510;MQ=60;set=variant4-variant6-variant9-variant14-variant16-variant17-variant22-variant23-variant24-variant27-variant30-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,11:26:99:293,0,360:9,6,6,5 chr1 55247097 . G A 1327.88 PASS AC=1;AF=0.529;AN=2;DP=1149;MQ=60;set=variant3-variant8-variant10-variant11-variant12-variant13-variant19-variant20-variant23-variant25-variant27-variant31-variant32-variant34-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:32,19:51:99:544,0,740:16,16,9,10 chr1 55248074 . A G 3803.92 PASS AC=1;AF=0.5;AN=2;DP=3595;MQ=60;set=variant3-variant8-variant10-variant11-variant12-variant13-variant19-variant20-variant23-variant25-variant27-variant31-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:83,113:196:99:2675,0,1813:47,36,62,51 chr1 55248184 . C T 2444.56 PASS AC=1;AF=0.5;AN=2;DP=410;FractionInformativeReads=1;MQ=60;set=variant9-variant23 GT:AD:DP:GQ:PL:SB 0/1:98,92:190:99:2231,0,2506:35,63,36,56 chr1 55250479 . C T 1835.03 PASS AC=1;AF=0.5;AN=2;DP=2082;MQ=60;set=variant3-variant8-variant10-variant11-variant12-variant13-variant19-variant20-variant23-variant25-variant27-variant31-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:90,71:161:99:1658,0,2391:43,47,33,38 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 1/1:0,74:74:99:2159,220,0:0,0,45,29 chr1 55252514 . C T 518.15 PASS AC=1;AF=0.5;AN=2;DP=486;MQ=60;set=variant3-variant8-variant10-variant11-variant12-variant13-variant19-variant20-variant23-variant25-variant27-variant31-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:25,15:40:99:332,0,699:16,9,10,5 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 0/1:47,49:96:99:1285,0,1318:29,18,23,26 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 1/1:0,84:84:99:2927,252,0:0,0,29,55 chr1 55266797 . G C 3869.4 PASS AC=1;AF=0.5;AN=2;DP=6830;MQ=60;set=variant-variant2-variant4-variant9-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant27-variant29-variant30-variant33-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:155,142:297:99:3190,0,3814:69,86,65,77 chr1 55272643 . C G 2716.71 PASS AC=1;AF=0.545;AN=2;DP=2241;FractionInformativeReads=1;MQ=60;set=variant3-variant10-variant11-variant12-variant17-variant20-variant23-variant25-variant26-variant31-variant40 GT:AD:DP:GQ:PL:SB 0/1:93,85:178:99:2067,0,2206:56,37,53,32 chr1 55273422 . A T 569.47 PASS AC=1;AF=0.5;AN=2;DP=477;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant9-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant27-variant29-variant30-variant33-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,17:27:99:562,0,283:5,5,7,10 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 1/1:0,128:128:99:3750,383,0:0,0,73,55 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 1/1:0,7:7:21:315,21,0:0,0,3,4 chr1 55279688 . G A 249.98 PASS AC=1;AF=0.5;AN=2;DP=202;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant14-variant19-variant22-variant23-variant27-variant30-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:155,0,355:2,8,3,3 chr1 55307501 . A G 1349.49 PASS AC=1;AF=0.523;AN=2;DP=2795;MQ=60;set=variant-variant2-variant4-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant27-variant29-variant30-variant32-variant33-variant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,57:113:99:1278,0,1519:21,35,25,32 chr1 55307640 . C T 736.83 PASS AC=1;AF=0.523;AN=2;DP=1744;MQ=60;set=variant-variant2-variant4-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant27-variant29-variant30-variant32-variant33-variant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,35:64:99:917,0,717:15,14,17,18 chr1 55307693 . C A 685.97 PASS AC=1;AF=0.523;AN=2;DP=1574;MQ=60;set=variant-variant2-variant4-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant27-variant29-variant30-variant32-variant33-variant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,38:62:99:964,0,501:11,13,21,17 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 1/1:0,19:19:57:641,57,0:0,0,14,5 chr1 55315611 . C G 434.54 PASS AC=2;AF=0.607;AN=2;DP=1256;MQ=60;set=variant-variant2-variant3-variant4-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant27-variant29-variant30-variant31-variant32-variant33-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1290,120,0:0,0,22,18 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 1/1:0,37:37:99:1209,111,0:0,0,16,21 chr1 55316322 . A G 315.05 PASS AC=2;AF=0.607;AN=2;DP=1416;MQ=60;set=variant-variant2-variant3-variant4-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant27-variant29-variant30-variant31-variant32-variant33-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1367,132,0:0,0,25,19 chr1 55316418 . G A 953.13 PASS AC=1;AF=0.5;AN=2;DP=594;MQ=60;set=variant3-variant9-variant10-variant11-variant17-variant20-variant23-variant31-variant40 GT:AD:DP:GQ:PL:SB 0/1:38,31:69:99:784,0,953:21,17,15,16 chr1 55317582 . A G 931.86 PASS AC=1;AF=0.5;AN=2;DP=568;FractionInformativeReads=1;MQ=60;set=variant3-variant9-variant10-variant11-variant17-variant20-variant23-variant31-variant40 GT:AD:DP:GQ:PL:SB 0/1:28,29:57:99:787,0,747:11,17,12,17 chr1 55317685 . G A 204.1 PASS AC=1;AF=0.523;AN=2;DP=776;MQ=60;set=variant-variant2-variant4-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant27-variant29-variant30-variant32-variant33-variant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,14:27:99:389,0,408:4,9,6,8 chr1 55318108 . C T 403.82 PASS AC=2;AF=0.593;AN=2;DP=1734;MQ=60;set=variant-variant2-variant3-variant4-variant9-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant27-variant29-variant30-variant31-variant32-variant33-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2317,230,0:0,0,28,49 chr1 55319008 . T C 46.75 PASS AC=2;AF=0.607;AN=2;DP=937;MQ=60;set=variant-variant2-variant3-variant4-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant27-variant29-variant30-variant31-variant32-variant33-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1085,96,0:0,0,24,8 chr1 55319935 . GA G 1069.84 PASS AC=1;AF=0.5;AN=2;DP=650;MQ=60;set=variant3-variant9-variant10-variant11-variant17-variant20-variant23-variant31-variant40 GT:AD:DP:GQ:PL:SB 0/1:18,36:54:99:958,0,395:7,11,13,23 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 1/1:0,49:49:99:1620,147,0:0,0,35,14 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 0/1:9,9:18:99:300,0,350:8,1,8,1 chr1 55337396 . G C 319.05 PASS AC=1;AF=0.5;AN=2;DP=29;FS=8.741;FractionInformativeReads=1;MQ=60;MQRankSum=0.161;QD=11;ReadPosRankSum=0.803;SOR=3.014;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:19,10:29:99:347,0,605:5,14,0,10 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 1/1:0,13:13:39:442,39,0:0,0,7,6 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 1/1:0,104:104:99:4571,322,0:0,0,62,42 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 1/1:0,104:104:99:4526,316,0:0,0,62,42 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 1/1:0,125:125:99:3793,372,0:0,0,75,50 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 1/1:0,95:95:99:3102,284,0:0,0,48,47 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 1/1:0,89:89:99:2856,267,0:0,0,41,48 chr1 55464743 . T C 2312.39 PASS AC=1;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 0/1:51,39:90:99:917,0,1411:34,17,23,16 chr1 55464790 . C G 3781.15 PASS AC=1;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 0/1:73,69:142:99:1645,0,1819:40,33,40,29 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 0/1:9,16:25:99:420,0,211:5,4,9,7 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 0/1:54,49:103:99:1232,0,1486:28,26,23,26 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 0/1:40,43:83:99:1089,0,1050:19,21,20,23 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 0/1:36,39:75:99:1098,0,814:19,17,20,19 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 0/1:22,30:52:99:855,0,609:9,13,14,16 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 0/1:31,32:63:99:792,0,710:16,15,17,15 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 0/1:29,52:81:99:1257,0,740:13,16,23,29 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 0/1:2,2:4:75:78,0,75:1,1,0,2 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 0/1:26,23:49:99:464,0,765:12,14,10,13 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 0/1:26,18:44:99:475,0,707:15,11,7,11 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 0/1:45,25:70:99:574,0,1197:23,22,11,14 chr1 55505647 . G T 2859.45 PASS AC=1;AF=0.5;AN=2;DP=1316;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant18-variant23-variant30-variant36 GT:AD:DP:GQ:PL:SB 0/1:97,76:173:99:1645,0,2377:44,53,34,42 chr1 55505732 . A G 4357.89 PASS AC=2;AF=0.955;AN=2;DP=5856;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3213,314,0:0,0,40,65 chr1 55505861 . G A 378.45 PASS AC=2;AF=0.615;AN=2;DP=943;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant28-variant30-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:823,75,0:0,0,9,16 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 1/1:0,96:96:99:2842,287,0:0,0,60,36 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 1/1:0,51:51:99:1518,153,0:0,0,30,21 chr1 55517883 . C G 774.29 PASS AC=2;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 1/1:0,61:61:99:1908,183,0:0,0,37,24 chr1 55518166 . G A 280.12 PASS AC=2;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 1/1:0,51:51:99:1840,153,0:0,0,31,20 chr1 55518190 . AC A,ACC 1031.66 PASS AC=2,0;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 1/1:59:99:0,0,35,24 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 1/1:1,63:64:99:1913,181,0:0,1,24,39 chr1 55521899 . GGGGCGGA G 98.97 PASS AC=2;AF=1;AN=2;DP=203;FS=0;MQ=60;MQRankSum=0.747;ReadPosRankSum=0.747;set=variant-variant2-variant3-variant8-variant16-variant19-variant22-variant23-variant26-variant28-variant29-variant32-variant34-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:19:263,19,0:0,0,0,6 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 1/1:0,90:90:99:2946,270,0:0,0,42,48 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 1/1:0,21:21:63:755,63,0:0,0,12,9 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 1/1:0,39:39:99:1199,117,0:0,0,20,19 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 1/1:0,32:32:96:985,96,0:0,0,11,21 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 1/1:0,25:25:75:739,75,0:0,0,9,16 chr1 55525400 . G A 707.07 PASS AC=2;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 1/1:0,25:25:75:755,75,0:0,0,11,14 chr1 55527323 . G A 1814.01 PASS AC=2;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 1/1:0,58:58:99:1955,174,0:0,0,19,39 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 1/1:0,7:7:21:221,21,0:0,0,2,5 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 1/1:0,129:129:99:4080,385,0:0,0,53,76 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 1/1:0,72:72:99:2247,216,0:0,0,39,33 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 1/1:0,83:83:99:2591,248,0:0,0,28,55 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 1/1:0,50:50:99:1701,150,0:0,0,21,29 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 1/1:0,44:44:99:1456,132,0:0,0,32,12 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 1/1:0,59:59:99:1849,177,0:0,0,25,34 chr1 55541340 . ACCACCACC A,AACCACC 121.03 PASS AC=0,2;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 2/2:9:28:0,0,2,7 chr1 55541343 . ACCAC AAC,ACAC,A 578.1 PASS AC=0,2,0;AF=0.167,0.25,0.167;AN=2;DP=97;MQ=60;set=variant4-variant18-variant23-variant24-variant28-variant39 GT:DP:GQ:SB 2/2:9:28:0,0,2,7 chr1 55541347 . C A 378.51 PASS AC=2;AF=0.75;AN=2;DP=20;FractionInformativeReads=1;MQ=60;MQRankSum=-0.717;ReadPosRankSum=-0.717;set=variant23-variant28 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:28:407,28,0:0,0,2,7 chr1 55541348 . C A 376.77 PASS AC=2;AF=0.75;AN=2;DP=20;FractionInformativeReads=1;MQ=60;MQRankSum=1.932;ReadPosRankSum=-1.031;set=variant23-variant28 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:405,27,0:0,0,2,7 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 1/1:0,17:17:51:582,51,0:0,0,4,13 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 1/1:0,7:7:21:274,21,0:0,0,6,1 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 1/1:0,16:16:48:539,48,0:0,0,12,4 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 1/1:0,29:29:87:1263,87,0:0,0,6,23 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 1/1:0,25:25:78:1169,78,0:0,0,4,21 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 1/1:0,5:5:15:169,15,0:0,0,1,4 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 1/1:0,7:7:21:286,21,0:0,0,7,0 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 1/1:0,5:5:15:214,15,0:0,0,5,0 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 1/1:0,14:14:42:630,42,0:0,0,13,1 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 1/1:0,6:6:18:249,18,0:0,0,6,0 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 1/1:1,88:89:99:2934,237,0:1,0,34,54 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 1/1:0,76:76:99:2345,228,0:0,0,47,29 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 1/1:0,7:7:21:271,21,0:0,0,6,1 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 1/1:0,14:14:42:630,42,0:0,0,12,2 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 1/1:0,8:8:24:300,24,0:0,0,7,1 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 1/1:0,79:79:99:2437,237,0:0,0,48,31 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 1/1:0,37:37:99:1272,111,0:0,0,9,28 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 1/1:0,59:59:99:1736,177,0:0,0,32,27 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 1/1:0,70:70:99:2095,210,0:0,0,37,33 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 1/1:0,27:27:81:891,81,0:0,0,13,14 chr1 57111169 . C G 1756.07 PASS AC=2;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 1/1:0,146:146:99:4180,437,0:0,0,69,77 chr1 57158293 . G A 241.76 PASS AC=2;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 1/1:0,13:13:39:521,39,0:0,0,1,12 chr1 57170229 . T C 197.93 PASS AC=2;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 1/1:0,13:13:39:541,39,0:0,0,2,11 chr1 57179521 . TAA TA,TAAA,T,TAAAA 254.71 PASS AC=1,1,0,0;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 1/2:42:85:6,4,15,17 chr1 57180867 . A G 6439.51 PASS AC=2;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 1/1:0,233:233:99:7068,699,0:0,0,120,113 chr1 57184465 . T G 1424.56 PASS AC=2;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 1/1:0,52:52:99:1488,156,0:0,0,28,24 chr1 57185818 . A G 3411.71 PASS AC=2;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 1/1:0,73:73:99:2506,219,0:0,0,47,26 chr1 57192353 . TAAA T 283.84 PASS AC=2;AF=0.553;AN=2;DP=293;MQ=60;set=variant-variant5-variant7-variant10-variant12-variant17-variant21-variant22-variant23-variant25-variant27-variant28-variant30-variant32-variant33-variant34-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:405,27,0:0,0,1,8 chr1 57219631 . G GA 355.57 PASS AC=1;AF=0.7;AN=2;DP=613;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:174,0,117:1,4,1,6 chr1 57221553 . G T 3909.68 PASS AC=1;AF=0.694;AN=2;DP=2646;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,24:48:99:848,0,1134:11,13,14,10 chr1 57221554 . A G 3909.68 PASS AC=1;AF=0.694;AN=2;DP=2660;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,24:48:99:848,0,1134:11,13,14,10 chr1 57224460 . G C 2933.88 PASS AC=1;AF=0.681;AN=2;DP=3568;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,32:77:99:762,0,1129:22,23,18,14 chr1 57232805 . T C 148.54 PASS AC=1;AF=0.615;AN=2;DP=66;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant8-variant11-variant16-variant20-variant23-variant27-variant32-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:37:81,0,37:1,0,2,0 chr1 57254900 . G A 39.46 PASS AC=1;AF=0.6;AN=2;DP=67;FractionInformativeReads=1;MQ=60;set=variant13-variant16-variant18-variant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:9,4:13:99:130,0,287:3,6,0,4 chr1 57320444 . G A 493.35 PASS AC=1;AF=0.5;AN=2;DP=77;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant23 GT:AD:DP:GQ:PL:SB 0/1:8,11:19:99:313,0,249:7,1,8,3 chr1 57340860 . G A 245.84 PASS AC=1;AF=0.531;AN=2;DP=307;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant7-variant10-variant14-variant18-variant21-variant22-variant23-variant24-variant28-variant36-variant37-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:221,0,268:2,6,1,6 chr1 57349407 . A T 241.62 PASS AC=1;AF=0.5;AN=2;DP=326;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant7-variant10-variant14-variant18-variant21-variant23-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:15,14:29:99:373,0,429:4,11,4,10 chr1 57349464 . T C 76.98 PASS AC=1;AF=0.5;AN=2;DP=121;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant7-variant10-variant14-variant18-variant21-variant23-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:99:107,0,218:2,5,1,3 chr1 57372591 . C T 1290.88 PASS AC=2;AF=0.792;AN=2;DP=1739;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1320,132,0:0,0,16,28 chr1 57373500 . GAGA G 620.64 PASS AC=2;AF=0.591;AN=2;DP=555;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant27-variant29-variant30-variant32-variant38-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:1016,69,0:0,0,19,4 chr1 57383358 . C T 240.13 PASS AC=1;AF=0.5;AN=2;DP=535;MQ=60;set=variant-variant11-variant12-variant15-variant18-variant23-variant30-variant32 GT:AD:DP:GQ:PL:SB 0/1:36,35:71:99:773,0,799:17,19,16,19 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 1/1:0,108:108:99:3039,324,0:0,0,54,54 chr1 57395294 . G A 1078.37 PASS AC=1;AF=0.5;AN=2;DP=188;FractionInformativeReads=1;MQ=60;set=variant7-variant23 GT:AD:DP:GQ:PL:SB 0/1:51,43:94:99:1057,0,1301:20,31,14,29 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 1/1:0,25:25:75:1009,75,0:0,0,22,3 chr1 57409329 . A G 1737.97 PASS AC=1;AF=0.5;AN=2;DP=477;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant23 GT:AD:DP:GQ:PL:SB 0/1:64,47:111:99:1117,0,1707:39,25,30,17 chr1 57415459 . A G 56.89 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=32;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.778;QD=1.78;ReadPosRankSum=-0.208;SOR=0.49;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:27,5:32:85:85,0,841:6,21,1,4 chr1 57417633 . G GGGATGTGTCCAAGGTCACACA 763.33 PASS AC=2;AF=0.757;AN=2;DP=401;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:33:494,33,0:0,0,8,1 chr1 57418056 . G C 346.01 PASS AC=1;AF=0.5;AN=2;DP=85;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant22-variant23-variant37 GT:AD:DP:GQ:PL:SB 0/1:7,8:15:99:227,0,257:0,7,2,6 chr1 57422484 . C T 6742.71 PASS AC=2;AF=0.932;AN=2;DP=9498;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,192:192:99:5617,575,0:0,0,87,105 chr1 57425888 . AG A 942.66 PASS AC=2;AF=0.545;AN=2;DP=910;MQ=60;set=variant-variant5-variant7-variant11-variant18-variant22-variant23-variant28-variant32-variant36-variant37 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2554,219,0:0,0,22,51 chr1 57463192 . CA C 4252.22 PASS AC=1;AF=0.5;AN=2;DP=1516;MQ=60;set=variant-variant9-variant12-variant23-variant36 GT:AD:DP:GQ:PL:SB 0/1:164,128:292:99:3474,0,4588:70,94,55,73 chr1 57463326 . C T 2531.21 PASS AC=1;AF=0.583;AN=2;DP=3268;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant13-variant16-variant18-variant21-variant23-variant24-variant30-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:87,65:152:99:1598,0,2270:39,48,30,35 chr1 57498844 . T TAC,TACAC,TACACAC 539.35 PASS AC=0,0,1;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 0/3:9:99:4,1,4,0 chr1 57528772 . A G 309.11 PASS AC=1;AF=0.898;AN=2;DP=1352;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:17,18:35:99:600,0,403:6,11,3,15 chr1 57535198 . C A 1408.5 PASS AC=1;AF=0.615;AN=2;DP=465;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant10-variant21-variant23-variant26-variant33-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:16,13:29:99:360,0,351:7,9,4,9 chr1 57536941 . A G 283.54 PASS AC=2;AF=0.625;AN=2;DP=118;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant7-variant8-variant10-variant21-variant23-variant26-variant33-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,1,1 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 1/1:0,9:9:27:317,27,0:0,0,7,2 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 1/1:0,75:75:99:2237,223,0:0,0,33,42 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 1/1:0,126:126:99:3762,377,0:0,0,62,64 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 1/1:0,109:109:99:3228,325,0:0,0,50,59 chr1 59120399 . T G 259.35 PASS AC=2;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 1/1:0,19:19:57:651,57,0:0,0,14,5 chr1 59120563 . A G 942.52 PASS AC=2;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 1/1:0,63:63:99:1771,188,0:0,0,31,32 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 1/1:0,61:61:99:2676,184,0:0,0,31,30 chr1 59120589 . C T 946.76 PASS AC=2;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 1/1:0,56:56:99:2550,175,0:0,0,31,25 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 1/1:0,71:71:99:2379,213,0:0,0,40,31 chr1 59120961 . G A 2837.18 PASS AC=2;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 1/1:3,178:181:99:5381,483,0:1,2,103,75 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 1/1:0,218:218:99:6705,655,0:0,0,118,100 chr1 59121144 . A AT 3652.26 PASS AC=2;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 1/1:0,169:169:99:5212,510,0:0,0,78,91 chr1 59121166 . G A 3402.31 PASS AC=2;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 1/1:0,142:142:99:4488,424,0:0,0,65,77 chr1 59121343 . T A 911.11 PASS AC=2;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 1/1:1,85:86:99:2816,212,0:0,1,41,44 chr1 59121768 . G C 815.07 PASS AC=2;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 1/1:0,47:47:99:1899,141,0:0,0,18,29 chr1 59122289 . T G 3457.18 PASS AC=2;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 1/1:1,200:201:99:6316,593,0:0,1,83,117 chr1 59122871 . C T 2293.81 PASS AC=2;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 1/1:0,133:133:99:4190,397,0:0,0,65,68 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 1/1:107:99:2,1,40,64 chr1 59124546 . A G 1741.88 PASS AC=2;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 1/1:0,105:105:99:3443,313,0:0,0,56,49 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 3/3:67:99:0,0,42,25 chr1 59124803 . C T 5764.57 PASS AC=2;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 1/1:0,269:269:99:8212,807,0:0,0,128,141 chr1 59125683 . C T 1049.05 PASS AC=2;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 1/1:0,61:61:99:1985,183,0:0,0,29,32 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 1/1:0,12:12:36:452,36,0:0,0,10,2 chr1 59127207 . T C 578.94 PASS AC=2;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 1/1:0,22:22:66:806,66,0:0,0,5,17 chr1 59131088 . A G 518.61 PASS AC=2;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 1/1:0,31:31:96:1431,96,0:0,0,24,7 chr1 59131089 . A C 518.61 PASS AC=2;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 1/1:0,32:32:96:1431,96,0:0,0,25,7 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 1/1:0,75:75:99:2301,224,0:0,0,27,48 chr1 59133024 . T G 64.09 PASS AC=2;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 1/1:0,9:9:27:356,27,0:0,0,1,8 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 1/1:97:99:0,0,46,51 chr1 59137783 . A G 502.75 PASS AC=2;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 1/1:0,13:13:39:497,39,0:0,0,2,11 chr1 59139223 . C G 1060.92 PASS AC=2;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 1/1:0,103:103:99:3139,308,0:0,0,62,41 chr1 59142713 . T C 1606.56 PASS AC=2;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 1/1:0,110:110:99:3262,330,0:0,0,43,67 chr1 59147420 . G A 365.29 PASS AC=2;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 1/1:0,14:14:42:527,42,0:0,0,11,3 chr1 59147926 . T C 1272.13 PASS AC=2;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 1/1:0,76:76:99:2631,228,0:0,0,37,39 chr1 59148118 . A T 2128.57 PASS AC=2;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 1/1:0,161:161:99:4993,483,0:0,0,72,89 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 1/1:0,54:54:99:1603,162,0:0,0,22,32 chr1 59150997 . TA T 48.61 PASS AC=2;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 1/1:0,20:20:60:515,60,0:0,0,7,13 chr1 59156155 . C T 397.55 PASS AC=2;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 1/1:0,22:22:66:690,66,0:0,0,8,14 chr1 59158632 . T C 904.75 PASS AC=2;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 1/1:0,52:52:99:1647,156,0:0,0,16,36 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 0/1:2,12:14:11:278,0,11:1,1,10,2 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 1/1:0,140:140:99:4884,420,0:0,0,39,101 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 1/1:0,64:64:99:1837,190,0:0,0,29,35 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 1/1:0,99:99:99:2904,296,0:0,0,46,53 chr1 59251097 . T G 540.12 PASS AC=1;AF=0.563;AN=2;DP=314;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant11-variant13-variant16-variant23-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:18,14:32:99:526,0,590:3,15,0,14 chr1 59364615 . G C 1133.15 PASS AC=1;AF=0.526;AN=2;DP=851;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant9-variant17-variant19-variant20-variant23-variant24-variant26-variant27-variant29-variant32-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,25:48:99:610,0,564:14,9,15,10 chr1 59364918 . G A 1573.4 PASS AC=1;AF=0.524;AN=2;DP=1387;MQ=60;set=variant2-variant4-variant5-variant9-variant13-variant17-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant29-variant32-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,26:45:99:627,0,507:11,8,14,12 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 0/1:75,53:128:99:1263,0,1685:39,36,30,23 chr1 60199133 . G GTTTT 291.73 PASS AC=2;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 1/1:0,6:6:18:256,18,0:0,0,0,6 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 1/1:0,119:119:99:5351,364,0:0,0,69,50 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 1/1:3,323:326:99:8324,933,0:3,0,164,159 chr1 60299125 . A G 1378.36 PASS AC=1;AF=0.5;AN=2;DP=353;MQ=60;set=variant2-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:43,63:106:99:1449,0,905:21,22,34,29 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 1/1:72:99:0,0,36,36 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 0/1:7,6:13:99:228,0,218:1,6,0,6 chr1 60466911 . ACAG A 925.35 PASS AC=2;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 1/1:3,64:67:70:2746,70,0:2,1,29,35 chr1 60466921 . C A 791.22 PASS AC=1;AF=0.5;AN=2;DP=72;FS=0.889;FractionInformativeReads=0.972;MQ=60;MQRankSum=-2.153;QD=10.99;ReadPosRankSum=0.471;SOR=0.821;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:37,33:70:99:819,0,806:18,19,15,18 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 1/1:0,52:52:99:1764,156,0:0,0,35,17 chr1 60503762 . T C 557.24 PASS AC=1;AF=0.567;AN=2;DP=803;MQ=60;set=variant-variant3-variant4-variant7-variant9-variant10-variant12-variant18-variant22-variant23-variant29-variant31-variant32-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:33,24:57:99:744,0,835:11,22,3,21 chr1 60505578 . A G 480.75 PASS AC=1;AF=0.909;AN=2;DP=992;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:254,0,319:8,5,7,2 chr1 61331160 . CTT CTTT,CT,C,CTTTT,CTTTTT 51.45 PASS AC=1,0,0,0,0;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 0/1:10:13:1,2,0,7 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 1/1:0,16:16:48:598,48,0:0,0,13,3 chr1 61553801 . C G 503.16 PASS AC=1;AF=0.5;AN=2;DP=476;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant11-variant22-variant23-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,22:48:99:546,0,743:17,9,15,7 chr1 61743160 . G A 3298.98 PASS AC=2;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 1/1:0,84:84:99:2424,251,0:0,0,39,45 chr1 61818422 . A G 384.2 PASS AC=2;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 1/1:0,3:3:9:132,9,0:0,0,0,3 chr1 61818428 . TACACACAC T,TACACACACACAC,TACACAC,TACACACACAC,TACACACACACACAC,TACAC 375.77 PASS AC=0,2,0,0,0,0;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 2/2:2:6:0,0,0,2 chr1 61869783 . G A 2951.53 PASS AC=1;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 0/1:104,73:177:99:1785,0,2719:63,41,46,27 chr1 61872228 . C T 107.49 PASS AC=1;AF=0.5;AN=2;DP=521;MQ=60;set=variant-variant2-variant4-variant7-variant8-variant10-variant14-variant16-variant18-variant23-variant26-variant27-variant33-variant34-variant39 GT:AD:DP:GQ:PL:SB 0/1:17,12:29:99:248,0,444:5,12,4,8 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 1/1:0,78:78:99:2902,235,0:0,0,33,45 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 0/1:144:99:12,13,59,60 chr1 61922046 . T TA,TAA 1569.72 PASS AC=1,0;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 0/1:39:44:3,3,18,15 chr1 61924359 . CTTT CTT,CTTTT,CT,C 509.74 PASS AC=1,0,0,0;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 0/1:73:99:22,34,5,12 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 1/1:0,57:57:99:1658,170,0:0,0,29,28 chr1 62148968 . C A 40.69 PASS AC=2;AF=0.7;AN=2;DP=33;FS=0;FractionInformativeReads=1;MQ=60;set=variant8-variant22-variant23-variant32-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:94,9,0:0,0,2,1 chr1 62149237 . C G 1338.7 PASS AC=1;AF=0.529;AN=2;DP=1321;MQ=60;set=variant4-variant8-variant9-variant12-variant14-variant16-variant18-variant21-variant22-variant23-variant27-variant28-variant29-variant32-variant36-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,27:76:99:603,0,1033:26,23,14,13 chr1 62160525 . T TTA,TTATA 150.99 PASS AC=1,0;AF=0.458,0.083;AN=2;DP=198;MQ=60;set=variant4-variant8-variant12-variant16-variant18-variant22-variant23-variant28-variant29-variant32-variant36-variant41 GT:DP:GQ:SB 0/1:9:88:1,2,2,4 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 1/1:0,8:8:24:342,24,0:0,0,2,6 chr1 62208244 . C G 670.13 PASS AC=1;AF=0.5;AN=2;DP=376;MQ=60;set=variant3-variant9-variant12-variant17-variant23-variant38 GT:AD:DP:GQ:PL:SB 0/1:34,27:61:99:627,0,813:15,19,11,16 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 1/1:0,44:44:99:1193,131,0:0,0,20,24 chr1 62208336 . TG T 74.62 PASS AC=1;AF=0.5;AN=2;DP=132;MQ=60;set=variant3-variant9-variant12-variant17-variant23-variant38 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:325,0,267:2,5,3,6 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 0/1:9,7:16:99:208,0,325:3,6,2,5 chr1 62208338 . C A 83.64 PASS AC=1;AF=0.5;AN=2;DP=125;MQ=60;set=variant3-variant9-variant12-variant17-variant23-variant38 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:325,0,267:2,5,3,6 chr1 62208340 . C A 83.59 PASS AC=1;AF=0.5;AN=2;DP=120;FractionInformativeReads=1;MQ=60;set=variant3-variant9-variant12-variant17-variant23-variant38 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:325,0,267:2,5,3,6 chr1 62231924 . T TTGA 403.5 PASS AC=2;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 1/1:0,17:17:51:765,51,0:0,0,16,1 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 1/1:0,66:66:99:1957,198,0:0,0,40,26 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 0/1:26,26:52:99:713,0,585:13,13,11,15 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 0/1:82,63:145:99:1471,0,1950:37,45,28,35 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 0/1:5,5:10:99:141,0,195:0,5,2,3 chr1 62329885 . AT A 95.59 PASS AC=2;AF=0.609;AN=2;DP=468;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant20-variant22-variant23-variant27-variant32-variant36-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:810,78,0:0,0,20,6 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 1/1:0,88:88:99:2847,264,0:0,0,43,45 chr1 62330374 . A T 1127.84 PASS AC=2;AF=0.636;AN=2;DP=1001;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant11-variant12-variant20-variant23-variant32-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,91:91:99:2859,271,0:0,0,34,57 chr1 62341157 . T C 570.04 PASS AC=1;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 0/1:2,10:12:55:392,0,55:0,2,0,10 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 0/1:22,18:40:99:376,0,531:14,8,11,7 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 0/1:12,11:23:99:323,0,357:1,11,1,10 chr1 62374267 . T C 361.25 PASS AC=2;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 1/1:0,14:14:42:485,42,0:0,0,4,10 chr1 62380124 . A G 631.18 PASS AC=1;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 0/1:9,10:19:99:254,0,262:7,2,6,4 chr1 62380223 . G T 1971.18 PASS AC=1;AF=0.583;AN=2;DP=2218;set=variant3-variant4-variant7-variant12-variant15-variant16-variant17-variant18-variant23-variant24-variant29-variant33-variant34-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,39:92:99:906,0,1279:30,23,23,16 chr1 62380270 . C T 3038.52 PASS AC=2;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 1/1:0,100:100:99:2851,299,0:0,0,51,49 chr1 62380298 . G A 2452.33 PASS AC=2;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 1/1:0,90:90:99:2596,268,0:0,0,39,51 chr1 62393394 . A G 4608.49 PASS AC=2;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 1/1:0,144:144:99:4266,432,0:0,0,76,68 chr1 62417951 . A AG 508.43 PASS AC=2;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 1/1:0,13:13:38:536,38,0:0,0,11,2 chr1 62417952 . A AGAGAGAG,AG,AGAGAGAGAG,AGAGAGAGAGAGAG,AGAGAGAGAGAGAGAGAGAG,AGAGAG,AGAGAGAGAGAGAGAGAG,AGAGAGAGAGAG 476.85 PASS AC=1,0,1,0,0,0,0,0;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 1/3:10:85:0,0,10,0 chr1 62456014 . G A 1779.64 PASS AC=1;AF=0.64;AN=2;DP=3977;MQ=60;set=variant-variant6-variant7-variant8-variant12-variant13-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant29-variant30-variant32-variant33-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,50:136:99:1139,0,2224:38,48,19,31 chr1 62456048 . G A 1438.78 PASS AC=1;AF=0.594;AN=2;DP=1995;MQ=60;set=variant-variant7-variant13-variant17-variant21-variant22-variant23-variant25-variant30-variant32-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:67,41:108:99:950,0,1782:26,41,15,26 chr1 62483415 . A G 235.36 PASS AC=1;AF=0.654;AN=2;DP=138;FS=0;set=variant7-variant8-variant12-variant13-variant22-variant23-variant26-variant29-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:23:112,0,23:1,0,3,0 chr1 62483599 . G A 1740.22 PASS AC=1;AF=0.625;AN=2;DP=2446;MQ=60;set=variant6-variant7-variant8-variant12-variant13-variant20-variant22-variant23-variant25-variant26-variant29-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,104:169:99:2481,0,1408:34,31,52,52 chr1 62516683 . G C 2314.36 PASS AC=1;AF=0.7;AN=2;DP=7336;set=variant-variant3-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,81:174:99:2023,0,2317:41,52,39,42 chr1 62545404 . T C 429.59 PASS AC=1;AF=0.5;AN=2;DP=143;FractionInformativeReads=1;MQ=60;set=variant4-variant16-variant18-variant19-variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:7,13:20:99:304,0,172:2,5,5,8 chr1 62550427 . G A 559.49 PASS AC=1;AF=0.5;AN=2;DP=131;FractionInformativeReads=1;MQ=60;set=variant4-variant16-variant18-variant23 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:291,0,240:3,7,3,7 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 1/1:0,10:10:30:276,30,0:0,0,6,4 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 1/1:0,39:39:99:1270,117,0:0,0,24,15 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 1/1:0,86:86:99:2710,258,0:0,0,45,41 chr1 62579891 . G T 302.97 PASS AC=1;AF=0.5;AN=2;DP=403;FractionInformativeReads=1;MQ=60;set=variant-variant17-variant21-variant23-variant40 GT:AD:DP:GQ:PL:SB 0/1:56,37:93:99:790,0,1254:27,29,15,22 chr1 62582847 . C G 1302.13 PASS AC=1;AF=0.5;AN=2;DP=483;FractionInformativeReads=1;MQ=60;set=variant4-variant16-variant18-variant23 GT:AD:DP:GQ:PL:SB 0/1:49,61:110:99:1343,0,1098:25,24,34,27 chr1 62587014 . T TA,TAAA,TAAAA,TAA 1025.01 PASS AC=1,0,1,0;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 1/3:62:99:1,1,23,37 chr1 62593893 . T C 118.67 PASS AC=1;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 0/1:7,4:11:99:137,0,245:1,6,0,4 chr1 62594593 . C T 1330.63 PASS AC=1;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 0/1:42,50:92:99:1075,0,1084:21,21,28,22 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 0/1:31,43:74:99:1115,0,857:9,22,16,27 chr1 62594753 . AATT A 145.89 PASS AC=1;AF=0.5;AN=2;DP=94;MQ=60;set=variant4-variant16-variant18-variant23 GT:AD:DP:GQ:PL:SB 0/1:11,14:25:99:544,0,359:4,7,3,11 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 1/1:1,284:285:99:8928,807,0:0,1,147,137 chr1 62629670 . GA G,GAAAA,GAAAAA 354.54 PASS AC=1,0,0;AF=0.346,0.077,0.077;AN=2;DP=511;MQ=60;set=variant4-filterInvariant7-filterInvariant10-variant16-variant18-filterInvariant21-filterInvariant22-variant23-variant27-variant29-variant30-variant36-variant41 GT:DP:GQ:SB 0/1:17:99:2,9,0,6 chr1 62644118 . A G 604.98 PASS AC=2;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 1/1:0,39:39:99:1389,117,0:0,0,9,30 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 0/1:43,44:87:99:1055,0,1117:21,22,22,22 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 1/1:0,23:23:69:772,69,0:0,0,6,17 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 1/1:0,9:9:27:405,27,0:0,0,7,2 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 1/1:0,53:53:99:1553,158,0:0,0,26,27 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 1/1:0,57:57:99:1762,171,0:0,0,28,29 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 1/1:0,43:43:99:1383,129,0:0,0,20,23 chr1 62675261 . G A 933.49 PASS AC=1;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 0/1:17,12:29:99:296,0,432:11,6,7,5 chr1 62675287 . G C 234.58 PASS AC=1;AF=0.545;AN=2;DP=353;FractionInformativeReads=1;MQ=60;set=variant7-variant8-variant11-variant17-variant18-variant19-variant21-variant23-variant27-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,21:33:99:446,0,307:5,7,12,9 chr1 62675385 . A G 410.99 PASS AC=1;AF=0.545;AN=2;DP=489;FractionInformativeReads=1;MQ=60;set=variant7-variant8-variant11-variant17-variant18-variant19-variant21-variant23-variant27-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,22:38:99:604,0,472:8,8,11,11 chr1 62675619 . C T 1758.46 PASS AC=1;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 0/1:21,26:47:99:768,0,561:10,11,16,10 chr1 62675709 . T C 599.89 PASS AC=1;AF=0.545;AN=2;DP=541;MQ=60;set=variant7-variant8-variant11-variant17-variant18-variant19-variant21-variant23-variant27-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:28,20:48:99:495,0,676:14,14,13,7 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 1/1:0,71:71:99:2120,213,0:0,0,33,38 chr1 62676091 . C A 952.99 PASS AC=1;AF=0.577;AN=2;DP=816;MQ=60;set=variant7-variant8-variant11-variant17-variant18-variant19-variant21-variant23-variant27-variant36-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,28:55:99:714,0,688:15,12,16,12 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 0/1:40,45:85:99:1143,0,1153:20,20,23,22 chr1 62677048 . G T 2298.47 PASS AC=1;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 0/1:48,43:91:99:1103,0,1156:24,24,25,18 chr1 62677723 . T C 292.03 PASS AC=1;AF=0.545;AN=2;DP=198;FractionInformativeReads=1;MQ=60;set=variant7-variant8-variant11-variant17-variant18-variant19-variant21-variant23-variant27-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:104,0,222:5,4,3,3 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 0/1:8,12:20:99:392,0,209:6,2,9,3 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 1/1:0,4:4:12:136,12,0:0,0,2,2 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 1/1:0,78:78:99:2384,234,0:0,0,39,39 chr1 62718954 . A G 685.11 PASS AC=1;AF=0.5;AN=2;DP=164;MQ=60;set=variant4-variant16-variant18-variant23 GT:AD:DP:GQ:PL:SB 0/1:11,20:31:99:629,0,407:0,11,3,17 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 0/1:36,42:78:99:870,0,768:19,17,25,17 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 0/1:42,39:81:99:1421,0,1525:25,17,22,17 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 0/1:36,44:80:99:1595,0,1345:22,14,23,21 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 0/1:56,45:101:99:1073,0,1478:35,21,22,23 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 0/1:73,29:102:99:647,0,1848:38,35,12,17 chr1 62732421 . T C 404.16 PASS AC=1;AF=0.567;AN=2;DP=1078;MQ=60;set=variant-variant5-variant6-variant7-variant12-variant17-variant18-variant19-variant23-variant26-variant29-variant31-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,38:63:99:898,0,521:12,13,17,21 chr1 62737125 . T C 756.14 PASS AC=1;AF=0.6;AN=2;DP=426;MQ=60;set=variant7-variant12-variant17-variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:31,50:81:99:1240,0,621:15,16,31,19 chr1 62738013 . C T 298.04 PASS AC=1;AF=0.567;AN=2;DP=475;MQ=60;set=variant-variant5-variant6-variant7-variant12-variant17-variant18-variant19-variant23-variant26-variant29-variant31-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,27:39:99:726,0,260:5,7,15,12 chr1 62738471 . T C 55.68 PASS AC=1;AF=0.571;AN=2;DP=155;FractionInformativeReads=1;set=variant-variant5-variant7-variant12-variant17-variant18-variant19-variant23-variant26-variant29-variant31-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,10:16:99:302,0,174:2,4,3,7 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 0/1:28,45:73:99:1158,0,613:13,15,24,21 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 0/1:59,58:117:99:2167,0,3632:30,29,32,26 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 0/1:61,56:117:99:2131,0,3668:31,30,32,24 chr1 62902874 . A G 2218.79 PASS AC=2;AF=0.806;AN=2;DP=5222;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,151:152:99:4676,409,0:1,0,70,81 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 1/1:0,54:54:99:1478,161,0:0,0,27,27 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 1/1:0,49:49:99:1610,147,0:0,0,32,17 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 1/1:0,5:5:15:141,15,0:0,0,3,2 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 1/1:0,19:19:57:593,57,0:0,0,8,11 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 1/1:0,7:7:21:239,21,0:0,0,1,6 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 1/1:0,12:12:36:461,36,0:0,0,10,2 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 1/1:0,3:3:9:131,9,0:0,0,3,0 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 1/1:0,10:10:29:315,29,0:0,0,3,7 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 1/1:0,18:18:54:777,54,0:0,0,0,18 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 1/1:0,79:79:99:2494,237,0:0,0,51,28 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 1/1:0,51:51:99:2046,153,0:0,0,24,27 chr1 63044645 . CA C,CAA 309.83 PASS AC=1,0;AF=0.4,0.1;AN=2;DP=1166;MQ=60;set=variant3-filterInvariant4-variant9-variant10-filterInvariant12-variant15-filterInvariant16-variant17-filterInvariant19-variant20-variant21-filterInvariant23-filterInvariant25-variant27-filterInvariant28-filterInvariant29-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-variant37-variant39-variant40-filterInvariant42-filterInvariant44 GT:DP:GQ:SB 0/1:28:71:7,13,3,5 chr1 63052344 . CTA C 529.56 PASS AC=2;AF=0.604;AN=2;DP=683;MQ=60;set=variant2-variant3-variant6-variant10-variant11-variant13-variant14-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant30-variant32-variant34-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:810,54,0:0,0,4,14 chr1 63085483 . T TA 30.2 PASS AC=2;AF=0.778;AN=2;DP=586;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:54:505,54,0:0,0,12,5 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 1/1:0,41:41:99:1217,123,0:0,0,18,23 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 1/1:0,8:8:24:305,24,0:0,0,6,2 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 1/1:0,9:9:27:316,27,0:0,0,7,2 chr1 63153866 . C G 2949.73 PASS AC=1;AF=0.5;AN=2;DP=1198;MQ=60;set=variant11-variant16-variant20-variant23-variant30-variant44 GT:AD:DP:GQ:PL:SB 0/1:104,109:213:99:2553,0,2613:59,45,57,52 chr1 63249975 . A G 314.9 PASS AC=2;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 1/1:0,21:21:63:675,63,0:0,0,6,15 chr1 63307303 . A G 61.77 PASS AC=2;AF=0.867;AN=2;DP=62;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant11-variant12-variant13-variant17-variant19-variant20-variant22-variant23-variant26-variant28-variant32-variant39-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,0,2 chr1 63330217 . G A 2491.98 PASS AC=2;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 1/1:2,201:203:99:5973,559,0:1,1,114,87 chr1 63331074 . G C 3266.18 PASS AC=2;AF=0.6;AN=2;DP=4945;MQ=60;set=variant-variant2-variant9-variant10-variant11-variant12-variant13-variant14-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant36-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,215:215:99:6127,644,0:0,0,103,112 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 0/1:174,177:351:99:4336,0,4314:87,87,93,84 chr1 63872032 . T C 983.01 PASS AC=1;AF=0.5;AN=2;DP=212;FractionInformativeReads=1;MQ=60;set=variant19-variant23-variant28 GT:AD:DP:GQ:PL:SB 0/1:30,34:64:99:871,0,743:12,18,16,18 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 0/1:19,15:34:99:411,0,544:14,5,11,4 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 0/1:19,34:53:99:860,0,516:7,12,13,21 chr1 63881552 . C T 531.09 PASS AC=2;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 1/1:0,37:37:99:1117,111,0:0,0,23,14 chr1 63902431 . A G 271.01 PASS AC=1;AF=0.5;AN=2;DP=206;FractionInformativeReads=1;MQ=60;set=variant8-variant12-variant23-variant31-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:22,9:31:99:305,0,634:15,7,9,0 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 0/1:25,31:56:99:831,0,545:12,13,11,20 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 0/1:17,19:36:99:735,0,943:8,9,9,10 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 0/1:140,123:263:99:3776,0,4392:68,72,62,61 chr1 63904294 . T C 756.89 PASS AC=2;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 1/1:0,19:19:57:739,57,0:0,0,3,16 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 0/1:27,21:48:99:624,0,788:20,7,17,4 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 0/1:31,38:69:99:740,0,692:13,18,16,22 chr1 63915343 . A G 386.9 PASS AC=1;AF=0.5;AN=2;DP=297;FractionInformativeReads=1;MQ=60;set=variant2-variant8-variant12-variant20-variant23-variant31-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,19:35:99:455,0,365:9,7,10,9 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 1/1:0,7:7:21:193,21,0:0,0,3,4 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 1/1:0,14:14:42:513,42,0:0,0,12,2 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 0/1:21,35:56:99:831,0,554:7,14,14,21 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 0/1:31,32:63:99:765,0,720:13,18,16,16 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 0/1:20,25:45:99:626,0,427:8,12,10,15 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 0/1:10,16:26:99:477,0,203:4,6,5,11 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 0/1:13,13:26:99:327,0,429:2,11,4,9 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 0/1:63,47:110:99:1042,0,1457:28,35,21,26 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 0/1:19,28:47:99:585,0,552:5,14,13,15 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 0/1:25,33:58:99:768,0,573:13,12,18,15 chr1 64120095 . T C 1055.25 PASS AC=1;AF=0.5;AN=2;DP=110;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.833;QD=9.59;ReadPosRankSum=1.065;SOR=0.75;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:66,44:110:99:1083,0,1679:28,38,18,26 chr1 64124999 . G T 179.65 PASS AC=1;AF=0.5;AN=2;DP=15;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.637;QD=11.98;ReadPosRankSum=-0.868;SOR=1.179;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:208,0,237:6,2,6,1 chr1 64474804 . C T 223.35 PASS AC=1;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 0/1:12,14:26:99:378,0,259:8,4,10,4 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 1/1:0,90:90:99:2657,270,0:0,0,50,40 chr1 64603231 . G A 1583.21 PASS AC=1;AF=0.55;AN=2;DP=961;MQ=60;set=variant2-variant6-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,19:34:99:529,0,428:2,13,6,13 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 1/1:1,146:147:99:4451,430,0:0,1,73,73 chr1 64608423 . G A 2110.44 PASS AC=1;AF=0.55;AN=2;DP=1842;MQ=60;set=variant2-variant6-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,46:87:99:1046,0,1019:16,25,24,22 chr1 64608563 . A G 1278.92 PASS AC=1;AF=0.55;AN=2;DP=988;MQ=60;set=variant2-variant6-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,23:37:99:637,0,361:4,10,8,15 chr1 64608778 . A G 4948.36 PASS AC=1;AF=0.55;AN=2;DP=3349;MQ=60;set=variant2-variant6-variant11-variant12-variant14-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:65,69:134:99:1685,0,1519:37,28,40,29 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 1/1:0,39:39:99:1394,117,0:0,0,30,9 chr1 64644707 . GAAA GA,GAA,G 556.75 PASS AC=0,1,0;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 0/2:41:99:5,12,9,15 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 0/1:19,15:34:99:420,0,541:6,13,4,11 chr1 64680682 . C G 1343.56 PASS AC=1;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 0/1:11,14:25:99:427,0,292:3,8,3,11 chr1 64726414 . A C 1725.72 PASS AC=1;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 0/1:20,20:40:99:533,0,591:4,16,6,14 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 1/1:0,107:107:99:3198,321,0:0,0,57,50 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 1/1:0,45:45:99:1252,135,0:0,0,28,17 chr1 65047890 . C T 1601.02 PASS AC=1;AF=0.5;AN=2;DP=132;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.369;QD=12.13;ReadPosRankSum=1.749;SOR=0.738;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:63,69:132:99:1629,0,1462:34,29,38,31 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 1/1:0,59:59:99:1853,177,0:0,0,20,39 chr1 65099701 . GT GTT,G,GTTT 282.86 PASS AC=1,0,0;AF=0.342,0.132,0.026;AN=2;DP=690;set=variant7-filterInvariant8-variant10-variant15-variant17-variant18-filterInvariant19-variant20-variant23-filterInvariant25-variant27-variant28-filterInvariant32-filterInvariant33-variant34-variant37-filterInvariant39-variant42-variant44 GT:DP:GQ:SB 0/1:41:99:14,9,12,6 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 1/1:0,41:41:99:1304,123,0:0,0,14,27 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 1/1:0,4:4:12:139,12,0:0,0,2,2 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 1/1:0,22:22:66:774,66,0:0,0,16,6 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 1/1:0,16:16:48:474,48,0:0,0,6,10 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 1/1:0,15:15:45:623,45,0:0,0,15,0 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 1/1:0,131:131:99:3942,392,0:0,0,61,70 chr1 65129220 . C T 231.95 PASS AC=1;AF=0.5;AN=2;DP=10;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.58;QD=23.19;ReadPosRankSum=-0.731;SOR=0.569;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:98:260,0,98:3,0,6,1 chr1 65326102 . CATTTATTT C 57.43 PASS AC=2;AF=1;AN=2;DP=19;FS=0;FractionInformativeReads=0.105;MQ=60;QD=3.02;SOR=0.693;set=variant23 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:8:95,8,0:0,0,1,1 chr1 65349304 . G A 716.58 PASS AC=1;AF=0.5;AN=2;DP=122;FractionInformativeReads=1;MQ=60;set=variant13-variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:13,18:31:99:544,0,315:4,9,5,13 chr1 65614260 . C T 2355.36 PASS AC=1;AF=0.5;AN=2;DP=2091;set=variant3-variant4-variant12-variant13-variant14-variant17-variant21-variant23-variant34-variant41 GT:AD:DP:GQ:PL:SB 0/1:98,87:185:99:1918,0,2183:49,49,37,50 chr1 65694404 . GTT GT,G 5488.65 PASS AC=0,1;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 0/2:363:99:85,83,111,84 chr1 65695716 . A G 775.23 PASS AC=1;AF=0.5;AN=2;DP=87;FractionInformativeReads=1;MQ=60;set=variant17-variant23 GT:AD:DP:GQ:PL:SB 0/1:15,19:34:99:492,0,456:8,7,11,8 chr1 65695853 . A G 824.63 PASS AC=1;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 0/1:32,20:52:99:460,0,716:16,16,9,11 chr1 65695930 . G A 1229.97 PASS AC=1;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 0/1:40,28:68:99:799,0,1177:29,11,20,8 chr1 65697059 . A G 159.52 PASS AC=1;AF=0.5;AN=2;DP=10;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.633;QD=15.95;ReadPosRankSum=-0.741;SOR=1.329;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:188,0,103:2,2,2,4 chr1 65697842 . A G 539.81 PASS AC=1;AF=0.5;AN=2;DP=51;FractionInformativeReads=1;MQ=60;set=variant17-variant23 GT:AD:DP:GQ:PL:SB 0/1:19,11:30:99:313,0,688:2,17,3,8 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 1/1:0,10:10:30:265,30,0:0,0,5,5 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 1/1:2,17:19:4:380,4,0:2,0,11,6 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 1/1:2,17:19:4:380,4,0:2,0,11,6 chr1 65830608 . T C 1135.18 PASS AC=1;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 0/1:7,12:19:99:350,0,217:1,6,3,9 chr1 65832014 . A G 266.82 PASS AC=1;AF=0.5;AN=2;DP=41;FS=0;FractionInformativeReads=1;MQ=60;set=variant10-variant23-variant36 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:167,0,197:1,5,1,5 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 1/1:0,90:90:99:2884,270,0:0,0,58,32 chr1 65845042 . A T 2290.53 PASS AC=1;AF=0.5;AN=2;DP=1373;MQ=60;set=variant-variant2-variant9-variant10-variant15-variant23-variant36-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:72,64:136:99:1502,0,1827:38,34,35,29 chr1 65845076 . C T 2469.82 PASS AC=1;AF=0.5;AN=2;DP=1473;MQ=60;set=variant-variant2-variant9-variant10-variant15-variant23-variant36-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:72,70:142:99:1590,0,1911:35,37,33,37 chr1 65852310 . A G 117.98 PASS AC=1;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 0/1:9,5:14:99:180,0,240:6,3,5,0 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 1/1:0,17:17:51:568,51,0:0,0,4,13 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 1/1:0,45:45:99:1381,134,0:0,0,30,15 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 1/1:0,61:61:99:1822,183,0:0,0,34,27 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 1/1:0,101:101:99:2922,302,0:0,0,42,59 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 1/1:0,56:56:99:1736,168,0:0,0,34,22 chr1 65879252 . A G 8635.31 PASS AC=1;AF=0.625;AN=2;DP=7383;MQ=60;set=variant-variant2-variant4-variant5-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant32-variant34-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:112,123:235:99:3157,0,2748:57,55,68,55 chr1 65881132 . AAC AACACAC,AACACACAC,A,AACAC 1833.54 PASS AC=0,0,0,1;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 0/4:52:99:6,9,19,18 chr1 65886398 . T C 5176.2 PASS AC=1;AF=0.63;AN=2;DP=6260;MQ=60;set=variant-variant2-variant4-variant5-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant32-variant34-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:90,90:180:99:2247,0,1884:52,38,58,32 chr1 65886448 . T C 5603.2 PASS AC=1;AF=0.63;AN=2;DP=7472;MQ=60;set=variant-variant2-variant4-variant5-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant32-variant34-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:113,131:244:99:3061,0,2642:61,52,65,66 chr1 65887013 . A C 3887.73 PASS AC=1;AF=0.63;AN=2;DP=2869;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant32-variant34-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:57,54:111:99:1261,0,1377:27,30,29,25 chr1 65897981 . G A 1049.13 PASS AC=1;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 0/1:23,40:63:99:1363,0,749:5,18,10,30 chr1 65898249 . TAA TAAA,T,TA 106.44 PASS AC=0,1,0;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 0/2:34:99:12,4,10,8 chr1 65898873 . G C 899.83 PASS AC=1;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 0/1:41,19:60:99:419,0,1373:10,31,8,11 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 1/1:0,51:51:99:1908,153,0:0,0,25,26 chr1 65898996 . C T 3057.21 PASS AC=1;AF=0.579;AN=2;DP=1317;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant8-variant12-variant15-variant23-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,34:54:99:1028,0,551:11,9,21,13 chr1 65900357 . G T 942.38 PASS AC=1;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 0/1:33,27:60:99:731,0,886:11,22,14,13 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 0/1:49,28:77:99:520,0,1342:17,32,3,25 chr1 65901119 . T C 620.05 PASS AC=1;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 0/1:8,14:22:99:552,0,278:0,8,0,14 chr1 66036441 . A G 2565.68 PASS AC=1;AF=0.6;AN=2;DP=1189;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant8-variant10-variant12-variant13-variant15-variant22-variant23-variant27-variant29-variant32-variant34-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,43:77:99:1184,0,923:12,22,15,28 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 1/1:0,31:31:93:1011,93,0:0,0,10,21 chr1 66037973 . GTT G,GT,GTTT,GTTTT 168.52 PASS AC=1,0,0,0;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 0/1:26:99:9,10,3,4 chr1 66037984 . T G 277.55 PASS AC=1;AF=0.5;AN=2;DP=747;set=variant4-variant7-variant9-variant12-variant17-variant19-variant20-variant23-variant25-variant26-variant28-variant32-variant33-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,12:30:99:229,0,461:9,9,5,7 chr1 66058513 . A G 3140.39 PASS AC=1;AF=0.696;AN=2;DP=3659;MQ=60;set=variant-variant3-variant6-variant8-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant27-variant29-variant31-variant32-variant34-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,50:125:99:1141,0,1916:32,43,18,32 chr1 66096106 . G A 83.07 PASS AC=2;AF=0.773;AN=2;DP=1505;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:701,69,0:0,0,16,7 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 0/1:81:99:14,35,3,29 chr1 66106763 . T G 94.73 PASS AC=1;AF=0.5;AN=2;DP=49;FractionInformativeReads=1;MQ=60;set=variant8-variant12-variant23-variant27-variant29-variant34 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:94:94,0,204:5,3,3,1 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 0/1:142,123:265:99:2821,0,3518:67,75,61,62 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 0/1:61,49:110:99:1050,0,1414:28,33,27,22 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 0/1:11,17:28:99:463,0,243:3,8,4,13 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 1/1:0,76:76:99:2331,228,0:0,0,28,48 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 0/1:52,39:91:99:939,0,1222:24,28,20,19 chr1 66838076 . C T 867.76 PASS AC=1;AF=0.5;AN=2;DP=150;FractionInformativeReads=1;MQ=60;set=variant23-variant28 GT:AD:DP:GQ:PL:SB 0/1:45,32:77:99:896,0,1150:23,22,20,12 chr1 66999216 . A ATAAT 784.25 PASS AC=1;AF=0.5;AN=2;DP=241;MQ=60;set=variant3-variant4-variant5-variant11-variant23-variant26-variant31-variant32 GT:AD:DP:GQ:PL:SB 0/1:15,6:21:99:185,0,927:5,10,3,3 chr1 67000103 . A G 1823.05 PASS AC=1;AF=0.5;AN=2;DP=995;MQ=60;set=variant3-variant4-variant5-variant11-variant23-variant26-variant31-variant32-variant36 GT:AD:DP:GQ:PL:SB 0/1:41,51:92:99:1304,0,1086:12,29,21,30 chr1 67000162 . T G 810.27 PASS AC=1;AF=0.5;AN=2;DP=439;MQ=60;set=variant3-variant4-variant5-variant11-variant23-variant26-variant31-variant32-variant36 GT:AD:DP:GQ:PL:SB 0/1:26,22:48:99:613,0,671:11,15,5,17 chr1 67094171 . G A 1037.54 PASS AC=1;AF=0.5;AN=2;DP=646;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant10-variant11-variant23-variant26-variant32-variant36 GT:AD:DP:GQ:PL:SB 0/1:32,40:72:99:1100,0,742:14,18,15,25 chr1 67099488 . G GA 77.69 PASS AC=1;AF=0.667;AN=2;DP=226;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant10-variant11-variant13-variant14-variant16-variant21-variant22-variant23-variant24-variant26-variant27-variant32-variant33-variant36-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:65:93,0,65:3,0,2,1 chr1 67101778 . AAC A 381.41 PASS AC=1;AF=0.5;AN=2;DP=85;FS=0;MQ=60;set=variant5-variant23-variant32 GT:AD:DP:GQ:PL:SB 0/1:13,12:25:99:461,0,853:2,11,1,11 chr1 67101802 . A G 238.66 PASS AC=1;AF=0.648;AN=2;DP=336;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant13-variant15-variant16-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:308,0,709:0,8,0,7 chr1 67109335 . A G 1635.78 PASS AC=1;AF=0.5;AN=2;DP=1254;MQ=60;set=variant3-variant4-variant5-variant10-variant11-variant23-variant26-variant32-variant36 GT:AD:DP:GQ:PL:SB 0/1:57,65:122:99:1540,0,1265:31,26,38,27 chr1 67125911 . A AGAGGGAGG,AGAGG 352.23 PASS AC=0,2;AF=0.6,0.15;AN=2;DP=185;FS=0;set=variant10-variant13-variant16-variant22-variant23-variant24-variant32-variant39-variant42-variant43 GT:DP:GQ:SB 2/2:15:48:0,0,15,0 chr1 67126114 . A G 2348.76 PASS AC=2;AF=0.654;AN=2;DP=3447;MQ=60;set=variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant22-variant23-variant24-variant25-variant26-variant28-variant32-variant34-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:3822,383,0:0,0,55,73 chr1 67133111 . T C 1208.16 PASS AC=1;AF=0.611;AN=2;DP=872;MQ=60;set=variant6-variant9-variant14-variant22-variant23-variant25-variant28-variant34-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,52:94:99:1345,0,937:19,23,26,26 chr1 67136537 . C T 405.62 PASS AC=1;AF=0.5;AN=2;DP=278;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant11-variant23-variant26-variant32-variant36 GT:AD:DP:GQ:PL:SB 0/1:21,21:42:99:524,0,564:15,6,14,7 chr1 67138877 . AG A 524.1 PASS AC=1;AF=0.611;AN=2;DP=308;FractionInformativeReads=1;MQ=60;set=variant6-variant9-variant14-variant22-variant23-variant25-variant28-variant34-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:562,0,525:12,4,12,5 chr1 67145322 . C A 625.43 PASS AC=2;AF=0.729;AN=2;DP=2471;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1830,186,0:0,0,38,24 chr1 67149706 . G C 236.4 PASS AC=2;AF=0.625;AN=2;DP=441;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant22-variant23-variant24-variant25-variant26-variant28-variant32-variant33-variant34-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:611,54,0:0,0,14,4 chr1 67154730 . CAA CA,C 199.59 PASS AC=0,2;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 2/2:28:58:0,2,17,9 chr1 67160336 . A G 2304.14 PASS AC=2;AF=0.714;AN=2;DP=4608;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:4089,363,0:0,0,56,65 chr1 67160938 . TA TAAAA,TAAA,TAAAAAAAAAAAA,TAAAAAAAAAA,TAA,TAAAAAAAAA,T,TAAAAAAAAAAA,TAAAAAAAAAAAAAAAAA,TAAAAA,TAAAAAAAAAAAAA 502.94 PASS AC=0,0,0,0,0,0,0,1,1,0,0;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 8/9:18:99:0,0,13,5 chr1 67241975 . T C 376.96 PASS AC=1;AF=0.5;AN=2;DP=37;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.41;QD=10.19;ReadPosRankSum=-1.109;SOR=0.616;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:19,18:37:99:405,0,429:12,7,11,7 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 1/1:0,76:76:99:2454,228,0:0,0,43,33 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 1/1:0,45:45:99:2086,141,0:0,0,30,15 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 1/1:0,51:51:99:2276,156,0:0,0,35,16 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 0/1:24,38:62:99:975,0,479:13,11,23,15 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 0/1:3,16:19:80:562,0,80:3,0,14,2 chr1 67313793 . G A 4148.51 PASS AC=1;AF=0.563;AN=2;DP=4688;MQ=60;set=variant-variant7-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant27-variant31-variant32-variant33-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:117,99:216:99:2330,0,2783:59,58,53,46 chr1 67396222 . T G 901.52 PASS AC=1;AF=0.898;AN=2;DP=1047;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:6,12:18:99:423,0,216:0,6,1,11 chr1 67437150 . A G 39.19 PASS AC=1;AF=0.571;AN=2;DP=85;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant23-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:177,0,199:5,1,5,0 chr1 67438535 . A T 1147.65 PASS AC=2;AF=0.567;AN=2;DP=1406;MQ=60;set=variant2-variant4-variant7-variant8-variant15-variant21-variant23-variant24-variant29-variant32-variant34-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:1971,200,0:0,0,43,24 chr1 67442210 . C T 649.37 PASS AC=1;AF=0.5;AN=2;DP=594;FractionInformativeReads=1;MQ=60;set=variant4-variant15-variant21-variant23-variant24-variant29-variant32-variant34-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,34:65:99:908,0,734:21,10,24,10 chr1 67442275 . C T 1230.12 PASS AC=2;AF=0.567;AN=2;DP=1943;MQ=60;set=variant2-variant4-variant7-variant8-variant15-variant21-variant23-variant24-variant29-variant32-variant34-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,114:114:99:3282,341,0:0,0,58,56 chr1 67447450 . A G 593.67 PASS AC=2;AF=0.567;AN=2;DP=806;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant8-variant15-variant21-variant23-variant24-variant29-variant32-variant34-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1322,129,0:0,0,29,14 chr1 67451497 . ATTTT ATTTTT,ATTT,AT,A 146.31 PASS AC=0,0,0,2;AF=0.111,0.194,0.167,0.139;AN=2;DP=475;set=variant-variant2-variant7-variant8-filterInvariant9-variant10-variant11-variant15-variant16-filterInvariant17-variant19-variant21-variant23-variant24-variant29-variant33-variant37-variant38 GT:DP:GQ:SB 4/4:7:21:0,0,3,4 chr1 67451602 . A C 839.33 PASS AC=2;AF=0.567;AN=2;DP=979;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant8-variant15-variant21-variant23-variant24-variant29-variant32-variant34-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1883,159,0:0,0,39,14 chr1 67451922 . C T 4050.5 PASS AC=2;AF=0.567;AN=2;DP=3023;MQ=60;set=variant2-variant4-variant7-variant8-variant15-variant21-variant23-variant24-variant29-variant32-variant34-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,173:173:99:7726,521,0:0,0,71,102 chr1 67451924 . G T 4050.5 PASS AC=2;AF=0.567;AN=2;DP=2994;MQ=60;set=variant2-variant4-variant7-variant8-variant15-variant21-variant23-variant24-variant29-variant32-variant34-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,170:170:99:7726,521,0:0,0,70,100 chr1 67452322 . G A 2557.41 PASS AC=2;AF=0.567;AN=2;DP=4322;set=variant2-variant4-variant7-variant8-variant15-variant21-variant23-variant24-variant29-variant32-variant34-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,248:248:99:7633,742,0:0,0,143,105 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 1/1:1,419:420:99:12657,1250,0:1,0,238,181 chr1 67453120 . A AT 5534.32 PASS AC=1;AF=0.571;AN=2;DP=3111;MQ=60;set=variant2-variant7-variant8-variant23-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:214,200:414:99:5232,0,5736:88,126,88,112 chr1 67465988 . A T 107.51 PASS AC=1;AF=0.545;AN=2;DP=175;set=variant4-variant15-variant22-variant23-variant24-variant26-variant31-variant33-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:21:85,0,21:2,0,5,1 chr1 67466606 . C A 329.38 PASS AC=1;AF=0.5;AN=2;DP=96;FractionInformativeReads=1;MQ=60;set=variant23-variant32 GT:AD:DP:GQ:PL:SB 0/1:24,14:38:99:358,0,704:9,15,7,7 chr1 67468124 . G C 4123.89 PASS AC=2;AF=0.567;AN=2;DP=5548;MQ=60;set=variant2-variant4-variant7-variant8-variant15-variant21-variant23-variant24-variant29-variant32-variant34-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,380:380:99:11188,1135,0:0,0,185,195 chr1 67469594 . C T 2701.44 PASS AC=1;AF=0.571;AN=2;DP=988;MQ=60;set=variant2-variant7-variant8-variant23-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:76,59:135:99:1378,0,1939:37,39,29,30 chr1 67487407 . GAC CAC,G 351.47 PASS AC=0,1;AF=0.4,0.5;AN=2;DP=146;FS=0;set=variant2-variant7-variant23-variant37-variant38 GT:DP:GQ:SB 0/2:13:24:0,2,3,8 chr1 67487439 . C T 68.9 PASS AC=1;AF=0.5;AN=2;DP=41;FS=0;set=variant23-variant32 GT:AD:DP:GQ:PL:SB 0/1:9,4:13:97:97,0,265:2,7,1,3 chr1 67518534 . C T 805.09 PASS AC=1;AF=0.5;AN=2;DP=815;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant22-variant23-variant32-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:50,35:85:99:775,0,1199:22,28,19,16 chr1 67519435 . C A 496.99 PASS AC=2;AF=0.6;AN=2;DP=615;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant22-variant23-variant30-variant32-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1044,104,0:0,0,23,12 chr1 67557817 . T C 153.38 PASS AC=1;AF=0.5;AN=2;DP=22;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant32 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:182,0,239:6,1,5,1 chr1 67557966 . G T 569.92 PASS AC=2;AF=0.793;AN=2;DP=2145;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1534,153,0:0,0,26,25 chr1 67558063 . C G 1515.86 PASS AC=2;AF=0.744;AN=2;DP=1671;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-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1368,122,0:0,0,21,20 chr1 67558169 . T C 3586.91 PASS AC=2;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 1/1:0,92:92:99:2740,273,0:0,0,55,37 chr1 67558377 . ACTATG A 4578.83 PASS AC=1;AF=0.55;AN=2;DP=2550;MQ=60;set=variant6-variant13-variant15-variant18-variant22-variant23-variant24-variant28-variant29-variant32 GT:AD:DP:GQ:PL:SB 0/1:111,103:214:99:3983,0,5874:61,50,53,50 chr1 67558739 . C T 2802.81 PASS AC=2;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 1/1:0,47:47:99:1648,141,0:0,0,18,29 chr1 67559929 . G A 5358.93 PASS AC=1;AF=0.694;AN=2;DP=18159;MQ=60;set=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-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:229,210:439:99:5191,0,5544:119,110,120,90 chr1 67560897 . A G 7471.05 PASS AC=2;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 1/1:0,188:188:99:6198,563,0:0,0,84,104 chr1 67560956 . C T 7237.36 PASS AC=2;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 1/1:0,192:192:99:5918,575,0:0,0,97,95 chr1 67561265 . T A 721.66 PASS AC=1;AF=0.694;AN=2;DP=2555;MQ=60;set=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-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,23:56:99:649,0,880:10,23,5,18 chr1 67561540 . T C 679.14 PASS AC=1;AF=0.5;AN=2;DP=577;FractionInformativeReads=1;set=variant2-variant5-variant7-variant8-variant10-variant23-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:37,39:76:99:956,0,968:26,11,22,17 chr1 67561772 . G A 1970.67 PASS AC=1;AF=0.5;AN=2;DP=1555;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant8-variant10-variant23-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:113,100:213:99:2309,0,2719:58,55,56,44 chr1 67562106 . G T 1111.7 PASS AC=2;AF=0.744;AN=2;DP=891;FractionInformativeReads=1;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-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:89:1110,89,0:0,0,5,25 chr1 67577367 . A T 647.1 PASS AC=2;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 1/1:0,62:62:99:1780,185,0:0,0,27,35 chr1 67579245 . G A 41.48 PASS AC=1;AF=0.7;AN=2;DP=282;FS=0;FractionInformativeReads=1;set=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-variant31-variant33-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,9:12:92:325,0,92:3,0,8,1 chr1 67579386 . A G 1248.24 PASS AC=2;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 1/1:0,53:53:99:1535,158,0:0,0,26,27 chr1 67591347 . A G 137.66 PASS AC=1;AF=0.7;AN=2;DP=375;FractionInformativeReads=1;set=variant2-variant4-variant5-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-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:99:147,0,257:7,0,3,1 chr1 67591660 . G A 201.16 PASS AC=2;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 1/1:0,9:9:27:315,27,0:0,0,2,7 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 0/1:115,44:159:99:484,0,4691:7,108,44,0 chr1 67600669 . T C 415.78 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2101;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:113,30:143:99:477,0,4694:4,109,30,0 chr1 67600686 . G T 876.54 PASS AC=1;AF=0.526;AN=2;DP=1949;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant12-variant13-variant15-variant16-variant18-variant20-variant21-variant23-variant24-variant25-variant28-variant32-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:65,44:109:99:1485,0,2584:0,65,1,43 chr1 67648460 . T C 896.25 PASS AC=2;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 1/1:0,20:20:60:684,60,0:0,0,16,4 chr1 67672567 . CTTT CTT,CT,CTTTT,C,CTTTTT 149.63 PASS AC=0,0,1,0,0;AF=0.146,0.042,0.292,0.021,0.021;AN=2;DP=829;set=variant-variant2-filterInvariant4-variant6-variant9-variant11-variant12-variant13-filterInvariant14-variant15-variant16-variant19-filterInvariant20-variant23-filterInvariant24-variant25-variant26-variant28-filterInvariant31-variant33-variant39-variant41-variant42-filterInvariant44 GT:DP:GQ:SB 0/3:18:99:6,3,7,2 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 1/1:0,60:60:99:1817,178,0:0,0,25,35 chr1 67685443 . G A 582.04 PASS AC=2;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 1/1:0,35:35:99:994,104,0:0,0,13,22 chr1 67702526 . T G 223.61 PASS AC=1;AF=0.583;AN=2;DP=202;MQ=60;set=variant5-variant7-variant17-variant23-variant30-variant42 GT:AD:DP:GQ:PL:SB 0/1:8,13:21:99:416,0,177:3,5,2,11 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 0/1:8,9:17:99:229,0,201:4,4,6,3 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 1/1:0,65:65:99:1926,195,0:0,0,36,29 chr1 67705958 . G A 416.42 PASS AC=1;AF=0.5;AN=2;DP=315;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant17-variant23-variant30-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,40:67:99:997,0,599:13,14,14,26 chr1 67773649 . T C 805.42 PASS AC=2;AF=0.661;AN=2;DP=546;MQ=60;set=variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:468,48,0:0,0,8,8 chr1 67785667 . G A 68.49 PASS AC=1;AF=0.5;AN=2;DP=26;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant23-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:34:120,0,34:1,1,3,0 chr1 67795319 . T C 4593.16 PASS AC=2;AF=0.977;AN=2;DP=5714;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,122:122:99:3662,366,0:0,0,60,62 chr1 67796641 . ATTAAC A 163.75 PASS AC=1;AF=0.5;AN=2;DP=99;MQ=60;set=variant3-variant13-variant14-variant15-variant16-variant22-variant23-variant26-variant28-variant32-variant33-variant41 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:78:78,0,133:0,2,0,2 chr1 67833527 . G C 462.54 PASS AC=1;AF=0.5;AN=2;DP=332;FractionInformativeReads=1;MQ=60;set=variant5-variant12-variant23-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:44,21:65:99:546,0,1112:23,21,12,9 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 1/1:0,9:9:27:302,27,0:0,0,3,6 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 0/1:133:99:31,34,40,28 chr1 67875103 . C CA 129.99 PASS AC=1;AF=0.5;AN=2;DP=452;set=variant5-variant8-variant10-filterInvariant12-variant14-variant16-variant22-variant23-variant27-filterInvariant30-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:121,0,244:7,2,5,5 chr1 67875104 . C A,CACACACA,CA 287.13 PASS AC=1,0,1;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 1/3:19:99:2,0,10,7 chr1 67875203 . C T 1485.53 PASS AC=1;AF=0.58;AN=2;DP=3041;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant28-variant30-variant32-variant33-variant34-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:51,67:118:99:1612,0,1071:26,25,35,32 chr1 67891029 . A C 52.67 PASS AC=1;AF=0.5;AN=2;DP=73;FractionInformativeReads=1;MQ=60;set=variant14-variant22-variant23-variant27-variant40 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:70:70,0,117:3,2,1,2 chr1 68151980 . T G 1608.69 PASS AC=1;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 0/1:26,21:47:99:702,0,751:21,5,19,2 chr1 68152363 . G A 349.91 PASS AC=1;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 0/1:8,9:17:99:233,0,309:0,8,2,7 chr1 68154086 . G C 731.07 PASS AC=1;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 0/1:15,9:24:99:246,0,480:3,12,1,8 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 0/1:50,29:79:99:787,0,1600:16,34,8,21 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 0/1:25,11:36:99:279,0,826:15,10,6,5 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 0/1:82,81:163:99:1970,0,2101:45,37,41,40 chr1 68517066 . C T 411.42 PASS AC=1;AF=0.886;AN=2;DP=849;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:9,9:18:99:226,0,302:8,1,6,3 chr1 68591104 . A G 3804.97 PASS AC=1;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 0/1:104,103:207:99:2536,0,2481:58,46,61,42 chr1 68591173 . A G 5592.93 PASS AC=1;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 0/1:147,142:289:99:3368,0,3803:83,64,78,64 chr1 68591253 . C T 4090.83 PASS AC=1;AF=0.578;AN=2;DP=13131;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant30-variant31-variant34-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:190,154:344:99:4030,0,4527:97,93,82,72 chr1 68591405 . G A 4623.36 PASS AC=1;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 0/1:103,121:224:99:3088,0,2454:43,60,47,74 chr1 68591884 . C T 1918.54 PASS AC=1;AF=0.5;AN=2;DP=557;FractionInformativeReads=1;MQ=60;set=variant11-variant23-variant31-variant32 GT:AD:DP:GQ:PL:SB 0/1:64,53:117:99:1379,0,1694:30,34,32,21 chr1 68593131 . C G 280.3 PASS AC=1;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 0/1:4,5:9:99:195,0,133:0,4,0,5 chr1 68603731 . A G 341.22 PASS AC=1;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 0/1:22,20:42:99:563,0,668:4,18,6,14 chr1 68613933 . C T 953.99 PASS AC=1;AF=0.556;AN=2;DP=680;MQ=60;set=variant-variant6-variant11-variant23-variant31-variant32-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,22:66:99:477,0,1094:20,24,10,12 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 1/1:0,41:41:99:1325,123,0:0,0,18,23 chr1 68620998 . C G 57.44 PASS AC=1;AF=0.55;AN=2;DP=140;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant11-variant21-variant23-variant31-variant32-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,9:17:99:354,0,273:1,7,0,9 chr1 68624878 . C T 1006.51 PASS AC=1;AF=0.586;AN=2;DP=3095;set=variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant30-variant34-variant36-variant37-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,48:94:99:1162,0,1121:19,27,24,24 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 0/1:4,6:10:98:188,0,98:0,4,1,5 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 0/1:2,5:7:70:204,0,70:2,0,5,0 chr1 68697540 . CGGGG CGGG,C,CG 333.05 PASS AC=0,0,1;AF=0.091,0.091,0.318;AN=2;DP=221;MQ=60;set=variant4-variant7-variant11-variant13-variant17-variant19-variant22-variant23-variant25-variant39-variant41 GT:DP:GQ:SB 0/3:8:92:3,1,4,0 chr1 68939744 . A G 759.61 PASS AC=1;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 0/1:27,26:53:99:852,0,791:20,7,21,5 chr1 68939908 . A G 11214 PASS AC=2;AF=0.977;AN=2;DP=13453;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,282:282:99:8564,845,0:0,0,147,135 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 1/1:0,204:204:99:9104,613,0:0,0,92,112 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 1/1:0,27:27:84:1260,84,0:0,0,17,10 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 1/1:0,28:28:84:1260,84,0:0,0,18,10 chr1 68943665 . T G 335.59 PASS AC=1;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 0/1:17,28:45:99:626,0,351:9,8,13,15 chr1 68944633 . A T 1682.45 PASS AC=1;AF=0.536;AN=2;DP=1543;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant9-variant10-variant16-variant19-variant20-variant23-variant29-variant34-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:60,35:95:99:856,0,1565:31,29,18,17 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 1/1:0,75:75:99:2376,225,0:0,0,33,42 chr1 68952564 . AACACACACAC AACACAC,AACACACAC,AACAC,A 93.24 PASS AC=0,2,0,0;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 2/2:12:34:0,0,8,4 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 1/1:0,15:15:45:464,45,0:0,0,4,11 chr1 68962931 . G T 977.44 PASS AC=1;AF=0.5;AN=2;DP=71;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-2.593;QD=13.77;ReadPosRankSum=0.408;SOR=0.602;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:35,36:71:99:1006,0,1092:9,26,10,26 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 0/1:43,48:91:99:1251,0,1278:31,12,32,16 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 1/1:0,171:171:99:7360,516,0:0,0,63,108 chr1 70144056 . T C 927.37 PASS AC=1;AF=0.5;AN=2;DP=324;FractionInformativeReads=1;MQ=60;set=variant23-variant34-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,39:83:99:956,0,1088:28,16,23,16 chr1 70225832 . G A 735.01 PASS AC=1;AF=0.5;AN=2;DP=712;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant7-variant12-variant17-variant20-variant22-variant23-variant26-variant28-variant31-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,21:32:99:596,0,295:6,5,12,9 chr1 70504360 . C T 890.68 PASS AC=1;AF=0.5;AN=2;DP=232;MQ=60;set=variant12-variant23-variant40 GT:AD:DP:GQ:PL:SB 0/1:44,29:73:99:738,0,1225:18,26,16,13 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 0/1:26,26:52:99:840,0,720:18,8,20,6 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 1/1:0,184:184:99:5520,552,0:0,0,100,84 chr1 70625069 . T C 1094.28 PASS AC=1;AF=0.5;AN=2;DP=305;FractionInformativeReads=1;MQ=60;set=variant3-variant23-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:37,28:65:99:630,0,808:20,17,18,10 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 0/1:55,26:81:99:526,0,1256:28,27,14,12 chr1 70653068 . A T 1027.29 PASS AC=1;AF=0.5;AN=2;DP=326;MQ=60;set=variant3-variant23-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:31,37:68:99:913,0,660:14,17,17,20 chr1 70654981 . GAAA GAA,GA,G,GAAAA 142.08 PASS AC=0,0,1,0;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 0/3:49:99:10,25,6,8 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 1/1:0,130:130:99:5876,400,0:0,0,69,61 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 0/1:56,72:128:99:1815,0,1478:35,21,46,26 chr1 70904523 . T TTGTG,TTGTGTG,TTGTGTGTG,TTG 645.31 PASS AC=0,1,0,0;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 0/2:33:99:3,19,2,9 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 0/1:2,4:6:73:92,0,73:0,2,1,3 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 0/1:22,23:45:99:515,0,498:13,9,16,7 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 0/1:1,9:10:16:362,0,16:0,1,0,9 chr1 71331220 . G A 757.32 PASS AC=1;AF=0.545;AN=2;DP=199;MQ=60;set=variant4-variant6-variant13-variant15-variant21-variant22-variant23-variant25-variant34-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,3:16:74:74,0,449:11,2,3,0 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 1/1:0,110:110:99:3349,329,0:0,0,50,60 chr1 71334870 . C T 1172.73 PASS AC=2;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 1/1:0,95:95:99:2741,282,0:0,0,55,40 chr1 71419499 . C T 1045.7 PASS AC=1;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 0/1:15,15:30:99:405,0,364:5,10,4,11 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 0/1:3,5:8:99:190,0,100:0,3,0,5 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 0/1:55,55:110:99:1406,0,1510:23,32,22,33 chr1 71529401 . C T 2108.47 PASS AC=1;AF=0.69;AN=2;DP=3281;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant32-variant33-variant34-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,51:90:99:1403,0,1157:18,21,23,28 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 0/1:47,55:102:99:1298,0,1032:24,23,27,28 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 1/1:0,220:220:99:6712,660,0:0,0,93,127 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 1/1:0,43:43:99:1299,129,0:0,0,16,27 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 1/1:0,18:18:54:604,54,0:0,0,13,5 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 1/1:0,23:23:69:740,69,0:0,0,14,9 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 1/1:0,85:85:99:2550,255,0:0,0,45,40 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 1/1:0,5:5:15:212,15,0:0,0,0,5 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 1/1:0,12:12:36:398,36,0:0,0,3,9 chr1 72400656 . A G 234.44 PASS AC=1;AF=0.545;AN=2;DP=134;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant10-variant11-variant12-variant14-variant23-variant29-variant31-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:99:228,0,99:2,1,6,1 chr1 72747844 . C T 78.07 PASS AC=1;AF=0.629;AN=2;DP=1490;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant33-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,15:45:99:396,0,945:23,7,13,2 chr1 72748084 . G C 3169.68 PASS AC=1;AF=0.5;AN=2;DP=226;FS=3.725;FractionInformativeReads=1;MQ=60;MQRankSum=-0.365;QD=14.03;ReadPosRankSum=0.833;SOR=0.779;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:107,119:226:99:3198,0,2929:51,56,64,55 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 1/1:0,106:106:99:3224,317,0:0,0,62,44 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 1/1:0,7:7:21:274,21,0:0,0,1,6 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 1/1:0,47:47:99:1328,141,0:0,0,25,22 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 0/1:20:98:5,6,5,4 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 1/1:0,72:72:99:2742,215,0:0,0,60,12 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 1/1:0,52:52:99:1714,156,0:0,0,15,37 chr1 74663709 . G A 374.6 PASS AC=2;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 1/1:0,70:70:99:2314,210,0:0,0,45,25 chr1 74663814 . C G 1136.42 PASS AC=2;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 1/1:0,115:115:99:3417,345,0:0,0,54,61 chr1 74664149 . T C 919.85 PASS AC=2;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 1/1:0,104:104:99:3221,312,0:0,0,39,65 chr1 74665493 . G A 1513.15 PASS AC=2;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 1/1:0,127:127:99:3875,381,0:0,0,50,77 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 1/1:0,7:7:21:236,21,0:0,0,6,1 chr1 74671519 . A G 4618.95 PASS AC=2;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 1/1:0,191:191:99:5996,573,0:0,0,100,91 chr1 74672323 . C A 4620.89 PASS AC=2;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 1/1:2,330:332:99:10343,974,0:1,1,174,156 chr1 74672474 . G A 3804.42 PASS AC=2;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 1/1:0,346:346:99:10719,1036,0:0,0,158,188 chr1 74672640 . T A 4971.62 PASS AC=2;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 1/1:0,373:373:99:11212,1117,0:0,0,199,174 chr1 74699099 . T G 1192.9 PASS AC=1;AF=0.5;AN=2;DP=343;FractionInformativeReads=1;MQ=60;set=variant5-variant23-variant31-variant38 GT:AD:DP:GQ:PL:SB 0/1:41,33:74:99:822,0,1072:25,16,17,16 chr1 74699331 . C G 1073.11 PASS AC=2;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 1/1:0,98:98:99:2915,294,0:0,0,42,56 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 1/1:0,6:6:18:180,18,0:0,0,2,4 chr1 74701950 . T A 354.72 PASS AC=2;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 1/1:0,44:44:99:1374,132,0:0,0,15,29 chr1 74705684 . G C 1122.42 PASS AC=1;AF=0.5;AN=2;DP=609;FractionInformativeReads=1;MQ=60;set=variant5-variant23-variant31-variant38 GT:AD:DP:GQ:PL:SB 0/1:71,96:167:99:2582,0,1769:41,30,56,40 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 1/1:0,79:79:99:2175,236,0:0,0,34,45 chr1 74836204 . C T 1087.95 PASS AC=1;AF=0.5;AN=2;DP=624;MQ=60;set=variant5-variant18-variant22-variant23-variant28-variant31-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:23,41:64:99:1192,0,703:14,9,18,23 chr1 74836916 . A G 2895.57 PASS AC=1;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 0/1:109,71:180:99:1664,0,2714:63,46,43,28 chr1 74836977 . A T 3743.5 PASS AC=1;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 0/1:146,104:250:99:2238,0,3499:70,76,55,49 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 1/1:0,138:138:99:6221,418,0:0,0,71,67 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 1/1:85:99:0,5,41,39 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 0/1:71,58:129:99:1623,0,1819:25,46,17,41 chr1 74840276 . C T 4950.21 PASS AC=1;AF=0.5;AN=2;DP=1983;MQ=60;set=variant5-variant23-variant28-variant31-variant38 GT:AD:DP:GQ:PL:SB 0/1:212,158:370:99:4157,0,5779:99,113,74,84 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 1/1:0,59:59:99:1991,176,0:0,0,32,27 chr1 74901739 . CTTT CTT,CT,C 256.31 PASS AC=0,2,0;AF=0.395,0.316,0.013;AN=2;DP=1553;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-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 2/2:23:69:0,0,15,8 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 1/1:0,83:83:99:2655,249,0:0,0,36,47 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 1/1:2,87:89:99:2608,215,0:1,1,44,43 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 1/1:0,144:144:99:4404,430,0:0,0,62,82 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 1/1:0,128:128:99:3959,384,0:0,0,71,57 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 1/1:0,185:185:99:5523,552,0:0,0,90,95 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 1/1:0,6:6:18:221,18,0:0,0,4,2 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 1/1:0,36:36:99:1098,108,0:0,0,12,24 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 1/1:0,105:105:99:3756,315,0:0,0,22,83 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 1/1:0,44:44:99:1818,132,0:0,0,2,42 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 0/1:95,103:198:99:2561,0,2322:43,52,45,58 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 1/1:0,125:125:99:3892,375,0:0,0,77,48 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 1/1:0,146:146:99:4649,438,0:0,0,86,60 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 0/1:59,68:127:99:1719,0,1373:29,30,29,39 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 0/1:76,66:142:99:1777,0,1900:43,33,34,32 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 0/1:6,10:16:99:313,0,172:4,2,8,2 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 0/1:60,47:107:99:1058,0,1412:30,30,26,21 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 0/1:6,12:18:99:312,0,127:3,3,4,8 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 0/1:35,27:62:99:550,0,860:14,21,12,15 chr1 75190452 . C T 2572.53 PASS AC=1;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 0/1:56,36:92:99:805,0,1277:31,25,20,16 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 0/1:21,17:38:99:420,0,570:12,9,8,9 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 1/1:0,38:38:99:1419,114,0:0,0,18,20 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 1/1:0,125:125:99:4081,374,0:0,0,47,78 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 0/1:14,13:27:99:414,0,408:3,11,4,9 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 0/1:22,22:44:99:556,0,575:14,8,14,8 chr1 75230606 . C T 261.78 PASS AC=1;AF=0.568;AN=2;DP=1185;MQ=60;set=variant-variant6-variant7-variant8-variant9-variant10-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant29-variant30-variant33-variant36-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,21:45:99:519,0,595:12,12,9,12 chr1 75230642 . G A 622.7 PASS AC=1;AF=0.5;AN=2;DP=46;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.714;QD=13.54;ReadPosRankSum=-1.076;SOR=0.867;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:23,23:46:99:651,0,546:12,11,13,10 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 0/1:7,10:17:99:277,0,143:4,3,7,3 chr1 75594348 . G C 344.57 PASS AC=1;AF=0.536;AN=2;DP=174;MQ=60;set=variant7-variant14-variant16-variant21-variant23-variant24-variant26-variant29-variant32-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,12:17:73:356,0,73:2,3,4,8 chr1 75600506 . ATT A,AT,ATTTT 392.99 PASS AC=0,1,0;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 0/2:20:73:2,3,9,6 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 1/1:0,84:84:99:2631,251,0:0,0,31,53 chr1 75609049 . A C 112.41 PASS AC=1;AF=0.538;AN=2;DP=247;MQ=60;set=variant7-variant14-variant16-variant21-variant23-variant24-variant26-variant29-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,9:10:16:340,0,16:0,1,0,9 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 0/1:23,20:43:99:379,0,469:9,14,7,13 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 0/1:62,58:120:99:1311,0,1596:32,30,29,29 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 1/1:0,29:29:87:1163,87,0:0,0,22,7 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 1/1:0,35:35:99:1400,105,0:0,0,3,32 chr1 75627354 . C CA,CAA 61.24 PASS AC=0,1;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 0/2:16:99:0,5,1,10 chr1 75680433 . G A 1839.74 PASS AC=2;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 1/1:0,53:53:99:1578,158,0:0,0,21,32 chr1 75680545 . T G 1085.63 PASS AC=2;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 1/1:0,30:30:90:915,90,0:0,0,11,19 chr1 75680565 . G A 1019.52 PASS AC=2;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 1/1:0,26:26:78:783,78,0:0,0,9,17 chr1 75681351 . A T 981.97 PASS AC=2;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 1/1:0,13:13:39:523,39,0:0,0,12,1 chr1 75681511 . T C 4173.6 PASS AC=2;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 1/1:0,108:108:99:2982,323,0:0,0,51,57 chr1 75685403 . T C 2428.61 PASS AC=2;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 1/1:0,66:66:99:2135,198,0:0,0,41,25 chr1 75716925 . C T 754.59 PASS AC=2;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 1/1:0,84:84:99:2513,250,0:0,0,33,51 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 1/1:0,17:17:51:551,51,0:0,0,5,12 chr1 76143443 . A G 233.22 PASS AC=1;AF=0.615;AN=2;DP=705;FractionInformativeReads=1;set=variant6-variant7-variant9-variant10-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,10:17:99:306,0,142:3,4,3,7 chr1 76143458 . T C 221.81 PASS AC=1;AF=0.565;AN=2;DP=541;set=variant6-variant9-variant10-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:306,0,144:2,4,2,7 chr1 76143505 . T C 345.13 PASS AC=1;AF=0.955;AN=2;DP=502;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:2,4:6:31:118,0,31:1,1,1,3 chr1 76189946 . G T 52.7 PASS AC=2;AF=0.679;AN=2;DP=77;FS=0;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant14-variant17-variant19-variant20-variant21-variant23-variant29-variant31-variant33-variant34-variant38-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:126,15,0:0,0,3,2 chr1 76190569 . C G 820.43 PASS AC=1;AF=0.635;AN=2;DP=2733;set=variant6-variant7-variant9-variant10-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:58,49:107:99:1245,0,1522:18,40,14,35 chr1 76194054 . C G 691.91 PASS AC=1;AF=0.58;AN=2;DP=1419;set=variant6-variant7-variant9-variant10-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:38,26:64:99:610,0,988:24,14,17,9 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 1/1:0,75:75:99:2569,226,0:0,0,22,53 chr1 76194306 . A G 1137.78 PASS AC=1;AF=0.943;AN=2;DP=781;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:3,5:8:99:184,0,111:0,3,0,5 chr1 76198436 . T C 894.23 PASS AC=1;AF=0.615;AN=2;DP=1887;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant9-variant10-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,33:75:99:835,0,1133:17,25,15,18 chr1 76198785 . G A 1387.49 PASS AC=1;AF=0.615;AN=2;DP=3765;MQ=60;set=variant6-variant7-variant9-variant10-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:66,67:133:99:1567,0,1590:31,35,27,40 chr1 76199345 . C G 1383.3 PASS AC=1;AF=0.615;AN=2;DP=2652;MQ=60;set=variant6-variant7-variant9-variant10-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:60,47:107:99:1104,0,1436:25,35,21,26 chr1 76205643 . C A 589.48 PASS AC=1;AF=0.58;AN=2;DP=1718;MQ=60;set=variant6-variant7-variant9-variant10-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,28:69:99:726,0,1151:28,13,20,8 chr1 76216330 . T C 125.93 PASS AC=1;AF=0.563;AN=2;DP=285;FractionInformativeReads=1;MQ=60;set=variant6-variant9-variant10-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:99:141,0,290:0,8,0,4 chr1 76227022 . A G 1253.93 PASS AC=1;AF=0.563;AN=2;DP=2208;MQ=60;set=variant6-variant9-variant10-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,41:81:99:1201,0,1147:11,29,11,30 chr1 76229120 . T C 3244.33 PASS AC=1;AF=0.5;AN=2;DP=4224;MQ=60;set=variant6-variant9-variant13-variant14-variant17-variant19-variant20-variant21-variant23-variant27-variant29-variant31-variant32-variant33-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:139,132:271:99:3015,0,3274:64,75,62,70 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 0/1:7,10:17:99:384,0,200:1,6,0,10 chr1 76234886 . A G 1056.39 PASS AC=1;AF=0.955;AN=2;DP=1855;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:28,13:41:99:338,0,611:12,16,3,10 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 0/1:13,10:23:99:340,0,415:11,2,9,1 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 0/1:111,89:200:99:2017,0,2738:47,64,38,51 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 0/1:18,20:38:99:528,0,433:12,6,12,8 chr1 76255228 . G A 405.76 PASS AC=1;AF=0.563;AN=2;DP=678;MQ=60;set=variant6-variant9-variant10-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,11:28:99:249,0,503:5,12,3,8 chr1 76257892 . A T 2559.55 PASS AC=1;AF=0.943;AN=2;DP=3603;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:34,25:59:99:688,0,885:20,14,17,8 chr1 76260837 . C T 1243.09 PASS AC=1;AF=0.563;AN=2;DP=1710;set=variant6-variant9-variant10-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,32:69:99:1100,0,1207:8,29,6,26 chr1 76260866 . CTTTTT CTT,CTTT,CT,CTTTT,CTTTTTT,C 222.11 PASS AC=0,0,1,0,1,0;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 3/5:15:90:0,1,5,9 chr1 76269372 . T C 303.56 PASS AC=1;AF=0.645;AN=2;DP=692;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,15:21:99:383,0,118:4,2,10,5 chr1 76276353 . T C 403.48 PASS AC=1;AF=0.563;AN=2;DP=773;MQ=60;set=variant6-variant9-variant10-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,20:34:99:474,0,370:10,4,11,9 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 1/1:0,3:3:9:94,9,0:0,0,2,1 chr1 76313874 . C T 593.8 PASS AC=1;AF=0.533;AN=2;DP=723;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant8-variant11-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,18:30:99:425,0,234:7,5,9,9 chr1 76333163 . T G 764.13 PASS AC=1;AF=0.563;AN=2;DP=1504;FractionInformativeReads=1;MQ=60;set=variant6-variant9-variant10-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,21:47:99:503,0,980:13,13,14,7 chr1 76333172 . T C 745.31 PASS AC=1;AF=0.5;AN=2;DP=309;FractionInformativeReads=1;MQ=60;set=variant11-variant19-variant20-variant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:24,24:48:99:620,0,867:15,9,11,13 chr1 76344011 . C A 2054.29 PASS AC=1;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 0/1:20,27:47:99:778,0,560:4,16,8,19 chr1 76344711 . A T 3982.71 PASS AC=1;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 0/1:43,41:84:99:960,0,980:21,22,25,16 chr1 76344856 . T C 704.69 PASS AC=1;AF=0.533;AN=2;DP=716;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant8-variant11-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,33:48:99:906,0,325:6,9,9,24 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 1/1:0,13:13:39:582,39,0:0,0,0,13 chr1 76346832 . T C 241.42 PASS AC=1;AF=0.5;AN=2;DP=72;FS=0;FractionInformativeReads=1;MQ=60;set=variant11-variant19-variant20-variant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:11,3:14:93:93,0,360:9,2,3,0 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 1/1:0,87:87:99:3918,265,0:0,0,58,29 chr1 76378359 . ATT A,AT 191.59 PASS AC=1,0;AF=0.429,0.071;AN=2;DP=167;set=variant19-variant20-variant21-variant22-variant23-variant31-variant40 GT:DP:GQ:SB 0/1:12:77:2,0,6,4 chr1 76378360 . T TA 120.9 PASS AC=1;AF=0.579;AN=2;DP=318;set=variant6-variant9-variant10-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,2:12:77:77,0,341:6,4,2,0 chr1 76378362 . T A 126.77 PASS AC=1;AF=0.6;AN=2;DP=354;set=variant6-variant9-variant10-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,4:14:77:77,0,341:6,4,3,1 chr1 76540291 . C G 143.51 PASS AC=1;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 0/1:6,10:16:99:277,0,222:4,2,7,3 chr1 76540306 . G A 77.7 PASS AC=1;AF=0.5;AN=2;DP=37;FS=0;FractionInformativeReads=1;set=variant16-variant18-variant20-variant23 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:178,0,402:7,3,4,2 chr1 76608491 . T C 886.36 PASS AC=1;AF=0.587;AN=2;DP=940;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant15-variant17-variant19-variant21-variant23-variant24-variant26-variant27-variant33-variant34-variant36-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,23:55:99:831,0,3357:19,13,15,8 chr1 76608507 . C G 940.24 PASS AC=1;AF=0.542;AN=2;DP=575;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant9-variant12-variant17-variant23-variant26-variant27-variant30-variant33-variant34-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,23:63:99:845,0,3940:24,16,15,8 chr1 76608508 . CT C,CTT 928.2 PASS AC=1,0;AF=0.5,0.042;AN=2;DP=594;MQ=60;set=variant2-variant6-variant9-variant12-variant17-variant23-variant26-variant27-variant32-variant33-variant34-variant44 GT:DP:GQ:SB 0/1:63:99:24,16,15,8 chr1 76608532 . T G 1060.31 PASS AC=1;AF=0.577;AN=2;DP=824;MQ=60;set=variant2-variant6-variant9-variant12-variant15-variant17-variant23-variant26-variant27-variant33-variant34-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,24:69:99:894,0,4058:27,18,15,9 chr1 76608777 . C T 417.52 PASS AC=1;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 0/1:8,6:14:99:147,0,231:2,6,2,4 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 1/1:0,44:44:99:1577,132,0:0,0,33,11 chr1 76779554 . T C 1229.77 PASS AC=1;AF=0.5;AN=2;DP=93;FS=0.783;FractionInformativeReads=1;MQ=60;MQRankSum=-1.288;QD=13.22;ReadPosRankSum=1.203;SOR=0.563;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:41,52:93:99:1258,0,1045:22,19,26,26 chr1 76878156 . C T 500.53 PASS AC=1;AF=0.567;AN=2;DP=669;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant9-variant13-variant17-variant23-variant27-variant28-variant33-variant34-variant36-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:14,24:38:99:671,0,375:5,9,6,18 chr1 77093010 . C T 1096.77 PASS AC=1;AF=0.615;AN=2;DP=883;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant26-variant29-variant31-variant32-variant33-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,10:23:99:412,0,942:10,3,6,4 chr1 77093011 . T G 1096.77 PASS AC=1;AF=0.615;AN=2;DP=900;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant26-variant29-variant31-variant32-variant33-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,11:25:99:412,0,942:11,3,7,4 chr1 77093180 . C A 4268.09 PASS AC=1;AF=0.615;AN=2;DP=4192;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant26-variant29-variant31-variant32-variant33-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,61:130:99:1318,0,1661:31,38,32,29 chr1 77094826 . A G 2026.72 PASS AC=1;AF=0.538;AN=2;DP=884;MQ=60;set=variant-variant4-variant10-variant11-variant13-variant20-variant22-variant23-variant31-variant32-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,52:75:99:1709,0,601:8,15,19,33 chr1 77094985 . C G 5440.92 PASS AC=1;AF=0.615;AN=2;DP=3698;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant26-variant29-variant31-variant32-variant33-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,63:127:99:1785,0,1718:39,25,39,24 chr1 77095754 . C T 1450.82 PASS AC=1;AF=0.5;AN=2;DP=88;FS=1.775;FractionInformativeReads=1;MQ=60;MQRankSum=-0.49;QD=16.49;ReadPosRankSum=-1.31;SOR=0.474;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:37,51:88:99:1479,0,1157:22,15,27,24 chr1 77096987 . CAA C,CA,CAAA 1869.49 PASS AC=1,0,0;AF=0.483,0.117,0.017;AN=2;DP=2054;set=variant-variant3-variant4-variant5-filterInvariant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-filterInvariant21-variant22-variant23-variant26-variant29-variant31-variant32-variant33-variant34-variant38-filterInvariant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:51:99:23,12,13,3 chr1 77097381 . T G 4946.35 PASS AC=1;AF=0.538;AN=2;DP=1376;MQ=60;set=variant-variant4-variant10-variant11-variant13-variant20-variant22-variant23-variant31-variant32-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,50:95:99:1419,0,1219:20,25,17,33 chr1 77097790 . A G 3066.33 PASS AC=1;AF=0.615;AN=2;DP=2564;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant26-variant29-variant31-variant32-variant33-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,39:71:99:1055,0,819:19,13,18,21 chr1 77098489 . AAAC A 3254.85 PASS AC=1;AF=0.5;AN=2;DP=1199;MQ=60;set=variant-variant10-variant23-variant44 GT:AD:DP:GQ:PL:SB 0/1:139,130:269:99:4781,0,5227:78,61,69,61 chr1 77098562 . A G 12223.8 PASS AC=2;AF=0.977;AN=2;DP=17186;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,315:316:99:9597,935,0:1,0,151,164 chr1 77098729 . G T 3408.85 PASS AC=1;AF=0.615;AN=2;DP=2809;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant26-variant29-variant31-variant32-variant33-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,51:96:99:1321,0,1314:11,34,23,28 chr1 77099691 . G A 20631.3 PASS AC=1;AF=0.615;AN=2;DP=13518;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant26-variant29-variant31-variant32-variant33-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:243,234:477:99:5936,0,6172:109,134,104,130 chr1 77100375 . T TAATATACTTGATATCCAAGTCGGAAACATATCCAGAATACTACTATAAACAATAACAAGAGAAAA,TAATATACTTGATATCCAAGTCGGAAACATATCCAGAATACTACTATAAACAATAACAAGAGAAAATGTTGG,TAATATACTTGATATCCAAGTCGGAAACATATCCAGAATACTACTATGAACAATAACAAGAGAAAATGTTGGTCTGCCTC,TAATATACTTGATATCCAAGTCGGAAACATATCCAGAATACTACTATAAACAATAACAAGAGAAAATGTTGGTCTGCC,TAATATACTTGATATCCAAGTCGGAAACATATCCAGAA,TAATATACTTGATATCCAAGTCGGAAACATATCCAGAATACTACTATGAACAATAACAAGAGAAAA,TAATATACTTGATATCCAAGTCGGAAACATATCCAGAATACTACTATAAACAA 1259.83 PASS AC=0,0,0,0,1,0,0;AF=0.143,0.071,0.071,0.143,0.071,0.071,0.071;AN=2;DP=229;set=variant5-variant11-variant17-variant22-variant23-variant26-variant31 GT:DP:GQ:SB 0/5:11:99:0,5,1,5 chr1 77557339 . A G 3580.53 PASS AC=1;AF=0.583;AN=2;DP=1212;FractionInformativeReads=1;MQ=60;set=variant3-variant12-variant17-variant23-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,88:174:99:2037,0,2136:41,45,42,46 chr1 77619958 . T C 4840.92 PASS AC=1;AF=0.6;AN=2;DP=1393;MQ=60;set=variant3-variant17-variant23-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:124,128:252:99:3184,0,3099:67,57,79,49 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 1/1:0,313:313:99:9177,936,0:0,0,146,167 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 1/1:0,44:44:99:1619,132,0:0,0,13,31 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 1/1:0,80:80:99:2270,240,0:0,0,44,36 chr1 77748664 . C T 2632.92 PASS AC=1;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 0/1:65,53:118:99:1235,0,1639:32,33,30,23 chr1 77748786 . A G 2926.04 PASS AC=1;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 0/1:40,66:106:99:1772,0,953:19,21,31,35 chr1 77749363 . G C 280.59 PASS AC=1;AF=0.593;AN=2;DP=527;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:10,11:21:99:391,0,300:3,7,1,10 chr1 77759380 . C G 230.64 PASS AC=1;AF=0.583;AN=2;DP=212;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant8-variant11-variant13-variant17-variant23-variant32-variant34-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:226,0,266:7,1,6,1 chr1 77759578 . A G 1126.99 PASS AC=1;AF=0.583;AN=2;DP=1307;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant8-variant11-variant13-variant17-variant23-variant32-variant34-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,60:91:99:1523,0,633:13,18,28,32 chr1 77763071 . A G 575.17 PASS AC=1;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 0/1:13,18:31:99:548,0,335:10,3,13,5 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 1/1:0,57:57:99:1712,171,0:0,0,25,32 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 1/1:0,41:41:99:1824,123,0:0,0,12,29 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 1/1:0,39:39:99:1755,117,0:0,0,12,27 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 1/1:0,20:20:60:652,60,0:0,0,7,13 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 1/1:0,6:6:18:226,18,0:0,0,2,4 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 1/1:0,30:30:90:986,90,0:0,0,22,8 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 1/1:0,86:86:99:3888,262,0:0,0,54,32 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 1/1:0,134:134:99:4148,400,0:0,0,65,69 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 1/1:0,182:182:99:8273,557,0:0,0,94,88 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 1/1:0,184:184:99:8273,557,0:0,0,96,88 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 1/1:0,77:77:99:3443,232,0:0,0,38,39 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 1/1:0,216:216:99:9753,662,0:0,0,113,103 chr1 78025459 . T C 5214.12 PASS AC=2;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 1/1:0,220:220:99:9766,662,0:0,0,112,108 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 1/1:0,184:184:99:5874,550,0:0,0,75,109 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 1/1:0,12:12:36:534,36,0:0,0,0,12 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 1/1:0,10:10:30:430,30,0:0,0,8,2 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 1/1:0,13:13:39:447,39,0:0,0,3,10 chr1 78046496 . T C 237.38 PASS AC=1;AF=0.5;AN=2;DP=32;FractionInformativeReads=1;MQ=60;set=variant23-variant28-variant30 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:266,0,212:6,3,7,1 chr1 78177213 . TACACAC TACAC,TAC,TACACACAC,T 1561.22 PASS AC=2,0,0,0;AF=0.795,0.08,0.034,0.023;AN=2;DP=2458;set=Intersection GT:DP:GQ:SB 1/1:49:99:0,1,31,17 chr1 78179032 . AT A 202.96 PASS AC=2;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 1/1:0,18:18:54:516,54,0:0,0,4,14 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 1/1:0,13:13:39:452,39,0:0,0,3,10 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 1/1:0,21:21:63:762,63,0:0,0,5,16 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 1/1:41:68:1,1,18,21 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 1/1:0,16:16:48:551,48,0:0,0,4,12 chr1 78414310 . CA C,CAA 383.11 PASS AC=1,0;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 0/1:150:99:71,43,25,11 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 1/1:0,56:56:99:2066,171,0:0,0,28,28 chr1 78444764 . C CGGCCG 1063.19 PASS AC=1;AF=0.545;AN=2;DP=664;MQ=60;set=variant-variant3-variant14-variant15-variant17-variant20-variant22-variant23-variant28-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,25:57:99:916,0,2119:17,15,13,12 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 1/1:0,5:5:15:166,15,0:0,0,0,5 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 1/1:0,33:33:99:1126,99,0:0,0,23,10 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 1/1:0,44:44:99:1503,132,0:0,0,31,13 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 1/1:1,198:199:99:5956,582,0:0,1,84,114 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 0/1:138:99:11,21,42,64 chr1 78602292 . CTTTTT CTTTT,CTTTTTTT,C,CT,CTTTTTT,CTTTTTTTT,CTTT,CTT 532.37 PASS AC=0,0,0,0,1,0,0,0;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 0/5:54:99:10,18,12,14 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 1/1:0,207:207:99:6198,620,0:0,0,116,91 chr1 78603279 . A G 10334.3 PASS AC=2;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 1/1:0,247:247:99:7988,740,0:0,0,103,144 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 1/1:0,210:210:99:6527,627,0:0,0,104,106 chr1 78603463 . T C 3270.62 PASS AC=2;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 1/1:1,228:229:99:7231,649,0:1,0,114,114 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 1/1:1,57:58:99:1673,139,0:0,1,27,30 chr1 79106967 . C T 1548.59 PASS AC=2;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 1/1:0,37:37:99:1192,111,0:0,0,14,23 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 0/1:11,9:20:99:207,0,369:10,1,5,4 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 0/1:73,42:115:99:1347,0,2591:33,40,18,24 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 1/1:0,122:122:99:3817,366,0:0,0,62,60 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 1/1:0,40:40:99:1273,120,0:0,0,19,21 chr1 79356179 . CT C 38.76 PASS AC=1;AF=0.5;AN=2;DP=93;MQ=60;set=filterInvariant23-variant28 GT:AD:DP:GQ:PL:SB 0/1:29,7:36:76:76,0,610:16,13,5,2 chr1 79357360 . G C 2697.83 PASS AC=2;AF=0.659;AN=2;DP=2847;MQ=60;set=variant3-variant4-variant5-variant6-variant8-variant10-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:3568,338,0:0,0,50,63 chr1 79383766 . G T 474.21 PASS AC=1;AF=0.5;AN=2;DP=280;MQ=60;set=variant4-variant10-variant23-variant24-variant29-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:13,21:34:99:553,0,281:6,7,8,13 chr1 79387242 . C T 1075.93 PASS AC=2;AF=0.659;AN=2;DP=1271;MQ=60;set=variant3-variant4-variant5-variant6-variant8-variant10-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant33-variant34-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1429,136,0:0,0,35,11 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 1/1:0,58:58:99:1812,174,0:0,0,38,20 chr1 81970883 . CCACACA CCA,CCACACACA,CCACA,C 124.73 PASS AC=0,1,0,0;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 0/2:5:48:2,0,2,1 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 0/1:18,21:39:99:729,0,611:12,6,16,5 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 0/1:164,156:320:99:3521,0,4126:80,84,76,80 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 0/1:14,9:23:99:336,0,813:8,6,7,2 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 1/1:0,28:28:84:1043,84,0:0,0,21,7 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 0/1:13,10:23:99:278,0,365:3,10,2,8 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 0/1:7,4:11:83:83,0,195:5,2,3,1 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 1/1:0,98:98:99:3158,294,0:0,0,59,39 chr1 82456585 . G A 1969.5 PASS AC=1;AF=0.5;AN=2;DP=808;FractionInformativeReads=1;MQ=60;set=variant2-variant11-variant23-variant26-variant29 GT:AD:DP:GQ:PL:SB 0/1:61,88:149:99:2099,0,1525:27,34,40,48 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 1/1:0,226:226:99:6500,675,0:0,0,98,128 chr1 84330635 . CGTGT CGTGTGTGT,CGTGTGTGTGTGTGT,CGTGTGTGTGTGTGTGTGTGT,CGTGTGTGTGT,CGTGTGT,C,CGTGTGTGTGTGT,CGT,CGTGTGTGTGTGTGTGT 157.51 PASS AC=0,0,0,0,1,0,0,0,1;AF=0.163,0.063,0.013,0.113,0.138,0.038,0.163,0.05,0.05;AN=2;DP=890;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-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 5/9:20:99:2,1,16,1 chr1 84331981 . A G 575.49 PASS AC=1;AF=0.649;AN=2;DP=2562;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,35:62:99:987,0,734:14,13,18,17 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 1/1:0,292:292:99:9036,874,0:0,0,145,147 chr1 84333213 . T TTG,TTGTG 2079.08 PASS AC=1,0;AF=0.618,0.013;AN=2;DP=8077;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:127:99:27,48,25,27 chr1 84333301 . G A 2479.7 PASS AC=1;AF=0.645;AN=2;DP=4601;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,76:153:99:2893,0,2857:34,43,39,37 chr1 84333310 . C T 2631.03 PASS AC=1;AF=0.645;AN=2;DP=4668;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,78:154:99:2988,0,2782:32,44,39,39 chr1 84335412 . C T 735.28 PASS AC=1;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 0/1:29,29:58:99:729,0,732:13,16,13,16 chr1 84355734 . AAGAACTTCAAGGAT A 670.65 PASS AC=1;AF=0.645;AN=2;DP=1648;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,28:66:99:1062,0,2413:18,20,11,17 chr1 84365788 . C A 783.97 PASS AC=1;AF=0.5;AN=2;DP=284;FractionInformativeReads=1;MQ=60;set=variant11-variant20-variant23-variant25-variant27-variant33-variant39 GT:AD:DP:GQ:PL:SB 0/1:26,16:42:99:437,0,763:19,7,12,4 chr1 84383079 . G A 811.73 PASS AC=1;AF=0.65;AN=2;DP=1221;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,23:39:99:619,0,424:11,5,16,7 chr1 84394792 . G A 470.57 PASS AC=1;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 0/1:43,31:74:99:675,0,1004:25,18,19,12 chr1 84464468 . C G 349.71 PASS AC=1;AF=0.65;AN=2;DP=809;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,14:28:99:356,0,465:10,4,10,4 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 1/1:0,50:50:99:1328,149,0:0,0,26,24 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 0/1:4,2:6:72:72,0,123:1,3,0,2 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 0/1:13,11:24:99:342,0,390:11,2,9,2 chr1 84641416 . CT C 1374.32 PASS AC=1;AF=0.5;AN=2;DP=667;MQ=60;set=variant11-variant20-variant23-variant25-variant33-variant39 GT:AD:DP:GQ:PL:SB 0/1:49,48:97:99:1084,0,1097:24,25,25,23 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 0/1:12,3:15:90:90,0,757:5,7,2,1 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 0/1:11,5:16:99:157,0,709:5,6,3,2 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 0/1:16,15:31:99:379,0,441:11,5,9,6 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 0/1:198,145:343:99:3324,0,4903:115,83,75,70 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 0/1:152,160:312:99:4050,0,3933:87,65,94,66 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 0/1:4,6:10:69:155,0,69:2,2,4,2 chr1 84768224 . TACACAC TACACACACAC,TACAC,TACACACAC,TAC,T 48.65 PASS AC=0,0,0,0,1;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 0/5:5:99:2,0,2,1 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 1/1:0,10:10:30:361,30,0:0,0,7,3 chr1 84810396 . A C 621.51 PASS AC=2;AF=0.886;AN=2;DP=658;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:768,63,0:0,0,17,4 chr1 84810815 . A G 4618.04 PASS AC=2;AF=0.977;AN=2;DP=5495;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:2935,296,0:0,0,53,46 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 1/1:0,33:33:99:1190,99,0:0,0,23,10 chr1 84816587 . A C 106.77 PASS AC=2;AF=0.956;AN=2;DP=152;FS=0;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:177,12,0:0,0,0,4 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 1/1:0,50:50:99:1582,150,0:0,0,32,18 chr1 84864256 . G C 1080.87 PASS AC=1;AF=0.574;AN=2;DP=2786;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant17-variant18-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,44:78:99:1025,0,954:16,18,20,24 chr1 84867610 . G A 594.95 PASS AC=1;AF=0.521;AN=2;DP=1200;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,22:45:99:602,0,479:13,10,14,8 chr1 84873835 . A G 1517.6 PASS AC=2;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 1/1:0,68:68:99:2100,204,0:0,0,42,26 chr1 84874242 . C G 746.03 PASS AC=1;AF=0.567;AN=2;DP=2593;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,26:68:99:716,0,1177:14,28,6,20 chr1 84876711 . C CA 2151.3 PASS AC=2;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 1/1:0,51:51:99:2044,153,0:0,0,12,39 chr1 84876731 . T G 1075.19 PASS AC=2;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 1/1:0,36:36:99:1313,108,0:0,0,8,28 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 0/1:35,45:80:99:1157,0,995:18,17,25,20 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 1/1:0,58:58:99:1822,173,0:0,0,20,38 chr1 84880380 . T C 1582.98 PASS AC=1;AF=0.583;AN=2;DP=3358;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,60:107:99:1652,0,1187:28,19,33,27 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 1/1:0,41:41:99:1561,123,0:0,0,5,36 chr1 84944989 . A G 606.02 PASS AC=2;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 1/1:0,57:57:99:1898,171,0:0,0,26,31 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 1/1:0,31:31:93:1049,93,0:0,0,8,23 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 1/1:0,34:34:99:973,102,0:0,0,22,12 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 0/1:3,9:12:61:249,0,61:1,2,3,6 chr1 85096592 . C T 1012.06 PASS AC=1;AF=0.5;AN=2;DP=1132;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant10-variant19-variant23-variant24-variant31-variant33-variant34-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,45:77:99:1111,0,805:11,21,20,25 chr1 85096920 . A G 391.14 PASS AC=1;AF=0.5;AN=2;DP=538;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant10-variant19-variant23-variant24-variant31-variant33-variant34-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,32:52:99:809,0,450:12,8,20,12 chr1 85097247 . T G 1249.98 PASS AC=1;AF=0.5;AN=2;DP=1254;MQ=60;set=variant-variant3-variant7-variant10-variant19-variant23-variant24-variant31-variant33-variant34-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,45:92:99:1131,0,1222:30,17,29,16 chr1 85097474 . G A 915.69 PASS AC=1;AF=0.5;AN=2;DP=63;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.565;QD=14.53;ReadPosRankSum=0.889;SOR=0.828;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:29,34:63:99:944,0,731:12,17,13,21 chr1 85110325 . C A 1867.36 PASS AC=2;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 1/1:0,63:63:99:2173,188,0:0,0,44,19 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 0/1:161,103:264:99:2338,0,4046:81,80,45,58 chr1 85113203 . T C 4118.59 PASS AC=2;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 1/1:0,121:121:99:3890,363,0:0,0,43,78 chr1 85113229 . A G 1543.68 PASS AC=1;AF=0.688;AN=2;DP=4490;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-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,54:113:99:1281,0,1619:18,41,21,33 chr1 85115852 . G T 10433.3 PASS AC=2;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 1/1:0,275:275:99:8195,823,0:0,0,153,122 chr1 85121255 . A G 651.58 PASS AC=1;AF=0.688;AN=2;DP=2523;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-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,27:51:99:616,0,601:9,15,11,16 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 1/1:0,3:3:9:86,9,0:0,0,2,1 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 0/1:25,27:52:99:763,0,672:7,18,12,15 chr1 85128280 . T C 1810.49 PASS AC=2;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 1/1:0,33:33:99:1081,99,0:0,0,13,20 chr1 85128305 . G C 582.67 PASS AC=1;AF=0.688;AN=2;DP=1297;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-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,14:26:99:355,0,318:3,9,6,8 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 0/1:3,4:7:74:147,0,74:2,1,4,0 chr1 85131982 . T G 435.13 PASS AC=2;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 1/1:0,17:17:51:608,51,0:0,0,3,14 chr1 85278106 . CTTTTTT CTTT,CTT,CTTTT,C 164.13 PASS AC=2,0,0,0;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 1/1:5:15:0,0,0,5 chr1 85278665 . A G 772.18 PASS AC=2;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 1/1:0,35:35:99:989,105,0:0,0,14,21 chr1 85278952 . T TTAAG 9889.36 PASS AC=2;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 1/1:0,137:137:99:6385,430,0:0,0,90,47 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 1/1:0,340:340:99:9514,1015,0:0,0,169,171 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 1/1:0,68:68:99:3051,205,0:0,0,23,45 chr1 85331918 . C G 76.73 PASS AC=1;AF=0.5;AN=2;DP=74;FractionInformativeReads=1;MQ=60;set=variant8-variant13-variant15-variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:5,10:15:91:317,0,91:2,3,3,7 chr1 85391575 . AT A,ATT 36.32 PASS AC=1,0;AF=0.25,0.25;AN=2;DP=235;set=variant-filterInvariant2-variant15-variant19-variant23-filterInvariant25-filterInvariant26-variant35-variant37-variant43 GT:DP:GQ:SB 0/1:13:92:1,7,2,3 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 1/1:0,44:44:99:1283,132,0:0,0,27,17 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 0/1:3,2:5:75:75,0,113:3,0,2,0 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 1/1:0,44:44:99:1568,132,0:0,0,11,33 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 1/1:0,115:115:99:3530,344,0:0,0,63,52 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 1/1:0,65:65:99:1932,195,0:0,0,40,25 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 1/1:0,3:3:9:132,9,0:0,0,0,3 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 1/1:0,106:106:99:3411,318,0:0,0,36,70 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 1/1:0,47:47:99:2082,147,0:0,0,17,30 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 1/1:0,47:47:99:2053,150,0:0,0,17,30 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 1/1:0,19:19:57:600,57,0:0,0,7,12 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 1/1:0,6:6:18:171,18,0:0,0,3,3 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 1/1:0,20:20:60:633,60,0:0,0,13,7 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 1/1:1,29:30:58:731,58,0:1,0,12,17 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 1/1:0,56:56:99:1800,168,0:0,0,34,22 chr1 85484473 . C T 2514.43 PASS AC=2;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 1/1:1,95:96:99:3002,242,0:1,0,54,41 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 1/1:0,100:100:99:3192,300,0:0,0,48,52 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 1/1:0,22:22:66:822,66,0:0,0,3,19 chr1 85491271 . TAA TA,TAAA,T 855.51 PASS AC=1,0,0;AF=0.476,0.024,0.012;AN=2;DP=6130;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-filterInvariant12-variant13-variant14-filterInvariant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-variant22-filterInvariant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-variant30-filterInvariant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-filterInvariant42-filterInvariant43-variant44 GT:DP:GQ:SB 0/1:123:99:63,40,12,8 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 1/1:0,13:13:39:454,39,0:0,0,3,10 chr1 85511057 . AAAC A 613.42 PASS AC=1;AF=0.5;AN=2;DP=324;MQ=60;set=variant-variant15-variant23-variant24-variant31-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,16:26:99:634,0,397:5,5,7,9 chr1 85514282 . T C 87.14 PASS AC=2;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 1/1:0,13:13:39:452,39,0:0,0,4,9 chr1 85527974 . G A 619.4 PASS AC=2;AF=0.886;AN=2;DP=1410;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1156,105,0:0,0,23,12 chr1 85528006 . C A 199.69 PASS AC=2;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 1/1:0,43:43:99:1431,129,0:0,0,27,16 chr1 85537502 . T A 376.59 PASS AC=2;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 1/1:0,8:8:24:310,24,0:0,0,7,1 chr1 85537522 . T C 713.3 PASS AC=2;AF=0.852;AN=2;DP=826;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:456,36,0:0,0,10,2 chr1 85538655 . A G 136.08 PASS AC=2;AF=0.881;AN=2;DP=230;FS=0;set=variant4-variant6-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant26-variant27-variant31-variant32-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:146,18,0:0,0,3,3 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 0/1:11,12:23:99:360,0,346:2,9,2,10 chr1 85547270 . A G 314.21 PASS AC=1;AF=0.77;AN=2;DP=938;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,10:13:95:311,0,95:0,3,1,9 chr1 85547945 . T C 429.33 PASS AC=1;AF=0.708;AN=2;DP=1219;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,7:25:99:240,0,558:12,6,7,0 chr1 85551468 . A ATCAGTTTTTCT 256.32 PASS AC=1;AF=0.77;AN=2;DP=495;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:357,0,267:7,0,6,1 chr1 85555672 . A C 94.69 PASS AC=1;AF=0.809;AN=2;DP=379;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:111,0,157:4,1,3,2 chr1 85559118 . CT C 1456.71 PASS AC=2;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 1/1:0,39:39:99:1214,117,0:0,0,25,14 chr1 85559440 . T A 1182.44 PASS AC=1;AF=0.5;AN=2;DP=77;FS=10.162;FractionInformativeReads=1;MQ=60;MQRankSum=0.559;QD=15.36;ReadPosRankSum=-0.904;SOR=0.179;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:30,47:77:99:1211,0,863:8,22,22,25 chr1 85559452 . A G 3058.4 PASS AC=2;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 1/1:0,78:78:99:2530,234,0:0,0,32,46 chr1 85560313 . T C 546.46 PASS AC=2;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 1/1:0,8:8:24:357,24,0:0,0,2,6 chr1 85561546 . T C 1568.45 PASS AC=2;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 1/1:0,50:50:99:1633,150,0:0,0,36,14 chr1 85564138 . A G 1552.49 PASS AC=2;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 1/1:0,32:32:94:929,94,0:0,0,21,11 chr1 85570157 . A T 398.78 PASS AC=1;AF=0.5;AN=2;DP=46;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.979;QD=8.67;ReadPosRankSum=0.66;SOR=0.838;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:29,17:46:99:427,0,817:21,8,13,4 chr1 85573705 . A AC,ACT 312.53 PASS AC=2,0;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 1/1:16:48:0,0,13,3 chr1 85574021 . G A 548.36 PASS AC=2;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 1/1:0,16:16:48:608,48,0:0,0,2,14 chr1 85589939 . GT G 1542.07 PASS AC=2;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 1/1:0,116:116:99:4340,349,0:0,0,43,73 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 1/1:0,13:13:39:366,39,0:0,0,8,5 chr1 85595645 . C T 1497.69 PASS AC=2;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 1/1:1,120:121:99:3602,351,0:1,0,71,49 chr1 85595975 . T C 851.55 PASS AC=2;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 1/1:0,66:66:99:2465,198,0:0,0,16,50 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 1/1:0,58:58:99:1768,174,0:0,0,37,21 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 1/1:0,159:159:99:4578,476,0:0,0,84,75 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 1/1:0,57:57:99:1675,171,0:0,0,22,35 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 1/1:0,21:21:63:674,63,0:0,0,16,5 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 1/1:0,134:134:99:4011,401,0:0,0,64,70 chr1 85648905 . T C 81 PASS AC=2;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 1/1:0,18:18:54:671,54,0:0,0,4,14 chr1 85723318 . A G 352.37 PASS AC=1;AF=0.583;AN=2;DP=267;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant14-variant18-variant23-variant25-variant31-variant32-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:308,0,258:1,6,1,8 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 0/1:47,37:84:99:1410,0,1817:19,28,17,20 chr1 85725426 . G T 596.3 PASS AC=1;AF=0.583;AN=2;DP=383;MQ=60;set=variant3-variant4-variant5-variant14-variant18-variant23-variant25-variant31-variant32-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,22:34:99:604,0,314:4,8,7,15 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 0/1:39,53:92:99:1378,0,1003:26,13,34,19 chr1 85732559 . CAAAAAAAAAA C,CAAAAAAAAA,CAAAAAAAA,CAAAAAAAAAAAA,CAAAAAAA,CAAAAA 576.09 PASS AC=0,1,0,0,0,0;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 0/2:13:52:4,1,8,0 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 0/1:140,128:268:99:2815,0,3285:66,74,60,68 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 0/1:12,12:24:99:264,0,287:7,5,7,5 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 1/1:0,151:151:99:4468,453,0:0,0,83,68 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 0/1:110,86:196:99:2085,0,2820:54,56,39,47 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 1/1:0,142:142:99:4477,426,0:0,0,68,74 chr1 85784936 . G A 1416.34 PASS AC=1;AF=0.542;AN=2;DP=863;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant14-variant23-variant25-variant31-variant32-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,21:48:99:567,0,781:15,12,11,10 chr1 85785550 . C CA 6742.14 PASS AC=2;AF=0.886;AN=2;DP=15466;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,340:340:99:13742,1026,0:0,0,176,164 chr1 85785655 . T C 3328.88 PASS AC=2;AF=0.756;AN=2;DP=9419;MQ=60;set=variant-variant2-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-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,225:225:99:6900,673,0:0,0,92,133 chr1 85785751 . T C 1400.9 PASS AC=1;AF=0.614;AN=2;DP=2054;MQ=60;set=variant-variant2-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant19-variant22-variant23-variant25-variant28-variant31-variant32-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,41:85:99:1283,0,1176:15,29,10,31 chr1 85786299 . T A 1422.51 PASS AC=1;AF=0.568;AN=2;DP=1941;MQ=60;set=variant-variant2-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant19-variant22-variant23-variant25-variant28-variant31-variant32-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,49:93:99:1270,0,1168:19,25,21,28 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 0/1:151:99:55,48,28,20 chr1 85786957 . T G,C 554.47 PASS AC=1,0;AF=0.543,0.022;AN=2;DP=898;set=variant-variant2-filterInvariant3-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant19-variant22-variant23-variant25-variant28-variant31-variant32-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:37:99:7,10,9,11 chr1 85786977 . G A 209.13 PASS AC=1;AF=0.568;AN=2;DP=681;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant19-variant22-variant23-variant25-variant28-variant31-variant32-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,10:23:99:265,0,322:7,6,6,4 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 1/1:0,63:63:99:2281,189,0:0,0,38,25 chr1 85787118 . G C 505.1 PASS AC=1;AF=0.571;AN=2;DP=1464;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant19-variant22-variant23-variant25-variant28-variant31-variant32-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,27:65:99:675,0,899:24,14,14,13 chr1 85787323 . T A 431.04 PASS AC=1;AF=0.571;AN=2;DP=841;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant19-variant22-variant23-variant25-variant28-variant31-variant32-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,8:21:99:242,0,431:2,11,1,7 chr1 85787334 . C T 311.8 PASS AC=1;AF=0.542;AN=2;DP=432;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant14-variant23-variant25-variant31-variant32-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,7:20:99:179,0,467:2,11,1,6 chr1 85790633 . G A 675.29 PASS AC=1;AF=0.571;AN=2;DP=1429;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant9-variant11-variant14-variant15-variant16-variant19-variant22-variant23-variant25-variant28-variant31-variant32-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,38:87:99:978,0,1332:17,32,13,25 chr1 85816134 . T C 1052.41 PASS AC=1;AF=0.542;AN=2;DP=1035;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant14-variant23-variant25-variant31-variant32-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,38:81:99:893,0,1156:25,18,21,17 chr1 85817295 . G A 2103.5 PASS AC=1;AF=0.542;AN=2;DP=2282;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant14-variant23-variant25-variant31-variant32-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,95:188:99:2323,0,2399:35,58,38,57 chr1 85930272 . GACAC G,GAC,GACACAC 821.22 PASS AC=0,2,0;AF=0.011,0.75,0.08;AN=2;DP=2144;set=Intersection GT:DP:GQ:SB 2/2:45:99:0,0,17,28 chr1 86047311 . G C 1989 PASS AC=1;AF=0.563;AN=2;DP=3186;MQ=60;set=variant5-variant7-variant9-variant11-variant13-variant14-variant17-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:78,84:162:99:1966,0,2005:32,46,33,51 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 1/1:0,52:52:99:1698,155,0:0,0,40,12 chr1 86119295 . A G 407.55 PASS AC=1;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 0/1:17,16:33:99:434,0,665:12,5,9,7 chr1 86119296 . C A 55.98 PASS AC=1;AF=0.621;AN=2;DP=1151;set=variant-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,16:32:99:421,0,624:9,7,11,5 chr1 86146672 . G A 115.17 PASS AC=1;AF=0.641;AN=2;DP=971;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:220,0,403:2,9,1,6 chr1 86167957 . C T 1270.42 PASS AC=1;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 0/1:17,18:35:99:427,0,440:6,11,8,10 chr1 86173298 . C T 1180.39 PASS AC=1;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 0/1:58,51:109:99:1147,0,1309:32,26,28,23 chr1 86173943 . C T 1075.77 PASS AC=1;AF=0.5;AN=2;DP=570;FractionInformativeReads=1;MQ=60;set=variant14-variant23-variant27-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:62,52:114:99:1320,0,1544:30,32,28,24 chr1 86174232 . G T 82.71 PASS AC=1;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 0/1:8,6:14:99:147,0,198:3,5,2,4 chr1 86194997 . C T 1204.39 PASS AC=2;AF=0.652;AN=2;DP=4506;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,108:108:99:2964,320,0:0,0,57,51 chr1 86195066 . A C 1532.54 PASS AC=2;AF=0.643;AN=2;DP=4805;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:2831,281,0:0,0,45,49 chr1 86201744 . C T 88.95 PASS AC=1;AF=0.5;AN=2;DP=71;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant11-variant15-variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,6:17:99:201,0,286:7,4,6,0 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 1/1:0,130:130:99:4245,389,0:0,0,75,55 chr1 86202102 . C A 1902.5 PASS AC=1;AF=0.5;AN=2;DP=1260;MQ=60;set=variant-variant3-variant11-variant15-variant22-variant23-variant30-variant42 GT:AD:DP:GQ:PL:SB 0/1:80,58:138:99:1351,0,2140:38,42,23,35 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 1/1:0,8:8:24:260,24,0:0,0,7,1 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 1/1:0,19:19:55:523,55,0:0,0,5,14 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 1/1:0,20:20:60:659,60,0:0,0,5,15 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 1/1:0,23:23:69:750,69,0:0,0,17,6 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 1/1:0,23:23:69:699,69,0:0,0,12,11 chr1 86249307 . T C 374.73 PASS AC=1;AF=0.5;AN=2;DP=39;FractionInformativeReads=1;MQ=60;set=variant3-variant23 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:113,0,200:2,4,0,5 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 1/1:0,60:60:99:1798,180,0:0,0,33,27 chr1 86252025 . A G 564.83 PASS AC=1;AF=0.656;AN=2;DP=1690;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,30:58:99:756,0,644:16,12,17,13 chr1 86334070 . T A 775.41 PASS AC=2;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 1/1:0,36:36:99:1139,107,0:0,0,25,11 chr1 86334316 . T C 1373.01 PASS AC=2;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 1/1:0,63:63:99:1938,189,0:0,0,22,41 chr1 86334675 . T C 286.03 PASS AC=2;AF=0.704;AN=2;DP=182;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,0,3 chr1 86340193 . G T 43.52 PASS AC=2;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 1/1:0,12:12:36:337,36,0:0,0,7,5 chr1 86340523 . T C 82.7 PASS AC=2;AF=0.863;AN=2;DP=358;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-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:99,12,0:0,0,2,2 chr1 86340794 . T C 669.63 PASS AC=2;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 1/1:0,11:11:33:333,33,0:0,0,7,4 chr1 86340892 . A G 1067.11 PASS AC=2;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 1/1:0,48:48:99:1586,144,0:0,0,30,18 chr1 86361384 . C T 175.08 PASS AC=2;AF=0.886;AN=2;DP=520;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:502,42,0:0,0,11,3 chr1 86361802 . C G 562 PASS AC=2;AF=0.775;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-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1760,171,0:0,0,23,34 chr1 86372839 . T TG 777.46 PASS AC=1;AF=0.611;AN=2;DP=1939;MQ=60;set=variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,26:54:99:622,0,685:16,12,17,9 chr1 86375654 . C G 1134.51 PASS AC=2;AF=0.775;AN=2;DP=3240;MQ=60;set=variant-variant2-variant3-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-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:2459,262,0:0,0,45,43 chr1 86375840 . G A 128.93 PASS AC=1;AF=0.563;AN=2;DP=72;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant9-variant13-variant15-variant20-variant21-variant23 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:75:75,0,76:0,2,0,2 chr1 86377028 . C T 637.12 PASS AC=1;AF=0.611;AN=2;DP=943;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant29-filterInvariant30-variant31-variant32-variant33-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,17:46:99:340,0,746:17,12,8,9 chr1 86435850 . T C 395.92 PASS AC=1;AF=0.591;AN=2;DP=455;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant9-variant11-variant13-variant15-variant20-variant21-variant22-variant23-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,17:36:99:410,0,526:13,6,10,7 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 0/1:14,20:34:99:511,0,344:5,9,10,10 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 0/1:27,48:75:99:1250,0,613:12,15,21,27 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 0/1:22,35:57:99:1370,0,1134:8,14,12,23 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 0/1:37,39:76:99:957,0,874:21,16,22,17 chr1 86515958 . C T 598.93 PASS AC=1;AF=0.545;AN=2;DP=358;MQ=60;set=variant3-variant4-variant6-variant16-variant19-variant21-variant23-variant24-variant25-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:487,0,452:4,12,4,13 chr1 86557967 . G A 646.44 PASS AC=1;AF=0.618;AN=2;DP=1402;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,20:45:99:397,0,579:13,12,10,10 chr1 86578449 . A C 320.88 PASS AC=1;AF=0.5;AN=2;DP=228;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant11-variant12-variant17-variant23-variant28-variant32-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:309,0,670:0,9,3,5 chr1 86578453 . C T 286.26 PASS AC=1;AF=0.5;AN=2;DP=207;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant11-variant12-variant17-variant23-variant28-variant32-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:312,0,638:0,8,3,5 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 1/1:0,89:89:99:2936,267,0:0,0,39,50 chr1 86590948 . A G 1172.71 PASS AC=1;AF=0.5;AN=2;DP=1248;MQ=60;set=variant3-variant5-variant6-variant7-variant11-variant12-variant17-variant23-variant32-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,43:89:99:1179,0,1267:21,25,21,22 chr1 86591837 . G A 3808.89 PASS AC=1;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 0/1:63,66:129:99:1723,0,1608:30,33,32,34 chr1 86621992 . C A 605.87 PASS AC=1;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 0/1:23,31:54:99:729,0,635:17,6,20,11 chr1 86814688 . C T 958.65 PASS AC=1;AF=0.6;AN=2;DP=1245;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:23,8:31:99:186,0,670:14,9,3,5 chr1 86814743 . C T 1900.13 PASS AC=1;AF=0.603;AN=2;DP=2194;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:41,19:60:99:465,0,997:23,18,12,7 chr1 86814920 . CA C 1774.73 PASS AC=1;AF=0.6;AN=2;DP=1658;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:21,31:52:99:901,0,548:8,13,16,15 chr1 86815022 . C G 1896.89 PASS AC=1;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 0/1:19,46:65:99:1139,0,390:11,8,25,21 chr1 86815303 . T C 1792.28 PASS AC=1;AF=0.5;AN=2;DP=1438;MQ=60;set=variant5-variant13-variant14-variant15-variant16-variant20-variant23-variant25-variant28-variant32-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:55,60:115:99:1563,0,1367:32,23,40,20 chr1 86815319 . A G 3329.52 PASS AC=1;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 0/1:67,69:136:99:1639,0,1696:39,28,40,29 chr1 86818572 . T C 3385.97 PASS AC=1;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 0/1:48,40:88:99:835,0,1205:22,26,19,21 chr1 86820267 . C T 3625.46 PASS AC=1;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 0/1:43,52:95:99:1247,0,1087:25,18,28,24 chr1 86821194 . A ACT 358.01 PASS AC=1;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 0/1:9,5:14:99:183,0,367:0,9,0,5 chr1 86821746 . A G 522.42 PASS AC=1;AF=0.5;AN=2;DP=191;MQ=60;set=variant12-variant22-variant23-variant24 GT:AD:DP:GQ:PL:SB 0/1:24,15:39:99:315,0,548:11,13,9,6 chr1 86838158 . C T 735.25 PASS AC=1;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 0/1:20,19:39:99:434,0,471:11,9,10,9 chr1 86847955 . G A 906.07 PASS AC=1;AF=0.617;AN=2;DP=1085;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:24,20:44:99:421,0,569:14,10,12,8 chr1 86852053 . A AT 572.41 PASS AC=1;AF=0.625;AN=2;DP=627;MQ=60;set=variant2-variant4-variant8-variant9-variant11-variant12-variant13-variant14-variant21-variant22-variant23-variant24-variant26-variant28-variant30-variant32-variant34-variant36-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,17:32:99:397,0,347:2,13,1,16 chr1 86890931 . T A 241.77 PASS AC=1;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 0/1:4,2:6:72:72,0,165:4,0,2,0 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 0/1:9,9:18:99:189,0,190:5,4,5,4 chr1 86894371 . G T 1946.26 PASS AC=1;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 0/1:24,29:53:99:773,0,651:10,14,7,22 chr1 86894496 . T C 196.93 PASS AC=1;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 0/1:5,3:8:99:105,0,123:2,3,0,3 chr1 86896354 . G A 737.82 PASS AC=1;AF=0.852;AN=2;DP=690;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:254,0,190:5,1,6,2 chr1 86896706 . C A 481.91 PASS AC=1;AF=0.619;AN=2;DP=461;FractionInformativeReads=1;set=variant2-variant4-variant8-variant9-variant11-variant12-variant13-variant14-variant21-variant22-variant23-variant24-variant26-variant28-variant30-variant32-variant34-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:179,0,274:0,7,2,5 chr1 86897970 . T A 556.77 PASS AC=1;AF=0.619;AN=2;DP=279;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant8-variant9-variant11-variant12-variant13-variant14-variant21-variant22-variant23-variant24-variant26-variant28-variant30-variant32-variant34-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:99:108,0,340:4,2,3,0 chr1 86897973 . T C 945.01 PASS AC=1;AF=0.852;AN=2;DP=659;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:6,3:9:99:108,0,340:4,2,3,0 chr1 86900332 . T C 6692.84 PASS AC=1;AF=0.619;AN=2;DP=5050;MQ=60;set=variant2-variant4-variant8-variant9-variant11-variant12-variant13-variant14-variant21-variant22-variant23-variant24-variant26-variant28-variant30-variant32-variant34-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:131,114:245:99:2462,0,3209:61,70,60,54 chr1 86900372 . C G 5977.55 PASS AC=1;AF=0.619;AN=2;DP=4355;MQ=60;set=variant2-variant4-variant8-variant9-variant11-variant12-variant13-variant14-variant21-variant22-variant23-variant24-variant26-variant28-variant30-variant32-variant34-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:107,106:213:99:2504,0,2622:47,60,46,60 chr1 86900491 . C T 1578.51 PASS AC=1;AF=0.619;AN=2;DP=974;set=variant2-variant4-variant8-variant9-variant11-variant12-variant13-variant14-variant21-variant22-variant23-variant24-variant26-variant28-variant30-variant32-variant34-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,15:36:99:430,0,686:3,18,3,12 chr1 86904993 . T A 49.74 PASS AC=1;AF=0.575;AN=2;DP=251;FractionInformativeReads=1;MQ=60;set=variant2-variant8-variant9-variant11-variant12-variant13-variant14-variant21-variant22-variant23-variant24-variant26-variant28-variant30-variant32-variant34-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,8:11:63:251,0,63:2,1,1,7 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 0/1:7,3:10:64:64,0,202:2,5,1,2 chr1 86909703 . T C 339.51 PASS AC=1;AF=0.595;AN=2;DP=459;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant8-variant9-variant11-variant12-variant13-variant21-variant22-variant23-variant24-variant26-variant28-variant30-variant32-variant34-variant36-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,4:14:99:138,0,334:2,8,0,4 chr1 86911543 . C T 591.98 PASS AC=1;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 0/1:5,2:7:61:61,0,197:0,5,0,2 chr1 86934176 . T G 6450.4 PASS AC=2;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 1/1:1,166:167:99:5400,455,0:0,1,72,94 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 1/1:0,77:77:99:2229,230,0:0,0,39,38 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 1/1:0,64:64:99:2173,192,0:0,0,45,19 chr1 86952324 . A G 694.29 PASS AC=1;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 0/1:28,41:69:99:986,0,621:13,15,18,23 chr1 86954591 . T C 671.81 PASS AC=1;AF=0.58;AN=2;DP=1483;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant11-variant16-variant19-variant21-variant22-variant23-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,17:37:99:501,0,586:15,5,12,5 chr1 86956772 . G A 88.71 PASS AC=1;AF=0.629;AN=2;DP=332;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant15-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:98:98,0,119:2,1,3,0 chr1 86956785 . C G 160.46 PASS AC=1;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 0/1:7,5:12:99:144,0,224:5,2,4,1 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 0/1:44,47:91:99:1164,0,1037:27,17,27,20 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 0/1:14,23:37:99:703,0,362:10,4,17,6 chr1 87025819 . T C 926.62 PASS AC=1;AF=0.5;AN=2;DP=830;MQ=60;set=variant4-variant5-variant9-variant10-variant14-variant17-variant19-variant20-variant23-variant26-variant29-variant30-variant33-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:31,26:57:99:738,0,864:19,12,18,8 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 1/1:0,158:158:99:4573,471,0:0,0,93,65 chr1 87036946 . C T 1062.69 PASS AC=1;AF=0.5;AN=2;DP=970;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant9-variant10-variant14-variant17-variant19-variant20-variant23-variant26-variant29-variant30-variant33-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:32,28:60:99:712,0,868:9,23,11,17 chr1 87038240 . T C 46.75 PASS AC=1;AF=0.65;AN=2;DP=48;FS=0;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant9-variant10-variant20-variant23-variant26-variant29-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:37:81,0,37:1,0,2,0 chr1 87045896 . TCCTACA T 3702.44 PASS AC=2;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 1/1:0,152:152:99:6418,457,0:0,0,80,72 chr1 87101245 . A G 467.54 PASS AC=1;AF=0.717;AN=2;DP=1367;MQ=60;set=variant-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:29,22:51:99:504,0,736:17,12,14,8 chr1 87101375 . C G 893.64 PASS AC=1;AF=0.717;AN=2;DP=3171;MQ=60;set=variant-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:47,48:95:99:1084,0,1033:21,26,22,26 chr1 87101649 . T C 525.19 PASS AC=1;AF=0.5;AN=2;DP=398;MQ=60;set=variant4-variant5-variant9-variant10-variant19-variant23-variant26-variant29-variant30-variant33-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:15,22:37:99:587,0,395:12,3,14,8 chr1 87200729 . C G 4877.75 PASS AC=1;AF=0.679;AN=2;DP=4195;MQ=60;set=variant3-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant29-variant30-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:85,56:141:99:1307,0,2174:47,38,32,24 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 1/1:0,79:79:99:2380,237,0:0,0,46,33 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 1/1:0,90:90:99:4075,274,0:0,0,47,43 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 1/1:0,105:105:99:4449,316,0:0,0,54,51 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 1/1:0,23:23:69:748,69,0:0,0,15,8 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 1/1:0,6:6:18:270,18,0:0,0,6,0 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 1/1:0,133:133:99:4495,398,0:0,0,72,61 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 1/1:2,90:92:99:2613,235,0:0,2,66,24 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 1/1:0,52:52:99:1638,156,0:0,0,19,33 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 1/1:0,108:108:99:3458,323,0:0,0,46,62 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 1/1:0,160:160:99:4859,480,0:0,0,100,60 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 1/1:0,13:13:39:555,39,0:0,0,10,3 chr1 87573820 . T C 1885.25 PASS AC=1;AF=0.5;AN=2;DP=569;FractionInformativeReads=1;MQ=60;set=variant-variant18-variant19-variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:46,51:97:99:1244,0,1332:17,29,21,30 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 1/1:0,73:73:99:2080,218,0:0,0,38,35 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 1/1:0,70:70:99:1962,210,0:0,0,34,36 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 1/1:0,81:81:99:2761,243,0:0,0,58,23 chr1 87598117 . T G 5674.04 PASS AC=2;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 1/1:0,125:125:99:4167,374,0:0,0,75,50 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 1/1:0,102:102:99:3127,306,0:0,0,47,55 chr1 87633761 . C T 151.4 PASS AC=2;AF=0.886;AN=2;DP=1099;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:543,51,0:0,0,12,5 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 1/1:1,60:61:99:1935,172,0:0,1,41,19 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 1/1:0,58:58:99:1668,173,0:0,0,30,28 chr1 89236029 . T A 494.97 PASS AC=1;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 0/1:33,16:49:99:409,0,986:24,9,13,3 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 1/1:0,3:3:9:84,9,0:0,0,1,2 chr1 89271574 . T C 2228.04 PASS AC=1;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 0/1:44,46:90:99:1198,0,1362:29,15,30,16 chr1 89280965 . A G 652.41 PASS AC=1;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 0/1:24,21:45:99:561,0,608:16,8,13,8 chr1 89298290 . ATTG ATTGTTG,A 690.12 PASS AC=0,1;AF=0.375,0.188;AN=2;DP=265;set=variant10-variant11-variant13-variant23-variant27-variant32-variant34-variant37 GT:DP:GQ:SB 0/2:28:99:10,6,8,4 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 1/1:0,169:169:99:5277,507,0:0,0,57,112 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 1/1:0,120:120:99:3647,359,0:0,0,58,62 chr1 89401613 . T G 3642.05 PASS AC=1;AF=0.5;AN=2;DP=2494;MQ=60;set=variant4-variant8-variant13-variant20-variant22-variant23-variant32-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:112,142:254:99:3816,0,2800:60,52,78,64 chr1 89426902 . G A 3248.64 PASS AC=1;AF=0.645;AN=2;DP=3693;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant31-variant32-variant34-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,61:100:99:1443,0,990:23,16,35,26 chr1 89430420 . A G 1399.15 PASS AC=1;AF=0.645;AN=2;DP=1563;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant31-variant32-variant34-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,26:45:99:716,0,411:11,8,17,9 chr1 89445551 . A G 2436 PASS AC=1;AF=0.5;AN=2;DP=816;FractionInformativeReads=1;MQ=60;set=variant4-variant8-variant20-variant22-variant23-variant32-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:40,50:90:99:1507,0,1215:19,21,29,21 chr1 89446508 . C G 4710.86 PASS AC=1;AF=0.5;AN=2;DP=3348;FractionInformativeReads=1;MQ=60;set=variant4-variant8-variant10-variant13-variant20-variant22-variant23-variant32-variant34-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:133,124:257:99:2681,0,3200:78,55,70,54 chr1 89449278 . C T 104.07 PASS AC=1;AF=0.5;AN=2;DP=1910;set=filterInvariant-variant2-variant3-variant4-variant5-variant9-filterInvariant11-variant15-variant16-variant18-variant20-filterInvariant21-variant22-variant23-variant26-variant28-variant29-filterInvariant32-variant34-variant37-filterInvariant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,16:73:99:218,0,1612:26,31,9,7 chr1 89449298 . C G 168 PASS AC=1;AF=0.5;AN=2;DP=2538;set=filterInvariant-variant2-variant3-variant4-variant5-filterInvariant7-filterInvariant8-variant9-variant11-filterInvariant12-variant15-variant16-variant18-filterInvariant19-variant20-variant21-variant22-variant23-filterInvariant24-variant26-variant28-variant29-variant32-variant34-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,22:79:99:348,0,1543:27,30,12,10 chr1 89449390 . T C 734.59 PASS AC=1;AF=0.5;AN=2;DP=3980;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,29:104:99:911,0,3429:38,37,13,16 chr1 89449399 . T C 746.58 PASS AC=1;AF=0.5;AN=2;DP=3913;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,25:100:99:812,0,3557:41,34,10,15 chr1 89458313 . G A 250.37 PASS AC=1;AF=0.5;AN=2;DP=200;FractionInformativeReads=1;MQ=60;set=variant18-variant23-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,47:88:99:1134,0,952:24,17,24,23 chr1 89473175 . T C 1983.13 PASS AC=2;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 1/1:0,147:147:99:4531,440,0:0,0,79,68 chr1 89473624 . G A 976.02 PASS AC=1;AF=0.594;AN=2;DP=542;MQ=60;set=variant-variant2-variant12-variant14-variant16-variant17-variant18-variant20-variant23-variant24-variant31-variant33-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,12:27:99:375,0,465:3,12,2,10 chr1 89474818 . A G 1222.41 PASS AC=2;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 1/1:0,54:54:99:1580,162,0:0,0,24,30 chr1 89475135 . C T 996.18 PASS AC=2;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 1/1:0,63:63:99:1858,189,0:0,0,37,26 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 1/1:0,20:20:60:694,60,0:0,0,15,5 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 1/1:0,111:111:99:3147,331,0:0,0,64,47 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 1/1:0,68:68:99:2413,204,0:0,0,50,18 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 1/1:0,5:5:15:225,15,0:0,0,5,0 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 1/1:0,141:141:99:4304,422,0:0,0,87,54 chr1 89518120 . A G 1893.05 PASS AC=2;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 1/1:0,161:161:99:4794,482,0:0,0,83,78 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 1/1:0,119:119:99:4815,360,0:0,0,50,69 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 1/1:0,105:105:99:4627,330,0:0,0,35,70 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 1/1:0,64:64:99:2051,191,0:0,0,21,43 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 1/1:0,33:33:99:1427,99,0:0,0,8,25 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 1/1:0,30:30:90:1328,90,0:0,0,7,23 chr1 89520658 . C T 197.34 PASS AC=2;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 1/1:0,25:25:75:872,75,0:0,0,6,19 chr1 89521841 . G C 2436.69 PASS AC=2;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 1/1:1,179:180:99:5463,528,0:1,0,67,112 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 1/1:0,192:192:99:6012,574,0:0,0,96,96 chr1 89523927 . C T 345.93 PASS AC=2;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 1/1:0,34:34:99:889,101,0:0,0,15,19 chr1 89525219 . CTT CT,CTTT,C 149.51 PASS AC=1,0,0;AF=0.438,0.031,0.063;AN=2;DP=1211;MQ=60;set=variant-filterInvariant3-variant4-variant5-variant6-filterInvariant7-variant8-variant10-filterInvariant11-variant12-filterInvariant13-filterInvariant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant32-filterInvariant33-variant34-variant36-filterInvariant40-variant42-filterInvariant43 GT:DP:GQ:SB 0/1:16:99:1,8,1,6 chr1 89525812 . C G 661.21 PASS AC=2;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 1/1:0,30:30:93:1356,93,0:0,0,22,8 chr1 89525820 . C T 655.21 PASS AC=2;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 1/1:0,33:33:99:1424,99,0:0,0,21,12 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 0/1:58,53:111:99:1172,0,1312:32,26,30,23 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 0/1:9,16:25:99:546,0,288:1,8,4,12 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 0/1:35,34:69:99:818,0,849:16,19,15,19 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 0/1:59,34:93:99:1250,0,13029:30,29,15,19 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 0/1:59,34:93:99:1250,0,13029:30,29,15,19 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 0/1:58,33:91:99:1250,0,13256:31,27,14,19 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 0/1:58,31:89:99:1205,0,13521:30,28,13,18 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 0/1:58,30:88:99:1202,0,13617:30,28,13,17 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 0/1:58,29:87:99:1082,0,13483:29,29,13,16 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 0/1:54,30:84:99:1088,0,13165:27,27,14,16 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 0/1:55,29:84:99:1094,0,12877:27,28,14,15 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 0/1:56,27:83:99:965,0,12920:28,28,13,14 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 0/1:51,52:103:99:1343,0,1281:23,28,18,34 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 0/1:3,8:11:59:216,0,59:2,1,7,1 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 1/1:0,25:25:75:969,75,0:0,0,4,21 chr1 89730723 . C T 678.67 PASS AC=2;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 1/1:0,37:37:99:1269,111,0:0,0,10,27 chr1 89731959 . G A 531.94 PASS AC=2;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 1/1:0,22:22:66:791,66,0:0,0,17,5 chr1 89733273 . T C 543.95 PASS AC=2;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 1/1:0,31:31:93:1018,93,0:0,0,11,20 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 1/1:0,266:266:99:7927,799,0:0,0,145,121 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 1/1:0,54:54:99:1622,162,0:0,0,35,19 chr1 89847153 . G A 344.27 PASS AC=1;AF=0.567;AN=2;DP=704;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant15-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant29-variant33-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,12:41:99:350,0,893:17,12,11,1 chr1 89847372 . G T 1246.92 PASS AC=1;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 0/1:59,67:126:99:1708,0,1461:32,27,35,32 chr1 89847411 . C T 1318.78 PASS AC=1;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 0/1:53,64:117:99:1697,0,1261:26,27,35,29 chr1 89847444 . A G 1338.45 PASS AC=1;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 0/1:59,63:122:99:1608,0,1352:28,31,33,30 chr1 89848323 . T G 1163.08 PASS AC=1;AF=0.5;AN=2;DP=101;FS=0.753;FractionInformativeReads=0.99;MQ=60;MQRankSum=-0.949;QD=11.52;ReadPosRankSum=-1.226;SOR=0.606;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:55,45:100:99:1191,0,1390:22,33,19,26 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 1/1:0,96:96:99:2824,287,0:0,0,52,44 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 1/1:0,60:60:99:2052,180,0:0,0,30,30 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 1/1:0,85:85:99:2746,255,0:0,0,43,42 chr1 89849574 . G A 1294.23 PASS AC=2;AF=0.859;AN=2;DP=1854;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-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1455,128,0:0,0,16,27 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 1/1:0,54:54:99:1446,161,0:0,0,25,29 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 1/1:0,3:3:9:74,9,0:0,0,0,3 chr1 89885854 . G A 883.42 PASS AC=2;AF=0.92;AN=2;DP=2484;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1696,168,0:0,0,23,33 chr1 89888530 . C T 3329.3 PASS AC=2;AF=0.92;AN=2;DP=5591;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,105:105:99:3509,315,0:0,0,70,35 chr1 89888552 . T A 4753.13 PASS AC=2;AF=0.92;AN=2;DP=7437;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,143:143:99:4498,427,0:0,0,92,51 chr1 89888585 . C G 8758.22 PASS AC=2;AF=0.92;AN=2;DP=9590;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,206:206:99:9257,623,0:0,0,117,89 chr1 89888588 . G T 8709.61 PASS AC=2;AF=0.92;AN=2;DP=9715;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,210:210:99:9343,632,0:0,0,119,91 chr1 90048248 . C T 2333.56 PASS AC=1;AF=0.55;AN=2;DP=3814;set=variant-variant2-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant21-variant23-variant24-variant27-variant30-variant31-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,77:163:99:1764,0,2112:41,45,39,38 chr1 90058885 . G A 429.45 PASS AC=1;AF=0.556;AN=2;DP=302;FractionInformativeReads=1;set=variant-variant7-variant8-variant10-variant12-variant15-variant19-variant22-variant23-variant25-variant26-variant28-variant31-variant33-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,14:21:99:547,0,236:7,0,13,1 chr1 90058936 . CAA CA,C,CAAA 336.11 PASS AC=1,0,0;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 0/1:46:99:12,9,21,4 chr1 90059357 . A C 4320.69 PASS AC=1;AF=0.5;AN=2;DP=931;MQ=60;set=variant23-variant24 GT:AD:DP:GQ:PL:SB 0/1:194,178:372:99:4349,0,4909:96,98,93,85 chr1 90059575 . G T 2373.23 PASS AC=1;AF=0.694;AN=2;DP=5160;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant15-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,69:129:99:1937,0,1773:14,46,22,47 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 1/1:0,201:201:99:6551,602,0:0,0,80,121 chr1 90061014 . C T 2746.11 PASS AC=1;AF=0.55;AN=2;DP=3455;MQ=60;set=variant-variant7-variant8-variant10-variant12-variant15-variant19-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:96,99:195:99:2477,0,2175:42,54,49,50 chr1 90063180 . C G 6590.93 PASS AC=1;AF=0.55;AN=2;DP=11724;set=variant-variant7-variant8-variant10-variant12-variant15-variant19-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:284,243:527:99:5829,0,7246:161,123,134,109 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 1/1:0,74:74:99:2211,222,0:0,0,35,39 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 1/1:0,73:73:99:2397,218,0:0,0,46,27 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 1/1:0,74:74:99:2422,222,0:0,0,41,33 chr1 90185106 . C G 816.84 PASS AC=2;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 1/1:0,42:42:99:1669,126,0:0,0,5,37 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 1/1:0,525:525:99:23070,1584,0:0,0,241,284 chr1 90287642 . A C 186.16 PASS AC=1;AF=0.542;AN=2;DP=239;FractionInformativeReads=1;MQ=60;set=variant12-variant13-variant18-variant20-variant23-variant27-variant28-variant29-variant32-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:3,12:15:42:322,0,42:2,1,5,7 chr1 90309517 . G GGATA 280.59 PASS AC=1;AF=0.611;AN=2;DP=302;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant12-variant16-variant17-variant19-variant21-variant23-variant26-variant28-variant29-variant31-variant33 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:153,0,515:1,4,1,3 chr1 90402116 . T C 5267.42 PASS AC=1;AF=0.625;AN=2;DP=1612;FractionInformativeReads=1;MQ=60;set=variant2-variant13-variant17-variant21-variant23-variant27-variant29-variant40 GT:AD:DP:GQ:PL:SB 0/1:97,97:194:99:2203,0,2126:41,56,47,50 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 1/1:0,56:56:99:1672,166,0:0,0,30,26 chr1 90459900 . A T 446.27 PASS AC=1;AF=0.6;AN=2;DP=243;FractionInformativeReads=1;MQ=60;set=variant8-variant23-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,28:51:99:644,0,551:9,14,11,17 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 0/1:36,22:58:99:516,0,869:18,18,11,11 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 0/1:10,19:29:99:467,0,241:4,6,9,10 chr1 91447985 . C T 3650.43 PASS AC=1;AF=0.932;AN=2;DP=4190;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:39,47:86:99:1097,0,1039:13,26,20,27 chr1 91727781 . C G 755.11 PASS AC=1;AF=0.611;AN=2;DP=928;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant17-variant19-variant23-variant24-variant25-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,13:31:99:379,0,494:9,9,4,9 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 1/1:0,91:91:99:2730,273,0:0,0,43,48 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 1/1:0,18:18:54:636,54,0:0,0,4,14 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 1/1:0,23:23:69:718,69,0:0,0,16,7 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 1/1:0,25:25:75:821,75,0:0,0,8,17 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 1/1:0,71:71:99:2270,213,0:0,0,47,24 chr1 91742055 . T C 343.76 PASS AC=1;AF=0.658;AN=2;DP=302;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant17-variant19-variant23-variant24-variant25-variant30-variant32-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,12:14:49:376,0,49:2,0,9,3 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 1/1:0,21:21:63:748,63,0:0,0,16,5 chr1 91781413 . T G 945.9 PASS AC=1;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 0/1:28,30:58:99:756,0,687:16,12,14,16 chr1 91781644 . C G 548.06 PASS AC=1;AF=0.605;AN=2;DP=979;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant17-variant19-variant22-variant23-variant24-variant25-variant31-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,15:41:99:268,0,577:13,13,7,8 chr1 91782031 . T C 570.51 PASS AC=1;AF=0.605;AN=2;DP=896;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant17-variant19-variant22-variant23-variant24-variant25-variant31-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,24:44:99:509,0,531:6,14,10,14 chr1 91784887 . G A 925.99 PASS AC=1;AF=0.614;AN=2;DP=1485;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant17-variant19-variant22-variant23-variant24-variant25-variant30-variant31-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,22:59:99:513,0,866:17,20,13,9 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 1/1:0,27:27:81:823,81,0:0,0,9,18 chr1 91818302 . A G 326.77 PASS AC=1;AF=0.5;AN=2;DP=153;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant10-variant13-variant16-variant20-variant23-variant29-variant32-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,13:19:99:412,0,153:1,5,2,11 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 1/1:0,28:28:84:957,84,0:0,0,6,22 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 1/1:0,79:79:99:2488,237,0:0,0,33,46 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 1/1:0,8:8:24:282,24,0:0,0,2,6 chr1 91851193 . G A 1249.59 PASS AC=1;AF=0.5;AN=2;DP=1074;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant10-variant13-variant16-variant20-variant23-variant29-variant32-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,41:77:99:967,0,847:16,20,18,23 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 1/1:0,67:67:99:2119,201,0:0,0,33,34 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 1/1:1,181:182:99:6482,536,0:0,1,91,90 chr1 91859801 . A G 1645.35 PASS AC=1;AF=0.595;AN=2;DP=3142;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant17-variant19-variant22-variant23-variant24-variant25-variant31-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:103,76:179:99:1747,0,2536:50,53,37,39 chr1 91866856 . C G 133.67 PASS AC=1;AF=0.583;AN=2;DP=33;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant13-variant23-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:34:82,0,34:0,1,2,1 chr1 91870410 . G C 3112.18 PASS AC=1;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 0/1:73,84:157:99:2199,0,1753:37,36,45,39 chr1 91870626 . C T 387.46 PASS AC=1;AF=0.528;AN=2;DP=749;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant7-variant9-variant11-variant12-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant31-variant32-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,17:39:99:407,0,667:5,17,5,12 chr1 91966445 . A G 2000.83 PASS AC=1;AF=0.537;AN=2;DP=2374;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:47,38:85:99:952,0,1184:26,21,26,12 chr1 91967142 . G GC 833.75 PASS AC=1;AF=0.533;AN=2;DP=862;MQ=60;set=variant5-variant10-variant11-variant13-variant19-variant20-variant21-variant23-variant25-variant28-variant32-variant36-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,22:57:99:649,0,1099:23,12,17,5 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 1/1:0,58:58:99:1708,173,0:0,0,22,36 chr1 91989572 . T G 1373.56 PASS AC=2;AF=0.955;AN=2;DP=1530;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1342,105,0:0,0,31,4 chr1 91991268 . T A 2034.93 PASS AC=2;AF=0.943;AN=2;DP=3088;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2289,255,0:0,0,22,63 chr1 92108274 . T TA,TAA 1057.41 PASS AC=1,0;AF=0.524,0.024;AN=2;DP=1063;MQ=60;set=variant2-variant13-variant14-variant20-variant21-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:53:99:21,13,13,6 chr1 92108899 . C T 2668.59 PASS AC=1;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 0/1:114,115:229:99:2679,0,2744:59,55,54,61 chr1 92148013 . C T 1399.29 PASS AC=1;AF=0.5;AN=2;DP=1492;MQ=60;set=variant2-variant5-variant6-variant7-variant17-variant21-variant22-variant23-variant25-variant26-variant31-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,26:68:99:678,0,1197:18,24,13,13 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 1/1:0,94:94:99:3354,282,0:0,0,49,45 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 0/1:106,90:196:99:2262,0,2577:45,61,35,55 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 0/1:9,9:18:99:304,0,330:2,7,1,8 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 0/1:16,24:40:99:777,0,506:6,10,11,13 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 0/1:9,11:20:99:313,0,221:4,5,3,8 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 0/1:10,12:22:99:376,0,370:2,8,4,8 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 0/1:10,9:19:99:240,0,432:4,6,2,7 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 1/1:0,14:14:42:547,42,0:0,0,3,11 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 0/1:6,6:12:99:158,0,194:1,5,1,5 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 0/1:14,4:18:73:73,0,425:9,5,3,1 chr1 92251600 . C G 87.2 PASS AC=1;AF=0.6;AN=2;DP=28;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant23-variant34-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:77:117,0,77:2,1,3,0 chr1 92262874 . T C 205.52 PASS AC=2;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 1/1:0,51:51:99:1703,153,0:0,0,37,14 chr1 92414993 . T C 772.68 PASS AC=2;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 1/1:0,27:27:80:799,80,0:0,0,16,11 chr1 92415118 . C A 1727.51 PASS AC=2;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 1/1:0,80:80:99:2567,240,0:0,0,47,33 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 1/1:0,22:22:66:732,66,0:0,0,6,16 chr1 92430435 . CGTGT CGT,CGTGTGT,C 64.96 PASS AC=0,0,2;AF=0.708,0.042,0.125;AN=2;DP=90;FS=0;MQ=60;set=variant5-variant9-variant11-variant16-variant17-variant19-variant21-variant23-variant31-variant32-variant33-variant36 GT:DP:GQ:SB 3/3:3:9:0,0,1,2 chr1 92445257 . C G 1386.25 PASS AC=2;AF=0.579;AN=2;DP=1857;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant8-variant10-variant11-variant12-variant14-variant17-variant20-variant21-variant23-variant27-variant28-variant33-variant36-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,83:83:99:2524,249,0:0,0,38,45 chr1 92446112 . T C 436.35 PASS AC=2;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 1/1:0,12:12:36:459,36,0:0,0,10,2 chr1 92446398 . T A 3255.89 PASS AC=2;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 1/1:0,59:59:99:1778,177,0:0,0,35,24 chr1 92446961 . T TTGTA 586.36 PASS AC=2;AF=0.575;AN=2;DP=643;MQ=60;set=variant-variant2-variant8-variant10-variant11-variant12-variant14-variant17-variant20-variant21-variant23-variant27-variant28-variant33-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:50:723,50,0:0,0,6,11 chr1 92447004 . A G 669.12 PASS AC=2;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 1/1:0,11:11:33:373,33,0:0,0,5,6 chr1 92457843 . C T 1518.79 PASS AC=2;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 1/1:0,48:48:99:1356,143,0:0,0,29,19 chr1 92457969 . CAAA CAA,CA,C 250.7 PASS AC=1,0,0;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 0/1:30:47:3,4,14,9 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 1/1:0,83:83:99:2604,249,0:0,0,44,39 chr1 92649842 . G A 1253.47 PASS AC=1;AF=0.5;AN=2;DP=108;FS=1.549;FractionInformativeReads=1;MQ=60;MQRankSum=-0.548;QD=11.61;ReadPosRankSum=-0.646;SOR=0.582;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:57,51:108:99:1282,0,1381:26,31,26,25 chr1 92650329 . T C 889.18 PASS AC=1;AF=0.5;AN=2;DP=84;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.447;QD=10.59;ReadPosRankSum=-0.131;SOR=0.775;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:48,36:84:99:917,0,1324:17,31,12,24 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 1/1:0,41:41:99:1375,123,0:0,0,18,23 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 1/1:0,32:32:96:1065,96,0:0,0,7,25 chr1 92799151 . C T 892.82 PASS AC=2;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 1/1:0,14:14:42:568,42,0:0,0,0,14 chr1 92852504 . A G 1851.13 PASS AC=2;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 1/1:0,53:53:99:1671,158,0:0,0,34,19 chr1 92940481 . A T 746.86 PASS AC=1;AF=0.5;AN=2;DP=56;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.155;QD=13.34;ReadPosRankSum=2.27;SOR=0.567;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:28,28:56:99:775,0,782:16,12,15,13 chr1 92941357 . A G 1676.83 PASS AC=2;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 1/1:0,48:48:99:1622,144,0:0,0,24,24 chr1 92944314 . CAGAGAGAGAG CAGAGAGAGAGAGAGAG,CAGAG,CAGAGAGAGAGAGAGAGAGAG,CAGAGAGAG,CAGAGAGAGAGAGAG,C,CAGAGAG,CAGAGAGAGAGAG,CAGAGAGAGAGAGAGAGAGAGAG 433.03 PASS AC=1,0,0,0,0,0,0,1,0;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 8/1:16:99:0,0,0,16 chr1 92946479 . G A 2506.75 PASS AC=2;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 1/1:0,86:86:99:2594,256,0:0,0,50,36 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 1/1:0,30:30:90:1179,90,0:0,0,23,7 chr1 92974595 . G A 4722.73 PASS AC=2;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 1/1:0,134:134:99:4213,401,0:0,0,59,75 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 0/1:6,18:24:84:360,0,84:1,5,5,13 chr1 92975244 . T A 3311.87 PASS AC=2;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 1/1:0,54:54:99:1548,160,0:0,0,28,26 chr1 92975262 . C A 3391.2 PASS AC=2;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 1/1:0,59:59:99:1784,177,0:0,0,29,30 chr1 92975493 . A G 5741.01 PASS AC=2;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 1/1:0,146:146:99:4646,437,0:0,0,83,63 chr1 92975938 . T C 12963.7 PASS AC=2;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 1/1:0,335:335:99:10018,1003,0:0,0,166,169 chr1 92976023 . T G 13045.3 PASS AC=2;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 1/1:0,312:312:99:10020,933,0:0,0,146,166 chr1 92976590 . G A 1497.69 PASS AC=2;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 1/1:0,55:55:99:1784,165,0:0,0,34,21 chr1 92977275 . A G 1616.84 PASS AC=2;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 1/1:0,33:33:99:1221,99,0:0,0,27,6 chr1 92978722 . TA T 3169.12 PASS AC=2;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 1/1:0,87:87:99:2444,261,0:0,0,56,31 chr1 92979354 . A G 3584.46 PASS AC=2;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 1/1:0,118:118:99:3526,352,0:0,0,59,59 chr1 92979681 . TTA T 130.95 PASS AC=2;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 1/1:0,6:6:18:253,18,0:0,0,0,6 chr1 93029453 . A G 546.35 PASS AC=2;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 1/1:0,21:21:63:687,63,0:0,0,6,15 chr1 93029479 . A T 178.71 PASS AC=1;AF=0.6;AN=2;DP=31;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant10-variant15-variant23 GT:AD:DP:GQ:PL:SB 0/1:2,8:10:60:227,0,60:0,2,2,6 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 1/1:0,28:28:84:1072,84,0:0,0,5,23 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 1/1:0,60:60:99:1890,180,0:0,0,25,35 chr1 93128514 . TA TAA,TAAA,T 248.87 PASS AC=2,0,0;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 1/1:17:24:0,1,3,13 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 1/1:0,26:26:78:839,78,0:0,0,17,9 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 1/1:0,108:108:99:3241,323,0:0,0,45,63 chr1 93163385 . A G 2269.55 PASS AC=2;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 1/1:0,46:46:99:1488,137,0:0,0,30,16 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 1/1:0,6:6:18:258,18,0:0,0,1,5 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 1/1:0,5:5:15:225,15,0:0,0,4,1 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 1/1:0,32:32:96:976,96,0:0,0,11,21 chr1 93306317 . G A 1665.5 PASS AC=2;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 1/1:0,128:128:99:3831,384,0:0,0,67,61 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 1/1:0,277:277:99:8605,829,0:0,0,136,141 chr1 93308168 . T TA 2521.14 PASS AC=2;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 1/1:0,193:193:99:7203,584,0:0,0,82,111 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 1/1:0,62:62:99:2210,186,0:0,0,23,39 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 1/1:0,43:43:99:1450,128,0:0,0,13,30 chr1 93311065 . GAAAA GAA,GA,GAAA,G 132.86 PASS AC=0,1,0,0;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 0/2:12:9:2,2,6,2 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 1/1:0,100:100:99:4747,328,0:0,0,65,35 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 1/1:0,113:113:99:4854,340,0:0,0,73,40 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 1/1:1,101:102:99:3377,295,0:1,0,56,45 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 1/1:1,120:121:99:3522,317,0:1,0,71,49 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 1/1:0,74:74:99:2327,222,0:0,0,49,25 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 1/1:1,103:104:99:3155,301,0:1,0,64,39 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 0/1:7:21:2,0,4,1 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 1/1:0,95:95:99:2757,284,0:0,0,58,37 chr1 93602814 . A G 2034.59 PASS AC=1;AF=0.5;AN=2;DP=1437;MQ=60;set=variant-variant3-variant5-variant6-variant15-variant23-variant29-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:67,59:126:99:1480,0,1710:43,24,42,17 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 1/1:212:99:0,0,100,112 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 1/1:1,555:556:99:17489,1620,0:0,1,271,284 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 1/1:0,214:214:99:6521,641,0:0,0,99,115 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 1/1:1,186:187:99:5627,550,0:1,0,97,89 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 1/1:0,171:171:99:5458,512,0:0,0,57,114 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 1/1:0,20:20:60:691,60,0:0,0,15,5 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 1/1:0,267:267:99:7937,800,0:0,0,148,119 chr1 93646418 . C T 3003.28 PASS AC=1;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 0/1:176,144:320:99:3267,0,4136:77,99,70,74 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 1/1:0,45:45:99:1756,135,0:0,0,40,5 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 1/1:1,20:21:29:734,29,0:1,0,3,17 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 1/1:0,26:26:78:804,78,0:0,0,8,18 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 1/1:0,42:42:99:1433,126,0:0,0,30,12 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 1/1:0,23:23:68:771,68,0:0,0,19,4 chr1 93676478 . A C 674.16 PASS AC=1;AF=0.5;AN=2;DP=75;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.055;QD=8.99;ReadPosRankSum=-0.691;SOR=0.706;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:43,32:75:99:702,0,1005:19,24,14,18 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 1/1:0,27:27:81:825,81,0:0,0,10,17 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 1/1:0,70:70:99:2042,210,0:0,0,32,38 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 1/1:0,123:123:99:3762,368,0:0,0,65,58 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 1/1:84:99:0,0,69,15 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 1/1:0,192:192:99:6384,576,0:0,0,65,127 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 1/1:29:24:0,3,13,13 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 1/1:0,65:65:99:2432,196,0:0,0,19,46 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 1/1:0,10:10:30:450,30,0:0,0,10,0 chr1 94037220 . A C 1157.9 PASS AC=1;AF=0.5;AN=2;DP=102;FS=0.743;FractionInformativeReads=1;MQ=60;MQRankSum=-1.031;QD=11.35;ReadPosRankSum=0.261;SOR=0.56;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:53,49:102:99:1186,0,1299:29,24,25,24 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 1/1:0,71:71:99:3068,213,0:0,0,18,53 chr1 94054382 . T C 376.29 PASS AC=1;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 0/1:22,16:38:99:356,0,570:14,8,6,10 chr1 94057720 . T A 223.42 PASS AC=1;AF=0.684;AN=2;DP=306;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant12-variant13-variant15-variant18-variant19-variant20-variant23-variant25-variant26-variant30-variant31-variant32-variant34-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:95:95,0,180:4,2,3,1 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 1/1:0,92:92:99:3420,277,0:0,0,55,37 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 1/1:0,78:78:99:3363,240,0:0,0,42,36 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 1/1:0,70:70:99:3172,214,0:0,0,34,36 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 1/1:0,58:58:99:2925,196,0:0,0,28,30 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 1/1:0,57:57:99:2655,178,0:0,0,27,30 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 1/1:0,51:51:99:2340,157,0:0,0,25,26 chr1 94312558 . G GC 952.73 PASS AC=1;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 0/1:30,17:47:99:630,0,1142:14,16,9,8 chr1 94312559 . CGGCTGGGTCGGGCG C 1337.73 PASS AC=1;AF=0.625;AN=2;DP=1908;MQ=60;set=variant2-variant3-variant6-variant7-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,30:48:99:1139,0,672:9,9,14,16 chr1 94312566 . G T 916.77 PASS AC=1;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 0/1:30,18:48:99:631,0,1141:14,16,9,9 chr1 94312567 . T C 916.77 PASS AC=1;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 0/1:30,17:47:99:631,0,1141:14,16,8,9 chr1 94312571 . G GC 952.73 PASS AC=1;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 0/1:30,17:47:99:624,0,1144:14,16,8,9 chr1 94312573 . G GC 907.73 PASS AC=1;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 0/1:30,17:47:99:666,0,1141:14,16,8,9 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 1/1:0,48:48:99:2205,147,0:0,0,22,26 chr1 94312579 . G GC,GT 817.73 PASS AC=1,1;AF=0.602,0.398;AN=2;DP=2357;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:DP:GQ:SB 2/1:47:99:0,0,22,25 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 1/1:0,48:48:99:2169,148,0:0,0,22,26 chr1 94333372 . G GTTTT,GTT 3243.07 PASS AC=1,0;AF=0.093,0.519;AN=2;DP=4701;set=variant2-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant32-variant34-variant36-variant37-variant39-variant40-variant42-variant44 GT:DP:GQ:SB 0/1:161:99:43,40,43,35 chr1 94333382 . A T 3794.42 PASS AC=1;AF=0.611;AN=2;DP=5155;set=variant2-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant32-variant34-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:88,88:176:99:3254,0,5976:47,41,48,40 chr1 94333546 . G C 683.7 PASS AC=1;AF=0.611;AN=2;DP=1821;set=variant2-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant32-variant34-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,20:45:99:560,0,819:4,21,5,15 chr1 94334537 . CTATTAT C 1315.42 PASS AC=1;AF=0.577;AN=2;DP=1254;set=variant2-variant3-variant4-variant6-variant7-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant32-variant34-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,14:29:99:284,0,942:10,5,9,5 chr1 94334766 . T TA 367.21 PASS AC=2;AF=0.775;AN=2;DP=2025;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-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1242,114,0:0,0,12,26 chr1 94334891 . A G 1129.72 PASS AC=1;AF=0.596;AN=2;DP=2726;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant32-variant34-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,56:99:99:1480,0,1084:26,17,37,19 chr1 94334954 . T C 1701.84 PASS AC=1;AF=0.596;AN=2;DP=4323;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant32-variant34-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,80:166:99:1911,0,1907:45,41,42,38 chr1 94335032 . A G 1772.2 PASS AC=1;AF=0.596;AN=2;DP=3751;set=variant2-variant3-variant4-variant6-variant7-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant32-variant34-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,63:133:99:1577,0,1738:28,42,22,41 chr1 94335194 . A T 1541.46 PASS AC=1;AF=0.611;AN=2;DP=3983;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant32-variant34-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,75:138:99:1680,0,1302:33,30,39,36 chr1 94335585 . G C 932.36 PASS AC=1;AF=0.5;AN=2;DP=771;MQ=60;set=variant2-variant9-variant16-variant21-variant23-variant34-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:44,47:91:99:1109,0,1092:23,21,24,23 chr1 94335643 . G GA 822.59 PASS AC=1;AF=0.596;AN=2;DP=2521;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant32-variant34-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,45:86:99:1139,0,1018:18,23,19,26 chr1 94337499 . G C 104.89 PASS AC=1;AF=0.5;AN=2;DP=103;FractionInformativeReads=1;MQ=60;set=variant2-variant21-variant23-variant34-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:226,0,313:8,1,6,1 chr1 94341137 . C T 96.2 PASS AC=1;AF=0.609;AN=2;DP=225;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant12-variant13-variant16-variant18-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant32-variant34-variant36-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:115,0,159:4,0,3,1 chr1 94341267 . A G 573.33 PASS AC=1;AF=0.611;AN=2;DP=1712;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant32-variant34-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,28:63:99:613,0,939:19,16,17,11 chr1 94343233 . T C 2428.49 PASS AC=2;AF=0.776;AN=2;DP=5899;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-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,151:151:99:4598,452,0:0,0,77,74 chr1 94344580 . C A 1211.26 PASS AC=2;AF=0.548;AN=2;DP=4406;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,148:148:99:4954,442,0:0,0,113,35 chr1 94344840 . A C 1870.96 PASS AC=1;AF=0.542;AN=2;DP=3565;MQ=60;set=variant-variant4-variant6-variant8-variant9-variant10-variant13-variant15-variant17-variant19-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:75,64:139:99:1883,0,2228:16,59,10,54 chr1 94344860 . G T 1280.4 PASS AC=1;AF=0.5;AN=2;DP=547;FractionInformativeReads=1;MQ=60;set=variant2-variant21-variant23-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:47,51:98:99:1599,0,1430:7,40,7,44 chr1 94350733 . G T 51.2 PASS AC=2;AF=0.813;AN=2;DP=64;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant8-variant9-variant17-variant21-variant23-variant24-variant25-variant26-variant29-variant33-variant34-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,1,1 chr1 94351062 . TAA T 1918.38 PASS AC=1;AF=0.542;AN=2;DP=1563;set=variant-variant4-variant6-variant8-variant9-variant10-variant13-variant15-variant17-variant19-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,31:56:99:1199,0,989:18,7,22,9 chr1 94351321 . T G 7450.21 PASS AC=1;AF=0.5;AN=2;DP=2187;set=variant2-variant21-variant23-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:199,195:394:99:4777,0,4996:103,96,91,104 chr1 94351328 . C T 5648.77 PASS AC=2;AF=0.569;AN=2;DP=12384;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant13-variant15-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,393:393:99:14770,1188,0:0,0,191,202 chr1 94351768 . CT CTT,C,CTTT 3340.2 PASS AC=1,1,0;AF=0.483,0.069,0.017;AN=2;DP=9800;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant13-variant15-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42 GT:DP:GQ:SB 2/1:286:99:2,1,129,154 chr1 94352237 . G GT 2103.37 PASS AC=2;AF=0.578;AN=2;DP=7699;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,169:169:99:4760,507,0:0,0,81,88 chr1 94352381 . C T 672.47 PASS AC=1;AF=0.5;AN=2;DP=297;FractionInformativeReads=1;MQ=60;set=variant2-variant21-variant23-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:26,29:55:99:726,0,711:7,19,9,20 chr1 94353029 . G GT,GTT 276.29 PASS AC=2,0;AF=0.577,0.051;AN=2;DP=2677;set=variant-variant2-variant3-variant4-filterInvariant5-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-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 1/1:41:30:1,3,13,24 chr1 94353449 . G T 1763.29 PASS AC=2;AF=0.569;AN=2;DP=4596;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant13-variant15-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,104:104:99:3370,310,0:0,0,60,44 chr1 94353573 . C T 4647.45 PASS AC=2;AF=0.569;AN=2;DP=12112;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant13-variant15-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,371:371:99:10780,1110,0:0,0,208,163 chr1 94360107 . C A 397.4 PASS AC=1;AF=0.542;AN=2;DP=935;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant8-variant9-variant10-variant13-variant15-variant17-variant19-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,20:33:99:600,0,320:8,5,16,4 chr1 94367097 . G A 644.78 PASS AC=2;AF=0.571;AN=2;DP=1089;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant13-variant15-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1064,108,0:0,0,22,14 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 1/1:0,132:132:99:4135,396,0:0,0,63,69 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 1/1:0,20:20:60:747,60,0:0,0,6,14 chr1 94487285 . AAC A 978.4 PASS AC=1;AF=0.5;AN=2;DP=1061;MQ=60;set=variant5-variant7-variant10-variant11-variant16-variant17-variant18-variant19-variant23-variant31-variant32-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,26:53:99:1006,0,1045:18,9,15,11 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 0/1:47,54:101:99:1267,0,1313:27,20,30,24 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 0/1:21,37:58:99:1439,0,821:8,13,16,21 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 0/1:21,35:56:99:1396,0,827:8,13,14,21 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 0/1:6,16:22:99:433,0,207:0,6,6,10 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 1/1:0,35:35:99:1120,104,0:0,0,25,10 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 0/1:22,36:58:99:1061,0,674:3,19,9,27 chr1 94497178 . G A 482.4 PASS AC=2;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 1/1:0,53:53:99:1564,159,0:0,0,32,21 chr1 94509226 . G T 267.15 PASS AC=2;AF=0.595;AN=2;DP=336;MQ=60;set=variant-variant7-variant10-variant14-variant16-variant17-variant22-variant23-variant29-variant31-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:504,39,0:0,0,2,11 chr1 94528363 . C T 268.06 PASS AC=2;AF=0.575;AN=2;DP=1190;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant10-variant11-variant15-variant16-variant23-variant27-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2064,195,0:0,0,24,41 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 1/1:0,11:11:36:351,36,0:0,0,2,9 chr1 94544233 . G A 839.22 PASS AC=1;AF=0.5;AN=2;DP=518;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant13-variant23-variant29-variant32-variant34 GT:AD:DP:GQ:PL:SB 0/1:37,29:66:99:674,0,1511:18,19,12,17 chr1 94544234 . T C 1390.66 PASS AC=1;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 0/1:29,39:68:99:1064,0,1090:12,17,19,20 chr1 94544276 . G A 709.48 PASS AC=1;AF=0.654;AN=2;DP=2299;MQ=60;set=variant-variant2-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,30:73:99:664,0,1009:20,23,13,17 chr1 94544326 . GT G 615.63 PASS AC=1;AF=0.654;AN=2;DP=1588;MQ=60;set=variant-variant2-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant20-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,23:50:99:711,0,829:9,18,9,14 chr1 94544805 . T TCA 343.19 PASS AC=1;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 0/1:11,8:19:99:239,0,297:8,3,7,1 chr1 94545160 . C T 431.31 PASS AC=1;AF=0.568;AN=2;DP=909;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant11-variant12-variant13-variant14-variant15-variant18-variant23-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,31:58:99:823,0,710:14,13,12,19 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 0/1:28,49:77:99:1309,0,614:11,17,18,31 chr1 94549083 . T C 507.26 PASS AC=2;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 1/1:0,39:39:99:1246,116,0:0,0,16,23 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 0/1:18,17:35:99:461,0,541:15,3,12,5 chr1 94568822 . T C 412.67 PASS AC=1;AF=0.607;AN=2;DP=2295;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant11-variant13-variant15-variant16-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:38,38:76:99:1067,0,995:12,26,11,27 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 0/1:21,14:35:99:323,0,595:12,9,10,4 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 0/1:16,25:41:99:640,0,374:10,6,17,8 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 1/1:0,49:49:99:1541,147,0:0,0,30,19 chr1 94638168 . GAT GATAT,GATATAT,GATATATAT,G,GATATATATAT 444.91 PASS AC=1,0,0,0,0;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 0/1:15:56:1,2,3,9 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 0/1:104,115:219:99:2850,0,2826:46,58,55,60 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 0/1:24,15:39:99:457,0,699:12,12,8,7 chr1 94639337 . A G 8972.4 PASS AC=2;AF=0.989;AN=2;DP=11704;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,197:197:99:6126,591,0:0,0,86,111 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 1/1:0,158:158:99:5000,472,0:0,0,75,83 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 1/1:0,11:11:33:314,33,0:0,0,2,9 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 0/1:59,60:119:99:1698,0,1490:29,30,26,34 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 1/1:0,101:101:99:3163,302,0:0,0,46,55 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 0/1:26,10:36:99:281,0,678:9,17,2,8 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 1/1:0,48:48:99:1770,144,0:0,0,31,17 chr1 94674726 . T C 570.55 PASS AC=1;AF=0.55;AN=2;DP=1042;FractionInformativeReads=1;MQ=60;set=variant4-variant12-variant14-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant32-variant33-variant36-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,21:52:99:491,0,746:19,12,13,8 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 0/1:78:99:41,26,6,5 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 0/1:8,12:20:99:413,0,213:6,2,11,1 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 0/1:63,58:121:99:1369,0,1410:33,30,28,30 chr1 94941376 . G A 241.6 PASS AC=1;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 0/1:1,11:12:10:395,0,10:0,1,1,10 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 1/1:0,70:70:99:1951,208,0:0,0,38,32 chr1 94982785 . A T 786.39 PASS AC=1;AF=0.6;AN=2;DP=580;MQ=60;set=variant-variant4-variant7-variant15-variant19-variant22-variant23-variant27-variant30-variant32-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:8,12:20:99:379,0,262:2,6,7,5 chr1 94983203 . C T 3313.7 PASS AC=1;AF=0.611;AN=2;DP=3626;MQ=60;set=variant-variant4-variant7-variant10-variant15-variant19-variant22-variant23-variant27-variant30-variant32-variant33-variant34-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:94,82:176:99:1963,0,2357:47,47,40,42 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 0/1:93:99:13,18,20,42 chr1 94995411 . C A 1207.81 PASS AC=1;AF=0.575;AN=2;DP=1546;set=variant-variant4-variant7-variant15-variant18-variant19-variant22-variant23-variant27-variant28-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,39:64:99:1291,0,641:6,19,5,34 chr1 94995629 . CAAAAA CAA,CA,CAAA,C 1218.1 PASS AC=1,1,0,0;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 2/1:40:99:0,1,37,2 chr1 94995713 . C T 3431.72 PASS AC=1;AF=0.5;AN=2;DP=651;MQ=60;set=variant23-variant32 GT:AD:DP:GQ:PL:SB 0/1:167,136:303:99:3460,0,4211:102,65,83,53 chr1 94995819 . C T 6410.1 PASS AC=1;AF=0.579;AN=2;DP=8911;MQ=60;set=variant-variant4-variant7-variant15-variant18-variant19-variant22-variant23-variant27-variant28-variant30-variant31-variant32-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:214,222:436:99:5433,0,5328:98,116,115,107 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 1/1:0,106:106:99:3206,318,0:0,0,53,53 chr1 95285897 . C CCCCAGA 638.77 PASS AC=2;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 1/1:0,14:14:42:572,42,0:0,0,5,9 chr1 95286085 . G A 2098.89 PASS AC=2;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 1/1:0,106:106:99:4705,328,0:0,0,57,49 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 1/1:0,114:114:99:4856,343,0:0,0,61,53 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 1/1:0,14:14:42:616,42,0:0,0,2,12 chr1 95290315 . A G 170.27 PASS AC=2;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 1/1:0,13:13:39:574,39,0:0,0,2,11 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 1/1:0,72:72:99:2179,216,0:0,0,43,29 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 0/1:58,37:95:99:850,0,1463:29,29,19,18 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 1/1:0,135:135:99:4194,405,0:0,0,77,58 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 0/1:42,56:98:99:1305,0,980:23,19,32,24 chr1 95332864 . C T 721.36 PASS AC=2;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 1/1:0,51:51:99:1460,153,0:0,0,29,22 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 1/1:0,46:46:99:1454,137,0:0,0,18,28 chr1 95360825 . A AT 2117.54 PASS AC=2;AF=0.989;AN=2;DP=4137;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,60:61:99:1558,154,0:0,1,17,43 chr1 95362927 . TAAAAA T,TA,TAAAAAA,TAAA,TAAAA,TAA 3416.45 PASS AC=0,0,0,1,0,0;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 0/4:76:99:19,17,18,22 chr1 95363663 . A C 563.68 PASS AC=1;AF=0.5;AN=2;DP=246;FractionInformativeReads=1;MQ=60;set=variant10-variant16-variant19-variant23-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,28:46:99:750,0,500:5,13,8,20 chr1 95367108 . ACC A,AC 353.37 PASS AC=0,1;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 0/2:13:99:4,1,7,1 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 1/1:0,17:17:51:615,51,0:0,0,11,6 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 0/1:16,19:35:99:446,0,330:6,10,8,11 chr1 95368574 . TA TAA,TAAA,T 151.39 PASS AC=0,1,0;AF=0.182,0.409,0.023;AN=2;DP=910;MQ=60;set=variant2-variant4-variant13-variant14-filterInvariant16-variant18-variant19-filterInvariant20-variant23-filterInvariant25-variant26-variant28-variant32-variant33-variant34-filterInvariant36-variant37-variant38-variant39-variant41-filterInvariant43-variant44 GT:DP:GQ:SB 0/2:24:99:9,5,9,1 chr1 95369211 . T G 2421.36 PASS AC=2;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 1/1:0,61:61:99:1899,183,0:0,0,22,39 chr1 95392588 . C T 1362.54 PASS AC=1;AF=0.577;AN=2;DP=955;MQ=60;set=variant4-variant13-variant14-variant19-variant23-variant26-variant33-variant34-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:51,33:84:99:861,0,1468:17,34,11,22 chr1 95427041 . ATT AT,A 82.87 PASS AC=1,1;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 2/1:17:99:0,0,4,13 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 0/1:12,15:27:99:502,0,370:11,1,12,3 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 0/2:46:99:21,5,14,6 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 0/1:11,14:25:99:329,0,290:3,8,6,8 chr1 95530709 . G A 157.17 PASS AC=1;AF=0.529;AN=2;DP=364;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant10-variant11-variant12-variant16-variant17-variant19-variant22-variant23-variant27-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:7,10:17:99:237,0,218:1,6,4,6 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 1/1:0,39:39:99:1202,117,0:0,0,23,16 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 1/1:0,8:8:24:319,24,0:0,0,6,2 chr1 95615748 . CT CTT,C,CTTTT 239.41 PASS AC=1,0,0;AF=0.385,0.077,0.038;AN=2;DP=466;set=variant5-variant8-variant10-variant11-variant16-variant18-variant19-variant23-variant34-variant36-variant37-variant39-variant42 GT:DP:GQ:SB 0/1:16:99:4,5,5,2 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 1/1:0,122:122:99:3886,367,0:0,0,43,79 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 0/1:157,151:308:99:3726,0,3993:90,67,94,57 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 0/1:96,111:207:99:2765,0,2518:28,68,40,71 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 0/1:51,44:95:99:1483,0,1771:18,33,14,30 chr1 95696612 . C T 719.18 PASS AC=1;AF=0.619;AN=2;DP=1427;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant11-variant15-variant16-variant19-variant20-variant23-variant27-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:31,27:58:99:735,0,862:10,21,6,21 chr1 95699594 . A G 106.77 PASS AC=2;AF=0.898;AN=2;DP=894;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:599,42,0:0,0,9,5 chr1 95699604 . G C 106.77 PASS AC=2;AF=0.909;AN=2;DP=974;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:633,45,0:0,0,9,6 chr1 95700044 . G C 115.68 PASS AC=1;AF=0.594;AN=2;DP=287;MQ=60;set=variant-variant5-variant8-variant11-variant15-variant16-variant19-variant23-variant27-variant31-variant33-variant36-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:141,0,311:1,8,2,4 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 1/1:0,38:38:99:1260,114,0:0,0,12,26 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 1/1:0,158:158:99:4770,474,0:0,0,85,73 chr1 95709939 . T G 4372.54 PASS AC=2;AF=0.909;AN=2;DP=5318;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3554,303,0:0,0,39,62 chr1 95712797 . G A 514.8 PASS AC=2;AF=0.898;AN=2;DP=740;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:516,42,0:0,0,2,12 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 1/1:0,5:5:15:214,15,0:0,0,4,1 chr1 96457579 . T C 1625.38 PASS AC=1;AF=0.606;AN=2;DP=2021;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,16:41:99:465,0,784:20,5,13,3 chr1 96488081 . T C 2790.31 PASS AC=1;AF=0.614;AN=2;DP=3135;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,49:103:99:1397,0,1424:38,16,33,16 chr1 96488261 . A T 8830.38 PASS AC=1;AF=0.943;AN=2;DP=10501;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:141,117:258:99:3001,0,3605:69,72,62,55 chr1 96488272 . C A 8693.69 PASS AC=1;AF=0.614;AN=2;DP=8546;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:143,120:263:99:3014,0,3727:71,72,62,58 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 1/1:2,264:266:99:8348,748,0:1,1,130,134 chr1 96912659 . A G 759.43 PASS AC=1;AF=0.571;AN=2;DP=488;FractionInformativeReads=1;set=variant12-variant17-variant23-variant25-variant27-variant28-variant31 GT:AD:DP:GQ:PL:SB 0/1:26,32:58:99:887,0,633:15,11,15,17 chr1 97189091 . G A 1821.83 PASS AC=1;AF=0.765;AN=2;DP=4769;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,55:116:99:1398,0,1509:30,31,31,24 chr1 97189288 . T A 117.12 PASS AC=1;AF=0.604;AN=2;DP=449;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant30-variant32-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,9:19:99:304,0,397:0,10,1,8 chr1 97235290 . A G 1014.05 PASS AC=1;AF=0.5;AN=2;DP=75;FS=0.9;FractionInformativeReads=1;MQ=60;MQRankSum=-1.073;QD=13.52;ReadPosRankSum=-1.617;SOR=0.547;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:33,42:75:99:1042,0,780:21,12,25,17 chr1 97236130 . G A 84.41 PASS AC=1;AF=0.848;AN=2;DP=136;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant10-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant31-variant32-variant36-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:73:162,0,73:2,0,4,0 chr1 97243023 . A G 233.14 PASS AC=1;AF=0.5;AN=2;DP=116;MQ=60;set=variant8-variant9-variant15-variant17-variant19-variant23-variant32 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:267,0,108:3,1,7,0 chr1 97278804 . G A 358.52 PASS AC=1;AF=0.765;AN=2;DP=1189;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,16:35:99:465,0,504:11,8,10,6 chr1 97279209 . T C 1135.57 PASS AC=1;AF=0.5;AN=2;DP=144;FS=0.648;FractionInformativeReads=0.986;MQ=59.68;MQRankSum=-3.116;QD=7.89;ReadPosRankSum=0.041;SOR=0.612;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:92,50:142:99:1164,0,3064:44,48,25,25 chr1 97279217 . CTTTTTTTTTTT CTTTTTTTTTT,CTTTTTT,C,CTTTTTTTTTTTT,CTTTTT,CTTTTTTTTTTTTTTTTTTTTT,CTTTT,CTTTTTTTTTTTTT,CTTTTTTTTT 163.08 PASS AC=0,1,0,0,0,0,0,0,0;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 0/2:121:99:27,32,29,33 chr1 97279692 . C T 7170.28 PASS AC=1;AF=0.765;AN=2;DP=19316;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:264,255:519:99:6315,0,6399:132,132,124,131 chr1 97280132 . A T 1266.14 PASS AC=1;AF=0.5;AN=2;DP=741;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant15-variant17-variant19-variant23-variant32 GT:AD:DP:GQ:PL:SB 0/1:59,57:116:99:1366,0,1596:26,33,26,31 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 0/1:150,132:282:99:3161,0,3659:87,63,74,58 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 1/1:0,34:34:99:1231,102,0:0,0,27,7 chr1 97700589 . C T 779.81 PASS AC=1;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 0/1:17,16:33:99:490,0,493:5,12,4,12 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 0/1:42,29:71:99:716,0,1088:12,30,9,20 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 1/1:0,267:267:99:7983,800,0:0,0,122,145 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 1/1:0,308:308:99:9543,922,0:0,0,178,130 chr1 98348885 . G A 2346.7 PASS AC=2;AF=0.875;AN=2;DP=3429;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,55:56:99:1503,157,0:1,0,26,29 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 1/1:34:99:0,0,15,19 chr1 99127205 . A G 247.45 PASS AC=2;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 1/1:0,18:18:54:578,54,0:0,0,9,9 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 1/1:0,92:92:99:2670,275,0:0,0,52,40 chr1 99150635 . G A 2324.93 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-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 1/1:0,71:71:99:2102,213,0:0,0,32,39 chr1 99156904 . T A 103.41 PASS AC=1;AF=0.6;AN=2;DP=26;FS=0;FractionInformativeReads=1;MQ=60;set=variant12-variant21-variant23-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:75:78,0,75:0,2,0,2 chr1 99164434 . G A 1398.86 PASS AC=1;AF=0.575;AN=2;DP=1690;MQ=60;set=variant-variant4-variant8-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:57,36:93:99:897,0,1448:28,29,21,15 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 1/1:0,101:101:99:3352,302,0:0,0,55,46 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 0/1:18,13:31:99:332,0,493:13,5,11,2 chr1 99356517 . A G 3540.25 PASS AC=1;AF=0.5;AN=2;DP=1975;MQ=60;set=variant6-variant12-variant13-variant17-variant23-variant28-variant30-variant31-variant39 GT:AD:DP:GQ:PL:SB 0/1:105,110:215:99:2900,0,2701:41,64,50,60 chr1 99356880 . T C 3253.45 PASS AC=1;AF=0.5;AN=2;DP=2147;MQ=60;set=variant12-variant17-variant23-variant28-variant30-variant31-variant39 GT:AD:DP:GQ:PL:SB 0/1:125,147:272:99:3928,0,3021:55,70,67,80 chr1 99356958 . A G 9680.75 PASS AC=1;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 0/1:114,98:212:99:2470,0,2887:48,66,41,57 chr1 99358358 . G T 968.14 PASS AC=1;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 0/1:53,41:94:99:1045,0,1329:27,26,21,20 chr1 99387628 . T TA 1588.11 PASS AC=1;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 0/1:20,32:52:99:771,0,444:6,14,10,22 chr1 99418948 . T TGTGTGA,TGTGA,TGTGTGTGA,TGA 362.04 PASS AC=1,0,0,0;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 0/1:11:99:1,4,1,5 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 0/1:41,45:86:99:1099,0,1126:10,31,16,29 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 0/1:29,18:47:99:492,0,781:19,10,14,4 chr1 100152443 . T C 1131.61 PASS AC=1;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 0/1:27,43:70:99:1121,0,673:11,16,19,24 chr1 100160177 . A T 1646.34 PASS AC=1;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 0/1:75,73:148:99:1988,0,1845:27,48,23,50 chr1 100184963 . CAA CA,CAAA,C 60.02 PASS AC=1,0,0;AF=0.395,0.132,0.026;AN=2;DP=289;set=variant-variant3-variant4-variant5-variant8-variant11-variant16-variant20-variant23-variant29-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant43 GT:DP:GQ:SB 0/1:11:25:0,3,6,2 chr1 100316589 . A G 2000.36 PASS AC=1;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 0/1:69,53:122:99:1387,0,1761:31,38,25,28 chr1 100316765 . C T 1140.97 PASS AC=1;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 0/1:17,22:39:99:647,0,373:7,10,5,17 chr1 100329889 . G C 3488.97 PASS AC=1;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 0/1:28,42:70:99:1109,0,693:18,10,29,13 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 0/1:7,12:19:99:387,0,226:7,0,10,2 chr1 100336361 . C T 1972.52 PASS AC=1;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 0/1:26,14:40:99:310,0,679:14,12,8,6 chr1 100340225 . G A 1813.63 PASS AC=1;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 0/1:41,35:76:99:780,0,1111:26,15,20,15 chr1 100342227 . C T 732.03 PASS AC=1;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 0/1:17,23:40:99:528,0,482:4,13,9,14 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 0/1:29,19:48:99:537,0,787:20,9,15,4 chr1 100345409 . C G 238.16 PASS AC=1;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 0/1:20,13:33:99:275,0,563:12,8,8,5 chr1 100346741 . T C 1368.33 PASS AC=1;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 0/1:41,35:76:99:910,0,1077:22,19,18,17 chr1 100353675 . G A 5773.43 PASS AC=1;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 0/1:106,74:180:99:1649,0,2507:50,56,37,37 chr1 100357141 . T A 637.43 PASS AC=1;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 0/1:16,11:27:99:359,0,523:15,1,10,1 chr1 100358200 . G A 1269.9 PASS AC=1;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 0/1:9,21:30:99:595,0,219:2,7,6,15 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 0/1:36:99:5,16,4,11 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 0/1:21,25:46:99:918,0,1053:9,12,10,15 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 0/1:19,21:40:99:825,0,1043:7,12,7,14 chr1 100381109 . A AT,ATT 54.15 PASS AC=0,1;AF=0.6,0.02;AN=2;DP=386;MQ=60;set=variant2-variant3-variant6-variant7-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant26-filterInvariant28-variant29-variant31-variant34-variant36-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:6:72:1,2,1,2 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 0/1:33,33:66:99:826,0,838:19,14,18,15 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 0/1:32,27:59:99:615,0,868:13,19,13,14 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 0/1:25,21:46:99:578,0,652:12,13,10,11 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 0/1:74,92:166:99:2360,0,1893:46,28,54,38 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 0/1:183,168:351:99:4347,0,4972:93,90,83,85 chr1 100515616 . T C 1319.16 PASS AC=1;AF=0.5;AN=2;DP=424;MQ=60;set=variant4-variant14-variant23-variant25-variant28 GT:AD:DP:GQ:PL:SB 0/1:43,38:81:99:893,0,1047:22,21,16,22 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 0/1:6,8:14:99:237,0,176:4,2,6,2 chr1 100545960 . T C 111.22 PASS AC=2;AF=0.75;AN=2;DP=16;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.825;ReadPosRankSum=0.289;set=variant23-variant24 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:139,12,0:0,0,3,1 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 0/1:105,95:200:99:2517,0,2677:54,51,48,47 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 0/1:158:99:59,58,19,22 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 0/1:45,57:102:99:1231,0,1025:23,22,29,28 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 1/1:0,138:138:99:6089,418,0:0,0,55,83 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 1/1:0,137:137:99:6089,418,0:0,0,54,83 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 1/1:0,31:31:93:1058,93,0:0,0,23,8 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 1/1:1,58:59:99:2432,168,0:0,1,3,55 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 0/7:14:94:3,2,3,6 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 0/1:19,17:36:99:510,0,414:10,9,8,9 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 1/1:0,99:99:99:2826,296,0:0,0,49,50 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 0/1:2,6:8:13:111,0,13:0,2,0,6 chr1 100715454 . G A 168.68 PASS AC=1;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 0/1:24,24:48:99:538,0,698:5,19,12,12 chr1 100731819 . C CA 1087.73 PASS AC=1;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 0/1:10,15:25:99:583,0,514:7,3,8,7 chr1 100731820 . G A 1096.77 PASS AC=1;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 0/1:10,15:25:99:583,0,514:7,3,8,7 chr1 100732450 . T C 1160.03 PASS AC=1;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 0/1:40,22:62:99:511,0,1035:16,24,9,13 chr1 100732526 . C G 554.22 PASS AC=1;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 0/1:20,11:31:99:258,0,496:8,12,3,8 chr1 100733207 . G GT,GTT 1677.46 PASS AC=1,1;AF=0.761,0.193;AN=2;DP=3656;set=Intersection GT:DP:GQ:SB 1/2:69:99:2,2,26,39 chr1 100733552 . T C 722.08 PASS AC=1;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 0/1:6,14:20:99:408,0,211:6,0,10,4 chr1 100742670 . A G 645.73 PASS AC=1;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 0/1:4,4:8:99:156,0,135:4,0,4,0 chr1 100750733 . AGTTTT A 4442.73 PASS AC=1;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 0/1:42,46:88:99:1771,0,2414:31,11,29,17 chr1 100758155 . T C 5671.07 PASS AC=1;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 0/1:70,67:137:99:1688,0,1674:45,25,46,21 chr1 100817384 . A G 1009.26 PASS AC=1;AF=0.594;AN=2;DP=1717;MQ=60;set=variant2-variant7-variant8-variant12-variant16-variant18-variant19-variant22-variant23-variant24-variant26-variant30-variant32-variant33-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:67,62:129:99:1345,0,1485:30,37,27,35 chr1 100817529 . AGTGTGTGTGTGTGT AGTGTGTGTGTGT,AGTGTGTGTGTGTGTGT,A,AGTGTGTGTGTGTGTGTGT,AGTGT,AGTGTGTGT,AGTGTGTGTGT 73.55 PASS AC=1,0,0,0,0,0,0;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 0/1:9:99:2,3,1,3 chr1 100817559 . T TGCGCGC,TGTGCGCGC 96.99 PASS AC=0,1;AF=0.583,0.167;AN=2;DP=58;MQ=60;set=variant8-variant19-variant23-variant24-variant33-variant40 GT:DP:GQ:SB 0/2:10:99:2,5,1,2 chr1 100818178 . G C 845.2 PASS AC=1;AF=0.6;AN=2;DP=2025;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant27-variant28-variant29-variant30-variant33-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,30:81:99:694,0,1302:23,28,14,16 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 1/1:0,99:99:99:3060,296,0:0,0,56,43 chr1 100818464 . T C 5085.1 PASS AC=2;AF=0.989;AN=2;DP=7771;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,177:177:99:5358,531,0:0,0,81,96 chr1 100819273 . T C 4249.93 PASS AC=1;AF=0.6;AN=2;DP=3069;MQ=60;set=variant2-variant7-variant8-variant10-variant12-variant13-variant16-variant18-variant19-variant22-variant23-variant24-variant26-variant30-variant32-variant33-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:65,76:141:99:1951,0,1602:34,31,38,38 chr1 100856479 . C T 828.78 PASS AC=1;AF=0.607;AN=2;DP=977;MQ=60;set=variant2-variant7-variant8-variant12-variant19-variant22-variant23-variant24-variant26-variant30-variant32-variant33-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:38,30:68:99:658,0,841:18,20,12,18 chr1 100908324 . A G 377.99 PASS AC=2;AF=0.788;AN=2;DP=226;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant32-variant33-variant34-variant37-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 100908577 . A T 1030.58 PASS AC=1;AF=0.6;AN=2;DP=1183;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant12-variant19-variant22-variant23-variant24-variant26-variant30-variant32-variant33-variant36-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:37,36:73:99:865,0,820:20,17,16,20 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 1/1:8:24:0,0,0,8 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 1/1:0,16:16:48:447,48,0:0,0,10,6 chr1 100963479 . CAG C 1208.82 PASS AC=1;AF=0.6;AN=2;DP=799;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant15-variant17-variant20-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant32-variant33-variant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,21:28:99:861,0,231:5,2,13,8 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 1/1:0,76:76:99:2378,228,0:0,0,48,28 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 1/1:0,97:97:99:3046,291,0:0,0,30,67 chr1 100984485 . C T 5648.94 PASS AC=1;AF=0.5;AN=2;DP=1615;MQ=60;set=variant4-variant14-variant23-variant28 GT:AD:DP:GQ:PL:SB 0/1:210,166:376:99:4048,0,5354:94,116,69,97 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 1/1:0,326:326:99:10598,981,0:0,0,136,190 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 1/1:0,11:11:33:320,33,0:0,0,8,3 chr1 101003762 . C A 1359.3 PASS AC=1;AF=0.682;AN=2;DP=1541;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,13:34:99:279,0,561:14,7,7,6 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 1/1:0,60:60:99:1806,180,0:0,0,26,34 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 0/1:5,6:11:99:178,0,111:2,3,3,3 chr1 101005090 . G A 4323.34 PASS AC=1;AF=0.662;AN=2;DP=5122;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,82:164:99:2026,0,1978:43,39,43,39 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 1/1:0,99:99:99:3284,296,0:0,0,58,41 chr1 101006577 . A G 16063.2 PASS AC=1;AF=0.58;AN=2;DP=11294;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant15-variant20-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant32-variant33-variant37-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:188,192:380:99:4519,0,4996:78,110,86,106 chr1 101007036 . T C 2984.85 PASS AC=1;AF=0.583;AN=2;DP=3661;MQ=60;set=variant-variant4-variant6-variant7-variant11-variant13-variant14-variant15-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:114,101:215:99:2303,0,2567:55,59,50,51 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 1/1:0,191:191:99:5714,573,0:0,0,85,106 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 1/1:0,12:12:36:444,36,0:0,0,2,10 chr1 101194965 . G GT 429.23 PASS AC=2;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 1/1:5,64:69:99:1560,102,0:2,3,26,38 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 1/1:0,5:5:15:222,15,0:0,0,5,0 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 1/1:0,130:130:99:3911,390,0:0,0,62,68 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 1/1:0,28:28:84:1171,84,0:0,0,1,27 chr1 101338324 . T C 9125.19 PASS AC=1;AF=0.692;AN=2;DP=12770;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-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:125,175:300:99:4570,0,3007:62,63,89,86 chr1 101338482 . A G 13209.6 PASS AC=1;AF=0.684;AN=2;DP=13819;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-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-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:155,181:336:99:4664,0,3902:80,75,91,90 chr1 101340134 . C T 406.78 PASS AC=1;AF=0.617;AN=2;DP=336;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:60:279,0,60:2,2,1,8 chr1 101342497 . T C 510.99 PASS AC=1;AF=0.632;AN=2;DP=713;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:110,0,201:3,5,1,4 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 0/1:32,30:62:99:788,0,646:15,17,19,11 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 1/1:0,4:4:12:168,12,0:0,0,0,4 chr1 101441384 . GTTTTTT GTTT,GTT,GT,GTTTT,GTTTTT,G 455.21 PASS AC=0,2,0,0,0,0;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 2/2:10:30:0,0,5,5 chr1 101444992 . CAAAAAA CAAAAA,CAAAA,C,CA,CAAAAAAA 452.53 PASS AC=0,1,0,0,0;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 0/2:112:99:42,38,23,9 chr1 101487373 . AACACACAC AACACACACACACAC,AACACACACAC,AACACACACACAC,AAC,A,AACAC 212.43 PASS AC=0,2,0,0,0,0;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 2/2:5:15:0,0,0,5 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 0/1:60,45:105:99:1125,0,1699:34,26,30,15 chr1 102252426 . C T 1696.14 PASS AC=1;AF=0.5;AN=2;DP=371;FractionInformativeReads=1;set=variant14-variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:45,42:87:99:987,0,1147:19,26,18,24 chr1 102269548 . C CT 3221.65 PASS AC=2;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 1/1:20,282:302:99:6972,486,0:8,12,129,153 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 0/1:71,63:134:99:1521,0,1731:31,40,28,35 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 0/1:104,78:182:99:2917,0,5466:47,57,34,44 chr1 103343274 . T C 5254.39 PASS AC=1;AF=0.667;AN=2;DP=457;FractionInformativeReads=1;MQ=60;set=variant6-variant20-variant23 GT:AD:DP:GQ:PL:SB 0/1:65,74:139:99:1886,0,1505:26,39,33,41 chr1 103343470 . G A 3188.24 PASS AC=1;AF=0.571;AN=2;DP=639;MQ=60;set=variant6-variant12-variant18-variant20-variant23-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:38,40:78:99:1102,0,983:20,18,19,21 chr1 103347380 . T C 379.75 PASS AC=1;AF=0.5;AN=2;DP=57;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant32 GT:AD:DP:GQ:PL:SB 0/1:15,15:30:99:408,0,417:4,11,4,11 chr1 103347416 . A G 119.71 PASS AC=1;AF=0.5;AN=2;DP=85;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant23-variant28-variant29-variant32-variant39 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:196,0,230:2,6,2,6 chr1 103353991 . T A 315.84 PASS AC=1;AF=0.571;AN=2;DP=88;FractionInformativeReads=1;MQ=60;set=variant6-variant12-variant18-variant20-variant23-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:9,5:14:99:143,0,210:5,4,4,1 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 1/1:0,50:50:99:1555,150,0:0,0,27,23 chr1 103354428 . A G 1759.29 PASS AC=2;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 1/1:0,105:105:99:2997,314,0:0,0,56,49 chr1 103354939 . CTG CTGTGTGTGTGTG,CTGTGTGTGTGTGTGTG,CTGTG,CTGTGTGTGTG,C,CTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTG 1303.42 PASS AC=0,1,1,0,0,0,0;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 3/2:31:99:1,1,20,9 chr1 103356072 . CA C 433.26 PASS AC=1;AF=0.5;AN=2;DP=306;MQ=60;set=variant6-filterInvariant7-filterInvariant12-variant18-variant20-variant23-variant28-filterInvariant36-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,8:27:99:147,0,460:8,11,4,4 chr1 103356168 . A C 61.77 PASS AC=2;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 1/1:0,7:7:21:267,21,0:0,0,1,6 chr1 103364396 . C T 89.37 PASS AC=1;AF=0.5;AN=2;DP=103;FractionInformativeReads=1;MQ=60;set=variant6-variant12-variant18-variant20-variant23-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:12,4:16:99:132,0,603:5,7,0,4 chr1 103364409 . A T 73.65 PASS AC=1;AF=0.5;AN=2;DP=84;FractionInformativeReads=1;MQ=60;set=variant6-variant12-variant18-variant20-variant23-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:11,3:14:90:90,0,606:4,7,0,3 chr1 103364618 . A T 407.9 PASS AC=2;AF=0.571;AN=2;DP=197;FS=0;FractionInformativeReads=1;MQ=60;set=variant6-variant12-variant18-variant20-variant23-variant36-variant41 GT:AD:DP:GQ:PL:SB 1/1:1,13:14:10:310,10,0:0,1,6,7 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 0/1:10,15:25:99:362,0,257:6,4,7,8 chr1 103380128 . G A 283.73 PASS AC=1;AF=0.5;AN=2;DP=210;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant23-variant28-variant29-variant32-variant33-variant39 GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:341,0,335:9,4,8,5 chr1 103380379 . TA TAA,T,TAAA 131.63 PASS AC=2,0,0;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 1/1:11:9:0,1,3,7 chr1 103381296 . T C 353.65 PASS AC=1;AF=0.5;AN=2;DP=227;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant23-variant28-variant29-variant32-variant33-variant39 GT:AD:DP:GQ:PL:SB 0/1:12,17:29:99:549,0,281:3,9,2,15 chr1 103388799 . TAC T 1024.16 PASS AC=1;AF=0.5;AN=2;DP=180;FractionInformativeReads=1;MQ=60;set=variant6-variant20-variant23 GT:AD:DP:GQ:PL:SB 0/1:29,27:56:99:987,0,1135:17,12,17,10 chr1 103388990 . TA T 121.62 PASS AC=1;AF=0.5;AN=2;DP=193;MQ=60;set=variant-variant8-variant23-variant28-variant29-variant32-variant33-variant39 GT:AD:DP:GQ:PL:SB 0/1:2,8:10:27:199,0,27:0,2,2,6 chr1 103399906 . G A 163.65 PASS AC=1;AF=0.5;AN=2;DP=161;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant23-variant28-variant29-variant32-variant33-variant39 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:231,0,172:5,1,6,2 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 1/1:0,35:35:99:1552,105,0:0,0,24,11 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 1/1:0,35:35:99:1552,105,0:0,0,24,11 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 0/1:25,21:46:99:496,0,613:16,9,14,7 chr1 103405892 . G A 761.43 PASS AC=1;AF=0.545;AN=2;DP=931;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant8-variant23-variant28-variant29-variant32-variant33-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:34,56:90:99:1306,0,904:17,17,27,29 chr1 103427381 . A G 1054.11 PASS AC=2;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 1/1:0,104:104:99:3005,311,0:0,0,55,49 chr1 103427407 . T C 1121.01 PASS AC=1;AF=0.5;AN=2;DP=631;MQ=60;set=variant23-variant28-variant29-variant32-variant33-variant39 GT:AD:DP:GQ:PL:SB 0/1:47,53:100:99:1149,0,1125:22,25,26,27 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 1/1:0,42:42:99:1391,126,0:0,0,12,30 chr1 103435626 . G A 64.18 PASS AC=2;AF=0.974;AN=2;DP=72;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.198;ReadPosRankSum=-0.198;set=variant2-variant3-variant6-variant7-variant8-variant13-variant15-variant17-variant19-variant22-variant23-variant24-variant25-variant31-variant32-variant33-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:87,6,0:0,0,2,0 chr1 103444497 . A G 628.88 PASS AC=2;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 1/1:0,45:45:99:1354,135,0:0,0,18,27 chr1 103445223 . G A 402.72 PASS AC=2;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 1/1:0,38:38:99:1102,114,0:0,0,15,23 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 1/1:0,11:11:33:330,33,0:0,0,7,4 chr1 103455217 . C T 626.36 PASS AC=1;AF=0.886;AN=2;DP=1689;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:21,13:34:99:356,0,521:8,13,3,10 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 1/1:0,37:37:99:1164,111,0:0,0,22,15 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 1/1:0,14:14:42:542,42,0:0,0,2,12 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 1/1:0,50:50:99:1576,150,0:0,0,33,17 chr1 103469989 . A G 399.36 PASS AC=1;AF=0.5;AN=2;DP=75;FS=0;FractionInformativeReads=1;MQ=60;set=variant6-variant23 GT:AD:DP:GQ:PL:SB 0/1:17,19:36:99:449,0,358:9,8,11,8 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 1/1:1,65:66:99:2802,163,0:0,1,31,34 chr1 103471734 . AAAATAAAT AAAATAAATAAATAAATAAAT,AAAATAAATAAAT,AAAATAAATAAATAAATAAATAAAT,AAAATAAATAAATAAAT,A 150.96 PASS AC=0,2,0,0,0;AF=0.6,0.06,0.16,0.08,0.04;AN=2;DP=312;FS=0;set=variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant19-variant21-variant23-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant38-variant39-variant42-variant43 GT:DP:GQ:SB 2/2:5:14:0,0,2,3 chr1 103477819 . A G 166.47 PASS AC=1;AF=0.5;AN=2;DP=31;FractionInformativeReads=1;MQ=60;set=variant6-variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:190,0,143:4,0,5,0 chr1 103477825 . A AT 85.17 PASS AC=1;AF=0.5;AN=2;DP=33;FS=0;FractionInformativeReads=1;MQ=60;set=variant6-variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:92:153,0,92:4,0,6,0 chr1 103483329 . T C 812.56 PASS AC=1;AF=0.5;AN=2;DP=164;FractionInformativeReads=1;MQ=60;set=variant6-variant23 GT:AD:DP:GQ:PL:SB 0/1:45,41:86:99:1080,0,1097:27,18,29,12 chr1 103487244 . T C 910.76 PASS AC=1;AF=0.5;AN=2;DP=661;MQ=60;set=variant6-variant16-variant22-variant23-variant34-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,56:100:99:1356,0,1013:19,25,31,25 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 1/1:2,20:22:41:511,41,0:2,0,4,16 chr1 103488173 . G A 264.37 PASS AC=1;AF=0.5;AN=2;DP=113;FractionInformativeReads=1;MQ=60;set=variant6-variant16-variant22-variant23-variant34-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,14:27:99:380,0,450:11,2,10,4 chr1 103491461 . T G 1479.98 PASS AC=1;AF=0.5;AN=2;DP=587;FractionInformativeReads=1;MQ=60;set=variant6-variant16-variant22-variant23-variant34-variant43 GT:AD:DP:GQ:PL:SB 0/1:57,37:94:99:913,0,1470:21,36,13,24 chr1 103491569 . G T 870.05 PASS AC=1;AF=0.5;AN=2;DP=173;FractionInformativeReads=1;MQ=60;set=variant6-variant16-variant22-variant23-variant34-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,6:20:99:208,0,1134:6,8,2,4 chr1 103491572 . C T 870.05 PASS AC=1;AF=0.5;AN=2;DP=173;FractionInformativeReads=1;MQ=60;set=variant6-variant16-variant22-variant23-variant34-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,7:21:99:223,0,1133:6,8,3,4 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 1/1:0,173:173:99:5002,518,0:0,0,89,84 chr1 103496792 . A G 569.97 PASS AC=1;AF=0.5;AN=2;DP=269;MQ=60;set=variant6-variant16-variant22-variant23-variant34-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,20:47:99:482,0,760:8,19,9,11 chr1 103496805 . GAA GA,GAAA,GAAAAA,G 493.06 PASS AC=1,1,0,0;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 1/2:32:99:0,0,10,22 chr1 103496875 . G A 76.65 PASS AC=1;AF=0.5;AN=2;DP=66;FractionInformativeReads=1;MQ=60;set=variant16-variant22-variant23-variant34-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:244,0,175:1,5,3,6 chr1 103548497 . A C 1388.7 PASS AC=1;AF=0.5;AN=2;DP=962;MQ=60;set=variant10-variant23-variant25-variant28-variant29-variant32-variant33-variant34-variant39 GT:AD:DP:GQ:PL:SB 0/1:34,63:97:99:1504,0,670:14,20,28,35 chr1 103573517 . CTT CT,CTTTT,C 85.73 PASS AC=1,0,0;AF=0.425,0.05,0.025;AN=2;DP=1248;set=filterInvariant4-filterInvariant5-filterInvariant7-filterInvariant9-filterInvariant10-variant11-filterInvariant14-filterInvariant16-filterInvariant17-filterInvariant20-filterInvariant21-variant23-filterInvariant26-filterInvariant27-filterInvariant31-filterInvariant33-variant34-filterInvariant36-variant37-filterInvariant44 GT:DP:GQ:SB 0/1:60:99:32,11,10,7 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 1/1:0,87:87:99:2752,259,0:0,0,53,34 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 1/1:0,22:22:65:693,65,0:0,0,11,11 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 1/1:0,26:26:78:793,78,0:0,0,12,14 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 1/1:0,15:15:45:470,45,0:0,0,7,8 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 0/2:36:99:12,9,8,7 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 1/1:0,47:47:99:1407,141,0:0,0,23,24 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 1/1:0,36:36:99:1200,108,0:0,0,10,26 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 1/1:0,78:78:99:2186,234,0:0,0,32,46 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 1/1:0,16:16:48:580,48,0:0,0,3,13 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 1/1:0,13:13:39:423,39,0:0,0,4,9 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 0/1:18,6:24:99:198,0,1020:3,15,3,3 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 0/1:67,32:99:99:725,0,1985:43,24,18,14 chr1 104120227 . T C 2675.45 PASS AC=1;AF=0.5;AN=2;DP=2436;set=variant6-variant7-variant20-variant23-variant32-variant39 GT:AD:DP:GQ:PL:SB 0/1:243,129:372:99:2783,0,6439:123,120,64,65 chr1 104166496 . T C 801.27 DRAGENHardSNP AC=1;AF=0.543;AN=2;DP=4857;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:39,86:125:99:1908,0,645:22,17,53,33 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 1/1:0,3:3:9:131,9,0:0,0,3,0 chr1 107600869 . G A 826.06 PASS AC=1;AF=0.556;AN=2;DP=1482;MQ=60;set=variant-variant3-variant4-variant5-variant9-variant13-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant33-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,34:63:99:999,0,854:14,15,18,16 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 1/1:0,27:27:80:885,80,0:0,0,25,2 chr1 107946324 . CA C,CAA,CAAA 41.34 PASS AC=1,0,0;AF=0.4,0.138,0.013;AN=2;DP=3092;set=filterInvariant2-variant3-variant4-variant5-variant6-filterInvariant7-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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:56:99:25,14,11,6 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 1/1:1,119:120:99:3851,322,0:1,0,66,53 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 1/1:0,174:174:99:5444,521,0:0,0,89,85 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 1/1:0,52:52:99:1832,155,0:0,0,32,20 chr1 107952914 . G A 8488.71 PASS AC=2;AF=0.989;AN=2;DP=10125;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,193:193:99:6323,577,0:0,0,93,100 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 1/1:0,82:82:99:2510,246,0:0,0,34,48 chr1 108024677 . CAAAAAAAAAAAAA C,CA,CAA,CAAA,CAAAAAA,CAAAAAAAA,CAAAAAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAAAAA,CAAAAA,CAAAA,CAAAAAAAAAAAAAA 1320.38 PASS AC=0,0,0,0,0,0,0,0,1,0,0;AF=0.025,0.1,0.063,0.275,0.05,0.013,0.075,0.013,0.013,0.013,0.013;AN=2;DP=2097;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-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/9:27:99:2,3,19,3 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 1/1:0,10:10:30:396,30,0:0,0,9,1 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 1/1:0,278:278:99:8205,833,0:0,0,156,122 chr1 108152630 . G T 661.75 PASS AC=1;AF=0.591;AN=2;DP=332;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant10-variant15-variant18-variant23-variant29-variant30-variant36-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,10:21:99:363,0,390:1,10,0,10 chr1 108185301 . C G 1998.27 PASS AC=1;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 0/1:48,40:88:99:1444,0,2407:25,23,21,19 chr1 108185309 . G A 2084.77 PASS AC=1;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 0/1:49,41:90:99:1477,0,2454:26,23,21,20 chr1 108292260 . A G 2358.08 PASS AC=1;AF=0.722;AN=2;DP=2427;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,28:57:99:696,0,782:8,21,9,19 chr1 108293874 . A G 573.02 PASS AC=1;AF=0.5;AN=2;DP=531;FractionInformativeReads=1;MQ=60;set=variant2-variant15-variant23-variant26-variant28-variant29-variant31-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,22:38:99:697,0,428:5,11,5,17 chr1 108293899 . T A 434.94 PASS AC=1;AF=0.5;AN=2;DP=369;FractionInformativeReads=1;MQ=60;set=variant2-variant15-variant23-variant26-variant28-variant29-variant31-variant36-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,18:26:99:680,0,288:0,8,2,16 chr1 108299775 . ATGTGTGTGTG ATGTGTGTG,ATGTGTG,ATG,ATGTGTGTGTGTG,A 1047.28 PASS AC=1,1,0,0,0;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 2/1:53:99:0,0,36,17 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 0/1:74:99:22,11,26,15 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 0/1:11,8:19:99:219,0,345:9,2,6,2 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 1/1:0,27:27:81:1001,81,0:0,0,20,7 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 1/1:0,77:77:99:2266,230,0:0,0,48,29 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 1/1:0,58:58:99:1778,174,0:0,0,29,29 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 1/1:0,40:40:99:1326,120,0:0,0,27,13 chr1 108507541 . GGCCGCC GGCC,G 437.99 PASS AC=1,0;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 0/1:45:99:7,21,4,13 chr1 108507636 . G A 138.41 PASS AC=1;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 0/1:9,4:13:92:92,0,313:2,7,1,3 chr1 108676570 . G A 558.3 PASS AC=1;AF=0.5;AN=2;DP=54;FS=4.162;FractionInformativeReads=1;MQ=60;MQRankSum=1.648;QD=10.34;ReadPosRankSum=-0.416;SOR=0.3;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:29,25:54:99:587,0,794:22,7,16,9 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 1/1:0,125:125:99:3761,373,0:0,0,75,50 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 1/1:0,100:100:99:2826,300,0:0,0,51,49 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 1/1:0,10:10:30:403,30,0:0,0,1,9 chr1 108766133 . A G 575.22 PASS AC=1;AF=0.581;AN=2;DP=581;FractionInformativeReads=1;set=variant-variant2-variant4-variant6-variant7-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:99:232,0,123:4,0,5,4 chr1 108766424 . A G 2920.4 PASS AC=1;AF=0.641;AN=2;DP=2390;set=variant-variant2-variant4-variant6-variant7-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,35:74:99:847,0,978:12,27,14,21 chr1 108771524 . C T 306.55 PASS AC=1;AF=0.531;AN=2;DP=841;FS=0;FractionInformativeReads=1;set=variant-variant2-variant4-variant6-variant7-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,10:21:99:378,0,375:11,0,10,0 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 0/1:170,58:228:99:856,0,4720:63,107,25,33 chr1 108994925 . A G 169.59 DRAGENHardSNP AC=2;AF=0.84;AN=2;DP=606;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:247,30,0:0,0,5,5 chr1 108994952 . G T 70.4 DRAGENHardSNP AC=2;AF=0.796;AN=2;DP=601;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:247,30,0:0,0,5,5 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 1/1:0,10:10:30:370,30,0:0,0,1,9 chr1 109143093 . C T 371.23 PASS AC=2;AF=0.625;AN=2;DP=96;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant23-variant29-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:947,87,0:0,0,19,10 chr1 109170746 . C T 588.81 PASS AC=2;AF=0.841;AN=2;DP=2148;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1560,120,0:0,0,34,6 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 1/1:0,263:263:99:11844,794,0:0,0,129,134 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 1/1:0,29:29:89:1291,89,0:0,0,1,28 chr1 109241669 . G A 518.67 PASS AC=1;AF=0.605;AN=2;DP=214;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant8-variant10-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant28-variant29-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,2:7:69:69,0,121:4,1,2,0 chr1 109242392 . A G 650.71 PASS AC=1;AF=0.5;AN=2;DP=99;FractionInformativeReads=1;MQ=60;set=variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:20,26:46:99:679,0,532:11,9,12,14 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 1/1:0,67:67:99:2144,201,0:0,0,39,28 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 1/1:0,93:93:99:3084,279,0:0,0,49,44 chr1 109270402 . G A 2417.25 PASS AC=1;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 0/1:24,31:55:99:954,0,671:16,8,24,7 chr1 109271674 . T A 127.46 PASS AC=1;AF=0.5;AN=2;DP=127;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant8-variant11-variant21-variant22-variant23-variant26-variant27-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:95:95,0,117:1,3,2,2 chr1 109273269 . A G 547.39 PASS AC=1;AF=0.5;AN=2;DP=42;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.201;QD=13.03;ReadPosRankSum=1.308;SOR=0.693;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:21,21:42:99:576,0,606:15,6,15,6 chr1 109273456 . A G 3296.02 PASS AC=1;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 0/1:39,48:87:99:1270,0,874:15,24,19,29 chr1 109273610 . G A 637.41 PASS AC=1;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 0/1:6,9:15:99:234,0,145:2,4,3,6 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 1/1:0,26:26:78:950,78,0:0,0,21,5 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 1/1:0,146:146:99:4249,438,0:0,0,81,65 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 1/1:0,94:94:99:2915,282,0:0,0,41,53 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 1/1:0,16:16:48:537,48,0:0,0,5,11 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 1/1:0,78:78:99:2272,233,0:0,0,33,45 chr1 109315211 . A G 104.64 PASS AC=2;AF=0.971;AN=2;DP=61;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.231;ReadPosRankSum=-0.358;set=variant3-variant4-variant6-variant7-variant13-variant16-variant21-variant23-variant24-variant25-variant26-variant27-variant33-variant34-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,4,0 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 1/1:0,44:44:99:1393,131,0:0,0,32,12 chr1 109325028 . T C 314.74 PASS AC=1;AF=0.5;AN=2;DP=654;MQ=60;set=variant2-variant3-variant8-variant13-variant16-variant18-variant21-variant22-variant23-variant24-variant27-variant28-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,27:52:99:612,0,670:16,9,17,10 chr1 109338861 . G C 1915.94 PASS AC=1;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 0/1:39,25:64:99:600,0,1046:22,17,16,9 chr1 109350198 . GT G,GTT 216.77 PASS AC=1,0;AF=0.382,0.118;AN=2;DP=2387;MQ=60;set=variant-variant2-filterInvariant3-filterInvariant4-filterInvariant8-filterInvariant9-variant10-filterInvariant11-variant12-filterInvariant13-filterInvariant15-variant16-filterInvariant17-variant18-filterInvariant20-variant21-variant23-variant24-filterInvariant25-filterInvariant26-variant27-variant28-variant29-variant31-filterInvariant32-filterInvariant34-filterInvariant37-filterInvariant38-filterInvariant39-variant40-variant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/1:47:99:5,24,3,15 chr1 109358755 . A AT 8409.33 PASS AC=1;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 0/1:100,101:201:99:2461,0,2443:50,50,48,53 chr1 109358958 . T C 485.33 PASS AC=1;AF=0.5;AN=2;DP=682;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant8-variant16-variant18-variant21-variant22-variant23-variant24-variant27-variant28-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:28,22:50:99:617,0,707:10,18,5,17 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 0/1:66,71:137:99:1819,0,1571:29,37,31,40 chr1 109366370 . C T 2462.52 PASS AC=2;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 1/1:0,99:99:99:3152,297,0:0,0,38,61 chr1 109369791 . G A 350.89 PASS AC=1;AF=0.556;AN=2;DP=240;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant8-variant16-variant21-variant22-variant23-variant27-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:154,0,151:4,1,4,1 chr1 109369797 . T G 240.81 PASS AC=2;AF=0.657;AN=2;DP=995;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:451,33,0:0,0,9,2 chr1 109369915 . G T 986.6 PASS AC=2;AF=0.643;AN=2;DP=2167;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1192,129,0:0,0,22,21 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 1/1:0,15:15:45:430,45,0:0,0,9,6 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 1/1:0,28:28:84:949,84,0:0,0,20,8 chr1 109377157 . TA T,TAA 1312.12 PASS AC=1,0;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 0/1:43:99:15,13,8,7 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 1/1:0,47:47:99:1587,141,0:0,0,25,22 chr1 109395105 . C T 1533.14 PASS AC=2;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 1/1:0,127:127:99:3785,381,0:0,0,72,55 chr1 109457151 . C T 275.3 PASS AC=2;AF=1;AN=2;DP=12;FS=0;FractionInformativeReads=1;MQ=60;set=variant15-variant23 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:222,15,0:0,0,1,4 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 1/1:0,52:52:99:1551,156,0:0,0,28,24 chr1 109472813 . T C 1540.18 PASS AC=2;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 1/1:0,60:60:99:1819,179,0:0,0,34,26 chr1 109474250 . TA TAAA,TAA,TAAAA,T 1116.05 PASS AC=0,0,0,1;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 0/4:165:99:74,61,15,15 chr1 109477462 . G C 1055.76 PASS AC=1;AF=0.5;AN=2;DP=109;FS=1.544;FractionInformativeReads=1;MQ=60;MQRankSum=-0.752;QD=9.69;ReadPosRankSum=-0.482;SOR=0.865;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:63,46:109:99:1084,0,1508:30,33,20,26 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 1/1:0,172:172:99:4979,513,0:0,0,94,78 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 1/1:0,168:168:99:5797,506,0:0,0,79,89 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 1/1:0,45:45:99:1385,135,0:0,0,15,30 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 0/1:2,2:4:78:78,0,80:0,2,1,1 chr1 109505835 . G T 459.75 PASS AC=1;AF=0.5;AN=2;DP=54;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant23 GT:AD:DP:GQ:PL:SB 0/1:18,10:28:99:311,0,606:15,3,9,1 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 0/1:184,167:351:99:4064,0,4654:99,85,87,80 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 0/1:11,10:21:99:294,0,311:3,8,1,9 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 1/1:0,19:19:57:855,57,0:0,0,3,16 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 1/1:0,28:28:84:807,84,0:0,0,16,12 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 1/1:0,16:16:48:513,48,0:0,0,5,11 chr1 109606778 . CAAAAAAAAAA C,CAAAAAAAAAAAAAA,CAAAAAAAAAAAAA,CAAAAAAAAAAAAAAA,CAAAAAAAAAAAA,CAAAAAAAA,CAAAAAAAAA,CAAAAAAAAAAA 1106.46 PASS AC=0,0,0,2,0,0,0,0;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 4/4:6:21:0,0,5,1 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 1/1:0,18:18:54:549,54,0:0,0,11,7 chr1 109635793 . C T 328.39 PASS AC=2;AF=0.667;AN=2;DP=37;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant23 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:32:360,32,0:0,0,2,9 chr1 109648503 . CAAAAA C,CAA,CAAA,CAAAA 67.78 PASS AC=0,0,0,1;AF=0.071,0.071,0.214,0.143;AN=2;DP=73;set=variant3-variant4-variant6-variant21-variant23-variant39-variant42 GT:DP:GQ:SB 0/4:9:28:1,2,5,1 chr1 109656038 . AAGAGAGAGAGAGAGAGAGAGAGAG AAGAGAGAGAGAGAGAGAG,AAGAGAGAGAGAGAGAGAGAGAGAGAG,AAGAGAGAGAGAGAGAGAGAGAG,A,AAGAG,AAGAGAGAGAGAG,AAGAGAGAGAGAGAGAGAGAGAGAGAGAG,AAGAGAGAGAGAGAGAG,AAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG,AAGAGAGAGAGAGAGAGAGAG,AAGAGAG,AAGAGAGAGAGAGAG,AAGAGAGAGAG 128.24 PASS AC=1,0,0,0,0,0,0,1,0,0,0,0,0;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 8/1:16:99:1,1,13,1 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 1/1:0,59:59:99:2033,177,0:0,0,46,13 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 1/1:0,137:137:99:4050,410,0:0,0,52,85 chr1 109714750 . T C 254.34 PASS AC=2;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 1/1:0,37:37:99:1382,111,0:0,0,6,31 chr1 109714919 . A G 73.25 PASS AC=2;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 1/1:0,7:7:21:274,21,0:0,0,6,1 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 1/1:0,15:15:45:510,45,0:0,0,11,4 chr1 109732080 . C T 857.2 PASS AC=2;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 1/1:0,23:23:69:868,69,0:0,0,8,15 chr1 109734157 . T C 1830.47 PASS AC=2;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 1/1:0,48:48:99:1707,144,0:0,0,14,34 chr1 109734225 . G T 1031.33 PASS AC=2;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 1/1:0,16:16:48:702,48,0:0,0,6,10 chr1 109734541 . C T 1434.12 PASS AC=2;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 1/1:0,59:59:99:2001,177,0:0,0,15,44 chr1 109735298 . T C 5745 PASS AC=2;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 1/1:0,146:146:99:4499,437,0:0,0,79,67 chr1 109735416 . A C 4164.01 PASS AC=2;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 1/1:0,161:161:99:4795,482,0:0,0,75,86 chr1 109735504 . T C 1263.74 PASS AC=2;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 1/1:0,63:63:99:2177,189,0:0,0,17,46 chr1 109737063 . C T 2169.67 PASS AC=2;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 1/1:1,57:58:99:1671,128,0:1,0,37,20 chr1 109737090 . G A 2999.2 PASS AC=2;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 1/1:1,74:75:99:2264,182,0:1,0,47,27 chr1 109737132 . T C 3718.04 PASS AC=2;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 1/1:1,102:103:99:3238,272,0:1,0,61,41 chr1 109737172 . C T 3670.25 PASS AC=2;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 1/1:1,107:108:99:3105,291,0:0,1,57,50 chr1 109737314 . T C 1235.95 PASS AC=2;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 1/1:0,32:32:96:1423,96,0:0,0,7,25 chr1 109737320 . G A 1138.05 PASS AC=2;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 1/1:0,30:30:90:1350,90,0:0,0,7,23 chr1 109740310 . AGT AGAGAGAGTGTGTGT,AGAGAGAGTGTGT,AGAGAGAGAGTGTGT,A 64.18 PASS AC=0,1,1,0;AF=0.3,0.1,0.1,0.075;AN=2;DP=479;set=variant-variant2-variant3-variant4-variant8-filterInvariant9-variant14-variant18-variant19-variant20-variant21-variant23-variant29-variant32-variant36-variant37-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 2/3:8:92:0,0,0,8 chr1 109740548 . G T 471.28 PASS AC=1;AF=0.545;AN=2;DP=1254;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant10-variant14-variant18-variant19-variant21-variant23-variant26-variant29-variant30-variant32-variant33-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,22:62:99:439,0,1064:20,20,12,10 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 1/1:0,23:23:69:829,69,0:0,0,5,18 chr1 109742452 . C T 151.77 PASS AC=2;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 1/1:0,7:7:21:266,21,0:0,0,6,1 chr1 109742485 . G A 450.06 PASS AC=2;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 1/1:0,21:21:63:838,63,0:0,0,19,2 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 0/1:18,21:39:99:625,0,662:1,17,6,15 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 1/1:0,58:58:99:2009,174,0:0,0,21,37 chr1 109771063 . T C 4837.82 PASS AC=1;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 0/1:65,35:100:99:782,0,1580:29,36,17,18 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 1/1:0,18:18:54:685,54,0:0,0,15,3 chr1 109773705 . ATT A 44.82 PASS AC=2;AF=0.929;AN=2;DP=38;FS=0;MQ=60;MQRankSum=-0.55;ReadPosRankSum=0.937;set=variant7-variant8-variant12-variant15-variant23-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:72,6,0:0,0,1,1 chr1 109778577 . T C 3158.67 PASS AC=1;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 0/1:42,42:84:99:1042,0,933:23,19,25,17 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 1/1:0,83:83:99:2451,248,0:0,0,40,43 chr1 109779621 . T TC 2449.43 PASS AC=1;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 0/1:29,25:54:99:768,0,918:8,21,7,18 chr1 109792735 . A ACGC 901.58 PASS AC=1;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 0/1:51,38:89:99:1442,0,1979:33,18,25,13 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 1/1:1,207:208:99:6473,578,0:0,1,91,116 chr1 109795026 . T C 3965.83 PASS AC=2;AF=0.955;AN=2;DP=6691;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,137:137:99:4281,411,0:0,0,71,66 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 1/1:0,205:205:99:6412,614,0:0,0,94,111 chr1 109796053 . C T 519.91 PASS AC=1;AF=0.523;AN=2;DP=1550;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant11-variant13-variant14-variant18-variant21-variant23-variant25-variant26-variant28-variant30-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,31:68:99:602,0,910:12,25,11,20 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 0/1:8,5:13:99:186,0,234:2,6,0,5 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 0/1:38,39:77:99:1068,0,1150:6,32,6,33 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 0/1:101,124:225:99:2953,0,2374:55,46,66,58 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 0/1:58,44:102:99:1077,0,1562:29,29,20,24 chr1 109810544 . C A 1415.56 PASS AC=1;AF=0.5;AN=2;DP=2543;MQ=60;set=variant2-variant4-variant5-variant8-variant10-variant11-variant14-variant21-variant23-variant26-variant28-variant30-variant36-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,72:161:99:1604,0,2078:45,44,37,35 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 0/1:16,16:32:99:476,0,422:9,7,13,3 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 0/1:56,39:95:99:1428,0,8065:28,28,18,21 chr1 109814880 . C T 2182.55 PASS AC=1;AF=0.536;AN=2;DP=3663;MQ=60;set=variant2-variant4-variant5-variant18-variant21-variant23-variant26-variant29-variant30-variant31-variant34-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:118,109:227:99:2381,0,2961:60,58,52,57 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 0/1:51,43:94:99:1032,0,1139:29,22,22,21 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 1/1:0,162:162:99:6081,486,0:0,0,57,105 chr1 109816189 . C T 3224.22 PASS AC=1;AF=0.5;AN=2;DP=673;MQ=60;set=variant3-variant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:58,88:146:99:2115,0,1280:24,34,30,58 chr1 109816863 . T TC 190.94 PASS AC=1;AF=0.545;AN=2;DP=366;MQ=60;set=variant2-variant4-variant5-variant19-variant21-variant23-variant26-variant29-variant30-variant31-variant34 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:202,0,264:5,6,4,5 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 0/1:62,49:111:99:1168,0,1504:36,26,27,22 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 0/1:51,61:112:99:1326,0,1280:26,25,29,32 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 0/1:33,28:61:99:712,0,811:16,17,12,16 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 0/1:18,5:23:99:156,0,532:10,8,4,1 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 0/1:78,53:131:99:1743,0,2671:39,39,29,24 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 1/1:0,102:102:99:3081,305,0:0,0,42,60 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 0/1:41,30:71:99:732,0,1064:14,27,11,19 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 0/1:9,13:22:99:438,0,249:7,2,11,2 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 0/1:19,26:45:99:806,0,457:14,5,21,5 chr1 109824250 . G A 1210.4 PASS AC=1;AF=0.5;AN=2;DP=1072;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant23-variant26-variant29-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,59:126:99:1425,0,1569:38,29,31,28 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 1/1:0,46:46:99:1555,138,0:0,0,25,21 chr1 109834938 . C T 47.97 PASS AC=1;AF=0.5;AN=2;DP=49;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant23-variant26-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:34:115,0,34:1,0,2,1 chr1 109835163 . C T 624.2 PASS AC=1;AF=0.5;AN=2;DP=353;MQ=60;set=variant2-variant5-variant23-variant26-variant29-variant36-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,14:32:99:364,0,454:6,12,6,8 chr1 109836842 . C G 5697.38 PASS AC=2;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 1/1:0,177:177:99:5118,531,0:0,0,81,96 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 1/1:0,13:13:39:434,39,0:0,0,4,9 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 1/1:0,13:13:39:410,39,0:0,0,9,4 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 1/1:0,99:99:99:2724,296,0:0,0,55,44 chr1 109839063 . AT A,ATT 332.92 PASS AC=1,0;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 0/1:19:99:3,7,2,7 chr1 109839392 . A G 975.91 PASS AC=1;AF=0.864;AN=2;DP=2844;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:19,34:53:99:792,0,718:11,8,19,15 chr1 109839400 . C T 840.14 PASS AC=1;AF=0.5;AN=2;DP=644;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant23-variant26-variant29-variant36-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,20:58:99:463,0,1411:22,16,11,9 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 1/1:0,78:78:99:2310,233,0:0,0,42,36 chr1 109839896 . C T 486.45 PASS AC=1;AF=0.5;AN=2;DP=816;MQ=60;set=variant2-variant5-variant6-variant13-variant15-variant18-variant21-variant23-variant34-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,26:45:99:692,0,607:2,17,8,18 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 1/1:0,15:15:45:562,45,0:0,0,7,8 chr1 109840169 . C T 609.13 PASS AC=1;AF=0.5;AN=2;DP=111;FractionInformativeReads=1;MQ=60;set=variant5-variant23 GT:AD:DP:GQ:PL:SB 0/1:22,42:64:99:954,0,496:12,10,20,22 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 0/1:78:99:17,21,16,24 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 0/1:146,114:260:99:2576,0,3592:78,68,60,54 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 0/1:65,74:139:99:2740,0,2324:28,37,39,35 chr1 109856843 . G T 525.29 PASS AC=1;AF=0.5;AN=2;DP=262;MQ=60;set=variant5-variant23-variant31-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,20:38:99:511,0,509:11,7,11,9 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 0/1:29,21:50:99:817,0,1255:9,20,7,14 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 0/1:32,21:53:99:518,0,783:14,18,8,13 chr1 109897100 . T C 1932.95 PASS AC=1;AF=0.5;AN=2;DP=528;FractionInformativeReads=1;MQ=60;set=variant5-variant23-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,65:127:99:1470,0,2395:31,31,37,28 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 0/1:69,62:131:99:1465,0,2605:38,31,32,30 chr1 109898267 . GC GCC,G,GCCC 569.21 PASS AC=0,1,0;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 0/2:13:99:2,4,1,6 chr1 109943579 . AG A 1043.83 PASS AC=1;AF=0.5;AN=2;DP=65;FS=9.297;FractionInformativeReads=1;MQ=60;MQRankSum=-0.455;QD=16.06;ReadPosRankSum=0.429;SOR=0.172;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:36,29:65:99:1081,0,2289:27,9,16,13 chr1 109943581 . A C 1052.86 PASS AC=1;AF=0.5;AN=2;DP=65;FS=9.297;FractionInformativeReads=1;MQ=60;MQRankSum=-0.508;QD=16.2;ReadPosRankSum=0.178;SOR=0.172;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:36,29:65:99:1081,0,2289:27,9,16,13 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 0/1:50,48:98:99:1389,0,1531:13,37,14,34 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 0/1:41,48:89:99:1458,0,1136:28,13,38,10 chr1 109955010 . C A 306.83 PASS AC=2;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 1/1:0,5:5:15:211,15,0:0,0,0,5 chr1 109955569 . T C 1143 PASS AC=1;AF=0.5;AN=2;DP=299;FractionInformativeReads=1;MQ=60;set=variant5-variant23-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,32:66:99:871,0,773:19,15,15,17 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 0/1:18,23:41:99:585,0,416:7,11,10,13 chr1 110009171 . C T 148.54 PASS AC=1;AF=0.833;AN=2;DP=537;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,8:11:99:197,0,104:2,1,5,3 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 0/1:41,39:80:99:1051,0,1165:29,12,25,14 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 0/1:77,66:143:99:1664,0,2020:33,44,30,36 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 1/1:0,39:39:99:1259,117,0:0,0,25,14 chr1 110019439 . A G 1683.61 PASS AC=1;AF=0.625;AN=2;DP=542;FractionInformativeReads=1;MQ=60;set=variant5-variant23-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,59:128:99:1466,0,1689:43,26,38,21 chr1 110020341 . C T 739.15 PASS AC=1;AF=0.6;AN=2;DP=432;MQ=60;set=variant5-variant23-variant34-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,46:93:99:1193,0,1424:30,17,29,17 chr1 110022060 . A G 2788.39 PASS AC=1;AF=0.5;AN=2;DP=247;FS=2.802;FractionInformativeReads=0.996;MQ=60;MQRankSum=1.654;QD=11.29;ReadPosRankSum=0.193;SOR=0.877;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:130,116:246:99:2817,0,2997:65,65,53,63 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 0/1:27,18:45:99:462,0,638:16,11,12,6 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 0/1:59,34:93:99:685,0,1423:33,26,20,14 chr1 110031188 . T G 239.19 PASS AC=1;AF=0.538;AN=2;DP=211;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant17-variant20-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,10:17:99:280,0,209:3,4,2,8 chr1 110032431 . T G 920.61 PASS AC=1;AF=0.625;AN=2;DP=340;MQ=60;set=variant5-variant23-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,57:82:99:1395,0,558:9,16,28,29 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 0/1:23,8:31:99:146,0,573:15,8,4,4 chr1 110036634 . C T 1139.09 PASS AC=1;AF=0.5;AN=2;DP=245;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant23-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,30:52:99:763,0,612:16,6,22,8 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 0/1:47,45:92:99:1107,0,1216:20,27,19,26 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 0/1:32,35:67:99:913,0,714:18,14,19,16 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 0/1:36,26:62:99:975,0,2278:15,21,9,17 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 0/1:34,26:60:99:977,0,2228:14,20,9,17 chr1 110041477 . TAAAA TAA,TAAAAA,TAAA,T 450.41 PASS AC=1,0,1,0;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 1/3:26:99:0,0,12,14 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 0/1:14,7:21:99:211,0,437:3,11,1,6 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 0/1:17,15:32:99:403,0,385:10,7,7,8 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 0/1:18,17:35:99:401,0,486:11,7,10,7 chr1 110049457 . G A 363.01 PASS AC=1;AF=0.5;AN=2;DP=189;FractionInformativeReads=1;MQ=60;set=variant5-variant23-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,29:54:99:782,0,601:9,16,14,15 chr1 110136458 . A G 17752.6 PASS AC=2;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 1/1:0,426:426:99:13366,1278,0:0,0,216,210 chr1 110145758 . ACCTGGGGGGTCTTCTAACTACTGG A 758.76 PASS AC=2;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 1/1:0,39:39:99:1728,120,0:0,0,34,5 chr1 110148974 . C T 1288.4 PASS AC=2;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 1/1:0,60:60:99:1731,178,0:0,0,35,25 chr1 110163076 . A G 256.95 PASS AC=2;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 1/1:0,27:27:81:863,81,0:0,0,8,19 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 0/1:53,55:108:99:1314,0,1229:27,26,29,26 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 0/1:116,80:196:99:1752,0,2894:62,54,37,43 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 0/1:32,43:75:99:1077,0,868:17,15,25,18 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 0/1:18,37:55:99:970,0,390:9,9,20,17 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 0/1:11,21:32:99:570,0,254:6,5,12,9 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 0/1:14,21:35:99:621,0,474:8,6,11,10 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 0/1:45,31:76:99:776,0,1245:28,17,21,10 chr1 110199172 . CTGTGTGTGTGTG CTGTGTGTGTGTGTGTG,CTGTGTGTGTG,CTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTG,CTGTGTG,CTGTG,CTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTG,C,CTGTGTGTGTGTGTGTGTGTGTGTG,CTG 426.42 PASS AC=1,0,0,0,0,1,0,0,0,0,0,0,0;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 6/1:26:99:1,0,14,11 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 0/1:17:99:8,0,8,1 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 0/1:136,139:275:99:3540,0,3615:67,69,65,74 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 1/1:0,204:204:99:6126,610,0:0,0,91,113 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 1/1:0,66:66:99:2333,198,0:0,0,22,44 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 1/1:1,94:95:99:4278,266,0:1,0,54,40 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 1/1:0,97:97:99:4310,295,0:0,0,55,42 chr1 110210780 . C G 2730.11 PASS AC=2;AF=0.898;AN=2;DP=7796;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,154:154:99:4897,462,0:0,0,58,96 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 0/1:43,37:80:99:418,0,1068:13,30,24,13 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 0/1:66,12:78:99:255,0,1600:30,36,2,10 chr1 110211835 . T C 1190.53 PASS AC=1;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 0/1:45,24:69:99:783,0,1488:37,8,23,1 chr1 110212293 . C A 544.44 PASS AC=1;AF=0.6;AN=2;DP=767;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant10-variant11-variant12-variant14-variant17-variant19-variant20-variant22-variant23-variant25-variant28-variant30-variant31-variant32-variant33-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,15:33:99:440,0,574:2,16,3,12 chr1 110252010 . T C 2780.01 PASS AC=1;AF=0.818;AN=2;DP=4014;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:38,33:71:99:810,0,957:20,18,18,15 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 0/1:19,21:40:99:624,0,685:3,16,3,18 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 0/1:45,37:82:99:1037,0,1126:23,22,19,18 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 0/1:18,39:57:99:992,0,489:7,11,20,19 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 0/1:31,27:58:99:670,0,811:14,17,11,16 chr1 110260742 . T C 1550.03 PASS AC=1;AF=0.559;AN=2;DP=1369;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant16-variant17-variant20-variant21-variant23-variant24-variant27-variant32-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,31:70:99:707,0,969:23,16,12,19 chr1 110276861 . T C 276.27 PASS AC=1;AF=0.5;AN=2;DP=365;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant16-variant20-variant23-variant24-variant27-variant32-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,16:24:99:405,0,248:5,3,7,9 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 0/1:33,43:76:99:1099,0,822:15,18,23,20 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 0/1:6:91:1,2,0,3 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 0/1:3,3:6:91:91,0,166:1,2,0,3 chr1 110278972 . C T 956.1 PASS AC=2;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 1/1:0,31:31:92:1032,92,0:0,0,15,16 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 0/1:31,21:52:99:567,0,871:21,10,14,7 chr1 110279053 . GT G 1080.93 PASS AC=2;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 1/1:0,84:84:99:2564,252,0:0,0,54,30 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 0/1:34,35:69:99:894,0,930:21,13,20,15 chr1 110279821 . C A 3203.75 PASS AC=2;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 1/1:0,108:108:99:3110,321,0:0,0,52,56 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 0/1:39,43:82:99:1171,0,1063:16,23,21,22 chr1 110281941 . G A 535.18 PASS AC=2;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 1/1:0,47:47:99:1445,140,0:0,0,30,17 chr1 110282972 . G T 1244.63 PASS AC=2;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 1/1:0,178:178:99:5318,532,0:0,0,76,102 chr1 110283785 . C T 355.34 PASS AC=2;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 1/1:0,14:14:42:566,42,0:0,0,1,13 chr1 110292856 . G C 464.42 PASS AC=2;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 1/1:0,47:47:99:1549,141,0:0,0,28,19 chr1 110295772 . T C 754.36 PASS AC=2;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 1/1:0,96:96:99:2754,287,0:0,0,46,50 chr1 110295890 . C G 70.68 PASS AC=2;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 1/1:0,32:32:96:1116,96,0:0,0,9,23 chr1 110299691 . G A 872.05 PASS AC=1;AF=0.5;AN=2;DP=595;FractionInformativeReads=1;MQ=60;set=variant5-variant9-variant10-variant13-variant23 GT:AD:DP:GQ:PL:SB 0/1:62,39:101:99:776,0,1457:32,30,21,18 chr1 110300277 . C T 663.37 PASS AC=1;AF=0.5;AN=2;DP=236;FractionInformativeReads=1;MQ=60;set=variant5-variant9-variant10-variant13-variant23 GT:AD:DP:GQ:PL:SB 0/1:23,17:40:99:479,0,729:9,14,7,10 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 0/1:44,29:73:99:647,0,1320:27,17,16,13 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 1/1:0,105:105:99:3192,315,0:0,0,54,51 chr1 110301260 . C T 738.52 PASS AC=1;AF=0.575;AN=2;DP=1708;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant13-variant16-variant17-variant18-variant21-variant23-variant24-variant27-variant32-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,42:78:99:1098,0,879:12,24,14,28 chr1 110301766 . AGTGTGTGTGT AGT,AGTGTGT,AGTGTGTGTGTGT,AGTGTGTGT,AGTGT,A 464.39 PASS AC=1,1,0,0,0,0;AF=0.216,0.239,0.034,0.33,0.114,0.011;AN=2;DP=1690;set=Intersection GT:DP:GQ:SB 1/2:25:99:0,1,21,3 chr1 110304537 . G A 428.74 PASS AC=1;AF=0.56;AN=2;DP=813;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant23-variant24-variant26-variant27-variant28-variant29-variant32-variant34-variant36-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,16:19:77:419,0,77:0,3,5,11 chr1 110466338 . C A 10561.2 PASS AC=1;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 0/1:208,199:407:99:4637,0,5022:98,110,105,94 chr1 110466466 . T C 2651.33 PASS AC=1;AF=0.62;AN=2;DP=5744;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant34-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:111,94:205:99:2410,0,2834:39,72,32,62 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 1/1:0,197:197:99:5772,590,0:0,0,84,113 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 1/1:0,60:60:99:1880,180,0:0,0,37,23 chr1 110468009 . C A 599.04 PASS AC=1;AF=0.542;AN=2;DP=204;FractionInformativeReads=1;MQ=60;set=variant6-variant12-variant13-variant17-variant18-variant21-variant22-variant23-variant24-variant29-variant32-variant34 GT:AD:DP:GQ:PL:SB 0/1:7,10:17:99:295,0,212:1,6,1,9 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 1/1:0,21:21:63:761,63,0:0,0,6,15 chr1 110469411 . A G 119.98 PASS AC=2;AF=0.704;AN=2;DP=292;MQ=60;set=variant-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant32-variant33-variant34-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:234,21,0:0,0,3,4 chr1 110471906 . C T 2690.31 PASS AC=1;AF=0.542;AN=2;DP=946;MQ=60;set=variant6-variant12-variant13-variant17-variant18-variant21-variant22-variant23-variant24-variant29-variant32-variant34 GT:AD:DP:GQ:PL:SB 0/1:30,42:72:99:1009,0,765:15,15,22,20 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 1/1:0,113:113:99:3635,339,0:0,0,52,61 chr1 110472956 . T G 781.37 PASS AC=1;AF=0.635;AN=2;DP=2533;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant34-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:52,45:97:99:1083,0,1324:26,26,22,23 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 1/1:0,77:77:99:3053,232,0:0,0,36,41 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 1/1:0,44:44:99:1718,132,0:0,0,14,30 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 0/1:84:99:34,32,11,7 chr1 110592048 . CTT CT,C 219.47 PASS AC=1,0;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 0/1:33:99:6,5,14,8 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 0/1:30,30:60:99:869,0,861:16,14,11,19 chr1 110693447 . T C 609.96 PASS AC=1;AF=0.841;AN=2;DP=1762;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:19,10:29:99:279,0,582:6,13,2,8 chr1 110709719 . T C 2372.71 PASS AC=1;AF=0.691;AN=2;DP=2565;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,21:48:99:801,0,1577:13,14,12,9 chr1 110709720 . G A 802.17 PASS AC=1;AF=0.617;AN=2;DP=2267;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,21:48:99:801,0,1577:13,14,12,9 chr1 110714436 . A T 75.67 PASS AC=1;AF=0.611;AN=2;DP=516;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:233,0,229:6,1,6,1 chr1 110716511 . C T 814.9 PASS AC=1;AF=0.617;AN=2;DP=1712;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,12:36:99:365,0,886:21,3,9,3 chr1 110735037 . T G 234.41 PASS AC=2;AF=0.731;AN=2;DP=1023;FractionInformativeReads=1;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-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:789,60,0:0,0,16,4 chr1 110738296 . G A 2385.65 PASS AC=2;AF=0.679;AN=2;DP=6423;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,187:187:99:5476,559,0:0,0,99,88 chr1 110740273 . G T 883.68 PASS AC=2;AF=0.679;AN=2;DP=2187;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,68:69:99:2097,175,0:1,0,29,39 chr1 110740406 . C T 422.9 PASS AC=2;AF=0.679;AN=2;DP=866;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,21:22:20:642,20,0:0,1,6,15 chr1 110740688 . C T 736.42 PASS AC=2;AF=0.679;AN=2;DP=1905;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1223,113,0:0,0,25,13 chr1 110741349 . G T 836.62 PASS AC=2;AF=0.724;AN=2;DP=2252;FractionInformativeReads=1;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-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1839,176,0:0,0,30,29 chr1 110741583 . C G 959.41 PASS AC=2;AF=0.724;AN=2;DP=3201;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-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2361,228,0:0,0,36,40 chr1 110742085 . T C 598.28 PASS AC=2;AF=0.737;AN=2;DP=2388;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-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1685,167,0:0,0,29,27 chr1 110742502 . A G 88.36 PASS AC=2;AF=0.781;AN=2;DP=124;set=variant3-variant4-variant8-variant11-variant15-variant16-variant17-variant21-variant23-variant24-variant26-variant28-variant33-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:70,6,0:0,0,2,0 chr1 110742615 . A G 246.94 PASS AC=2;AF=0.679;AN=2;DP=717;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:559,51,0:0,0,12,5 chr1 110742992 . T G 370.51 PASS AC=2;AF=0.679;AN=2;DP=1340;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1254,111,0:0,0,22,15 chr1 110744874 . G A 918.52 PASS AC=1;AF=0.5;AN=2;DP=296;FractionInformativeReads=1;MQ=60;set=variant3-variant9-variant11-variant23-variant38 GT:AD:DP:GQ:PL:SB 0/1:17,28:45:99:646,0,345:7,10,12,16 chr1 110765535 . C G 358.85 PASS AC=2;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 1/1:0,39:39:99:1479,117,0:0,0,31,8 chr1 110881083 . ACT A 201.24 PASS AC=2;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 1/1:0,50:50:99:2176,151,0:0,0,30,20 chr1 110882444 . A G 3056.91 PASS AC=2;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 1/1:0,126:126:99:3776,377,0:0,0,67,59 chr1 110888948 . G A 472.46 PASS AC=2;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 1/1:0,54:54:99:1511,161,0:0,0,29,25 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 0/2:63:99:30,5,25,3 chr1 110917734 . G C 152.6 PASS AC=2;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 1/1:0,6:6:18:189,18,0:0,0,4,2 chr1 110922140 . G A 180.3 PASS AC=2;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 1/1:0,8:8:24:238,24,0:0,0,3,5 chr1 110949566 . G T 283.55 PASS AC=2;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 1/1:0,19:19:57:610,57,0:0,0,13,6 chr1 110949720 . C T 527.24 PASS AC=2;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 1/1:0,34:34:99:1063,102,0:0,0,14,20 chr1 110949857 . A T 872.21 PASS AC=2;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 1/1:0,71:71:99:2127,211,0:0,0,47,24 chr1 110950462 . G A 2756.85 PASS AC=2;AF=0.563;AN=2;DP=1600;MQ=60;set=variant-variant10-variant22-variant23-variant35-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,180:180:99:5054,537,0:0,0,85,95 chr1 110993739 . C A 1542.6 PASS AC=1;AF=0.5;AN=2;DP=694;MQ=60;set=variant3-variant23-variant25-variant26-variant32-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,20:55:99:616,0,1184:30,5,17,3 chr1 110999705 . C T 334.47 PASS AC=1;AF=0.5;AN=2;DP=82;FractionInformativeReads=1;MQ=60;set=variant18-variant23-variant32-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,6:19:99:165,0,456:3,10,1,5 chr1 111059812 . CGA CGAGA,C 551.28 PASS AC=1,0;AF=0.5,0.032;AN=2;DP=1635;set=variant-variant2-variant4-filterInvariant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-variant19-variant20-variant23-variant24-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant39-variant41-variant43 GT:DP:GQ:SB 0/1:43:99:13,1,22,7 chr1 111060669 . T C 1565.12 PASS AC=2;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 1/1:0,157:157:99:5083,470,0:0,0,66,91 chr1 111061062 . T C 1258.06 PASS AC=2;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 1/1:0,85:85:99:2777,255,0:0,0,40,45 chr1 111061653 . A G 159.64 PASS AC=1;AF=0.5;AN=2;DP=192;FractionInformativeReads=1;MQ=60;set=variant8-variant14-variant20-variant21-variant22-variant23-variant36 GT:AD:DP:GQ:PL:SB 0/1:5,16:21:99:521,0,120:1,4,9,7 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 1/1:0,28:28:84:992,84,0:0,0,23,5 chr1 111148416 . G C 88.5 PASS AC=1;AF=0.607;AN=2;DP=222;MQ=60;set=variant-variant4-variant8-variant9-variant10-variant12-variant13-variant14-variant17-variant19-variant23-variant28-variant33-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:377,0,308:5,7,2,9 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 1/1:0,4:4:12:180,12,0:0,0,4,0 chr1 111215472 . A C 3554.35 PASS AC=2;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 1/1:0,58:58:99:2273,174,0:0,0,15,43 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 0/2:22:99:10,5,4,3 chr1 111436857 . T G 2446.77 PASS AC=2;AF=0.739;AN=2;DP=5768;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:5745,388,0:0,0,77,52 chr1 111436858 . C T 2446.77 PASS AC=2;AF=0.739;AN=2;DP=5788;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:5745,388,0:0,0,76,52 chr1 111437129 . A C 539.19 PASS AC=2;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 1/1:0,54:54:99:1792,162,0:0,0,21,33 chr1 111437176 . G GA 678.17 PASS AC=2;AF=0.739;AN=2;DP=1209;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1035,96,0:0,0,10,22 chr1 111437421 . C A 1466.73 PASS AC=2;AF=0.784;AN=2;DP=1941;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:855,81,0:0,0,19,8 chr1 111441829 . C T 5138.69 PASS AC=2;AF=0.739;AN=2;DP=8626;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,207:207:99:6287,620,0:0,0,101,106 chr1 111442529 . A AAC 5980.9 PASS AC=2;AF=0.784;AN=2;DP=4820;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:4796,322,0:0,0,32,75 chr1 111442555 . G C 3345.2 PASS AC=2;AF=0.784;AN=2;DP=2893;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2183,192,0:0,0,16,48 chr1 111490542 . T A 2837.44 PASS AC=1;AF=0.5;AN=2;DP=273;FS=1.445;FractionInformativeReads=1;MQ=60;MQRankSum=1.823;QD=10.39;ReadPosRankSum=-0.313;SOR=0.602;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:145,128:273:99:2866,0,3550:69,76,64,64 chr1 111492807 . G A 685.84 PASS AC=2;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 1/1:0,22:22:66:812,66,0:0,0,3,19 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 1/1:0,72:72:99:2415,216,0:0,0,45,27 chr1 111663003 . CAAAAAAAAAAAAAAAAAAAAAA CA,CAAAAAAAAAAAAAAA,CAAAA,C,CAAAAAAAAA,CAAAAAAAAAAAAA,CAAAAAAAAAAAA 92.3 PASS AC=0,2,0,0,0,0,0;AF=0.182,0.182,0.045,0.182,0.091,0.045,0.045;AN=2;DP=92;MQ=60;set=variant2-variant3-variant16-variant18-variant20-variant21-variant22-variant23-variant34-variant37-variant42 GT:DP:GQ:SB 2/2:2:12:0,0,2,0 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 1/1:0,16:16:48:543,48,0:0,0,13,3 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 1/1:1,351:352:99:10331,1041,0:1,0,160,191 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 1/1:0,292:292:99:9504,886,0:0,0,154,138 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 1/1:0,43:43:99:1317,129,0:0,0,26,17 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 1/1:0,30:30:89:911,89,0:0,0,10,20 chr1 111727469 . CTT CTTT,CT,C 318.24 PASS AC=0,1,0;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 0/2:127:99:34,51,18,24 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 1/1:0,72:72:99:2445,216,0:0,0,20,52 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 1/1:0,38:38:99:1214,113,0:0,0,26,12 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 1/1:0,6:6:18:222,18,0:0,0,5,1 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 1/1:0,13:13:39:442,39,0:0,0,9,4 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 1/1:0,41:41:99:1564,123,0:0,0,27,14 chr1 111742841 . A G 506.46 PASS AC=1;AF=0.545;AN=2;DP=513;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant11-variant21-variant23-variant25-variant34-variant36-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,25:41:99:736,0,333:10,6,17,8 chr1 111743540 . C T 1052.55 PASS AC=1;AF=0.5;AN=2;DP=774;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant15-variant20-variant23-variant26-variant31-variant32-variant36-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,27:65:99:585,0,1068:18,20,11,16 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 0/1:78,69:147:99:1532,0,1881:46,32,38,31 chr1 111770423 . T G 3588.33 PASS AC=2;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 1/1:0,134:134:99:3928,401,0:0,0,61,73 chr1 111772303 . CAAAAA C,CAAAA,CAAAAAAAAAAA,CAAAAAA,CAAAAAAAAAAAA,CAA,CAAA 304.32 PASS AC=1,0,0,0,0,0,0;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 0/1:11:67:2,0,9,0 chr1 111773568 . G C 1203.62 PASS AC=2;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 1/1:0,78:78:99:2483,234,0:0,0,28,50 chr1 111773600 . A G 843.87 PASS AC=1;AF=0.5;AN=2;DP=429;MQ=60;set=variant3-variant7-variant20-variant22-variant23-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,20:48:99:532,0,858:7,21,8,12 chr1 111773830 . A T 822.41 PASS AC=2;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 1/1:1,57:58:99:1739,141,0:1,0,27,30 chr1 111778187 . A G 2318.79 PASS AC=2;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 1/1:1,58:59:99:1677,166,0:1,0,28,30 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 1/1:0,62:62:99:1864,185,0:0,0,32,30 chr1 111778824 . T C 822.72 PASS AC=2;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 1/1:0,19:19:57:659,57,0:0,0,4,15 chr1 111783942 . C T 771.59 PASS AC=1;AF=0.5;AN=2;DP=354;MQ=60;set=variant3-variant7-variant20-variant22-variant23-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,28:50:99:724,0,557:14,8,19,9 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 0/1:79:99:24,15,21,19 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 1/1:0,87:87:99:2591,261,0:0,0,47,40 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 0/1:54,42:96:99:986,0,1333:23,31,21,21 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 1/1:1,92:93:99:3230,237,0:1,0,43,49 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 0/1:51,35:86:99:769,0,1144:22,29,19,16 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 0/1:27,19:46:99:425,0,663:10,17,7,12 chr1 111785126 . C T 1670.08 PASS AC=1;AF=0.5;AN=2;DP=747;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant20-variant22-variant23-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,37:91:99:789,0,1332:26,28,17,20 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 0/1:16,24:40:99:840,0,530:5,11,8,16 chr1 111785930 . T C 2402.04 PASS AC=2;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 1/1:0,93:93:99:2825,279,0:0,0,40,53 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 0/1:26,27:53:99:684,0,599:11,15,8,19 chr1 111825883 . T C 1644.34 PASS AC=1;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 0/1:30,46:76:99:1102,0,615:16,14,21,25 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 0/1:31,27:58:99:621,0,795:14,17,10,17 chr1 111826023 . C G 786.78 PASS AC=1;AF=0.528;AN=2;DP=1230;FractionInformativeReads=1;set=variant2-variant4-variant5-variant7-variant10-variant12-variant13-variant14-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant31-variant32-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,25:47:99:615,0,495:9,13,11,14 chr1 111833270 . C T 597.61 PASS AC=1;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 0/1:4,7:11:99:222,0,141:4,0,7,0 chr1 111833441 . G A 3642.99 PASS AC=1;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 0/1:77,62:139:99:1397,0,1804:37,40,28,34 chr1 111833488 . C CCT 3386.9 PASS AC=1;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 0/1:55,34:89:99:1228,0,2140:19,36,12,22 chr1 111833517 . G A 1810.55 PASS AC=1;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 0/1:34,22:56:99:506,0,988:9,25,8,14 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 1/1:0,11:11:33:411,33,0:0,0,9,2 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 1/1:0,57:57:99:1766,171,0:0,0,39,18 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 1/1:0,7:7:21:271,21,0:0,0,5,2 chr1 111857087 . C T 899.79 PASS AC=2;AF=0.652;AN=2;DP=1598;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant36-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1230,111,0:0,0,26,11 chr1 111857107 . A G 879.61 PASS AC=1;AF=0.5;AN=2;DP=388;FractionInformativeReads=1;MQ=60;set=variant9-variant17-variant22-variant23-variant25-variant29-variant40 GT:AD:DP:GQ:PL:SB 0/1:26,19:45:99:454,0,713:18,8,10,9 chr1 111857120 . C A 1091.9 PASS AC=1;AF=0.5;AN=2;DP=458;FractionInformativeReads=1;MQ=60;set=variant9-variant17-variant22-variant23-variant25-variant29-variant40 GT:AD:DP:GQ:PL:SB 0/1:30,21:51:99:436,0,828:20,10,10,11 chr1 111857154 . T C 1357.66 PASS AC=2;AF=0.744;AN=2;DP=3645;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-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2325,219,0:0,0,43,30 chr1 111857208 . G A 1356.79 PASS AC=1;AF=0.5;AN=2;DP=883;MQ=60;set=variant9-variant17-variant22-variant23-variant25-variant29-variant40 GT:AD:DP:GQ:PL:SB 0/1:64,45:109:99:1039,0,1596:33,31,23,22 chr1 111857276 . T C 2174.66 PASS AC=1;AF=0.556;AN=2;DP=2262;MQ=60;set=variant3-variant7-variant9-variant11-variant13-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant29-variant30-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:49,50:99:99:1101,0,1145:21,28,26,24 chr1 111857685 . G C 165.95 PASS AC=1;AF=0.526;AN=2;DP=339;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant8-variant9-variant10-variant17-variant20-variant22-variant23-variant25-variant26-variant29-variant31-variant32-variant33-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,3:10:64:64,0,248:6,1,2,1 chr1 111858291 . T C 2730.59 PASS AC=2;AF=0.654;AN=2;DP=4162;MQ=60;set=variant3-variant4-variant6-variant7-variant9-variant12-variant13-variant14-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant27-variant29-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,152:152:99:4299,454,0:0,0,79,73 chr1 111858444 . C T 1490.99 PASS AC=2;AF=0.782;AN=2;DP=7252;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-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:4100,425,0:0,0,67,75 chr1 111858499 . A G 1072.51 PASS AC=2;AF=0.647;AN=2;DP=4545;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,97:99:99:2977,220,0:2,0,34,63 chr1 111858525 . TAAATATAAGAATAAGA T 1032.7 PASS AC=2;AF=0.647;AN=2;DP=3262;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,73:75:99:2255,175,0:1,1,24,49 chr1 111858542 . CACTATCCTTGGCTT C 1071.54 PASS AC=2;AF=0.647;AN=2;DP=2950;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,73:75:99:2254,174,0:1,1,24,49 chr1 111858589 . G T 944.7 PASS AC=2;AF=0.654;AN=2;DP=1182;MQ=60;set=variant3-variant4-variant6-variant7-variant9-variant12-variant13-variant14-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant27-variant29-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1481,135,0:0,0,14,31 chr1 111858603 . G T 792.32 PASS AC=2;AF=0.654;AN=2;DP=922;MQ=60;set=variant3-variant4-variant6-variant7-variant9-variant12-variant13-variant14-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant27-variant29-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1234,110,0:0,0,10,27 chr1 111861475 . A G 475.59 PASS AC=1;AF=0.5;AN=2;DP=255;FractionInformativeReads=1;MQ=60;set=variant9-variant17-variant22-variant23-variant25-variant29-variant40 GT:AD:DP:GQ:PL:SB 0/1:14,16:30:99:507,0,447:4,10,3,13 chr1 111861508 . T C 562.1 PASS AC=1;AF=0.625;AN=2;DP=372;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant7-variant12-variant13-variant14-variant16-variant19-variant23-variant24-variant25-variant27-variant33-variant34-variant36-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:307,0,333:0,9,5,5 chr1 111861714 . T A 580.92 PASS AC=2;AF=0.731;AN=2;DP=1925;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-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1342,126,0:0,0,27,15 chr1 111861841 . A G 993.55 PASS AC=2;AF=0.744;AN=2;DP=3939;FractionInformativeReads=1;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-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2679,258,0:0,0,42,44 chr1 111861974 . T C 795.53 PASS AC=1;AF=0.7;AN=2;DP=3204;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,59:97:99:1527,0,784:17,21,30,29 chr1 111862074 . C T 559.69 PASS AC=1;AF=0.5;AN=2;DP=416;FractionInformativeReads=1;MQ=60;set=variant9-variant17-variant22-variant23-variant25-variant29-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:26,16:42:99:334,0,666:9,17,6,10 chr1 111862952 . T G 1390.45 PASS AC=2;AF=0.744;AN=2;DP=5676;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-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,131:131:99:4027,392,0:0,0,67,64 chr1 111863306 . C T 227.73 PASS AC=1;AF=0.5;AN=2;DP=182;FractionInformativeReads=1;MQ=60;set=variant9-variant17-variant22-variant23-variant25-variant29-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:8,9:17:99:285,0,273:1,7,1,8 chr1 111890244 . C T 37.96 PASS AC=1;AF=0.542;AN=2;DP=840;set=filterInvariant2-variant3-variant4-filterInvariant5-variant6-variant8-filterInvariant10-filterInvariant11-filterInvariant14-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant31-variant33-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,8:27:99:261,0,472:14,5,7,1 chr1 111892905 . T C 621.48 PASS AC=1;AF=0.587;AN=2;DP=571;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant14-variant16-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant31-variant32-variant33-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,12:18:99:317,0,165:1,5,5,7 chr1 111893708 . G A 79.68 PASS AC=1;AF=0.543;AN=2;DP=223;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant14-variant16-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant31-variant32-variant33-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:73:162,0,73:2,0,4,0 chr1 111893788 . GTTTTT GTTT,GTT,G,GTTTT,GTTTTTT,GT 117.88 PASS AC=0,0,1,0,0,0;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 0/3:31:99:6,5,13,7 chr1 111893958 . A G 1346.77 PASS AC=1;AF=0.565;AN=2;DP=2768;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant14-variant16-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant31-variant32-variant33-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,37:104:99:823,0,1855:34,33,19,18 chr1 111894180 . G A 1046.88 PASS AC=1;AF=0.571;AN=2;DP=888;MQ=60;set=variant3-variant4-variant6-variant14-variant16-variant19-variant22-variant23-variant25-variant27-variant33-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,27:66:99:577,0,974:19,20,13,14 chr1 111895487 . C T 4918.48 PASS AC=1;AF=0.69;AN=2;DP=3511;set=variant3-variant4-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,43:102:99:1083,0,1644:27,32,17,26 chr1 111957097 . C G 1133.92 PASS AC=2;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 1/1:0,63:63:99:1819,189,0:0,0,32,31 chr1 111957245 . G A 2232 PASS AC=1;AF=0.625;AN=2;DP=2588;MQ=60;set=variant2-variant3-variant8-variant11-variant13-variant14-variant16-variant19-variant20-variant22-variant23-variant25-variant28-variant29-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,65:135:99:1374,0,1721:41,29,36,29 chr1 111957501 . CTCACAGACTGATGACTCACAGGGG C 2277.44 PASS AC=1;AF=0.611;AN=2;DP=3207;set=variant2-variant3-variant4-variant11-variant13-variant16-variant19-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,99:162:99:2504,0,3070:31,32,57,42 chr1 111957547 . GGGTCAGGGTCTTTTCCCCAGGGGTCACAGACTGATAACCCACAGA G 1923.93 PASS AC=1;AF=0.605;AN=2;DP=3268;set=variant2-variant3-variant4-variant11-variant13-variant16-variant19-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,65:138:99:2449,0,3741:38,35,32,33 chr1 111957688 . T C 1655.65 PASS AC=1;AF=0.545;AN=2;DP=1658;set=variant4-variant6-variant15-variant22-variant23-variant25-variant26-variant30-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:83,79:162:99:1962,0,2068:37,46,38,41 chr1 111957693 . A G 1449.04 PASS AC=2;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 1/1:2,158:160:99:5935,440,0:1,1,73,85 chr1 111958885 . C A 208.65 PASS AC=1;AF=0.5;AN=2;DP=227;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant15-variant18-variant23-variant25-variant26-variant30-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:13,8:21:99:195,0,361:10,3,6,2 chr1 111962209 . G A 794.1 PASS AC=1;AF=0.5;AN=2;DP=861;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant15-variant18-variant23-variant25-variant26-variant30-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:42,38:80:99:972,0,1032:21,21,21,17 chr1 111962256 . G T 793.69 PASS AC=1;AF=0.5;AN=2;DP=790;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant15-variant23-variant25-variant26-variant30-variant38 GT:AD:DP:GQ:PL:SB 0/1:46,46:92:99:941,0,1245:20,26,25,21 chr1 111964262 . G A 1484 PASS AC=1;AF=0.5;AN=2;DP=931;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant15-variant23-variant25-variant26-variant30-variant38 GT:AD:DP:GQ:PL:SB 0/1:40,52:92:99:1221,0,918:19,21,27,25 chr1 111966291 . C T 1114.15 PASS AC=1;AF=0.5;AN=2;DP=1248;MQ=60;set=variant3-variant11-variant13-variant16-variant19-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,34:73:99:879,0,984:18,21,15,19 chr1 111968316 . G A 213.97 PASS AC=2;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 1/1:0,10:10:30:401,30,0:0,0,1,9 chr1 111968327 . T C 187.23 PASS AC=2;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 1/1:0,9:9:27:402,27,0:0,0,0,9 chr1 111969294 . A G 2351.11 PASS AC=2;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 1/1:0,138:138:99:3991,413,0:0,0,65,73 chr1 111969307 . G C 2056.84 PASS AC=2;AF=0.6;AN=2;DP=3256;MQ=60;set=variant3-variant4-variant6-variant11-variant13-variant15-variant16-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:3985,419,0:0,0,65,75 chr1 111969719 . A G 2643.83 PASS AC=2;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 1/1:1,181:182:99:5263,533,0:0,1,85,96 chr1 111970431 . TACACACACACACACACACAC TACACACACACACACACACACAC,TACACACACACACACACAC,TACACACACACACACAC,TACACACACACACACACACACACACACACAC,TACACACACACAC,TACACACACACACAC,TACACACACACACACACACACACACACAC,TACACACACAC,TACACACACACACACACACACACACACACACACAC,TACACACACACACACACACACACAC,TACACACACACACACACACACACACACACACAC,TACACACACACACACACACACACACAC,T,TACACACAC 100.39 PASS AC=0,0,0,0,0,0,0,0,0,1,0,0,0,0;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 0/10:26:59:1,3,7,15 chr1 111982604 . T A 6639.67 PASS AC=1;AF=0.5;AN=2;DP=5645;MQ=60;set=variant3-variant11-variant13-variant16-variant19-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:170,154:324:99:3745,0,3967:86,84,78,76 chr1 111985229 . G T 1496.34 PASS AC=2;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 1/1:0,110:110:99:3386,330,0:0,0,65,45 chr1 111990265 . T C 1090.09 PASS AC=1;AF=0.5;AN=2;DP=1080;FractionInformativeReads=1;MQ=60;set=variant3-variant11-variant13-variant16-variant19-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,35:56:99:888,0,483:7,14,13,22 chr1 111991768 . G A 4200.53 PASS AC=1;AF=0.5;AN=2;DP=1825;MQ=60;set=variant4-variant6-variant15-variant23-variant25-variant26-variant30-variant38 GT:AD:DP:GQ:PL:SB 0/1:133,85:218:99:1855,0,3417:76,57,44,41 chr1 111991845 . C A 3165.86 PASS AC=2;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 1/1:3,203:206:99:5992,556,0:2,1,92,111 chr1 111992019 . T A 1385.44 PASS AC=1;AF=0.5;AN=2;DP=1944;MQ=60;set=variant4-variant6-variant9-variant15-variant18-variant22-variant23-variant25-variant26-variant30-variant32-variant34-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:51,55:106:99:1354,0,1288:24,27,29,26 chr1 111992095 . C T 2268.78 PASS AC=2;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 1/1:0,123:123:99:3611,368,0:0,0,63,60 chr1 111997063 . G T 652.15 PASS AC=1;AF=0.5;AN=2;DP=174;MQ=60;set=variant16-variant19-variant22-variant23-variant40 GT:AD:DP:GQ:PL:SB 0/1:23,10:33:99:246,0,532:10,13,4,6 chr1 112004122 . C G 4902.88 PASS AC=2;AF=0.6;AN=2;DP=5588;MQ=60;set=variant3-variant4-variant6-variant11-variant13-variant15-variant16-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,247:247:99:7997,740,0:0,0,83,164 chr1 112004523 . GA G,GAA 77.98 PASS AC=0,1;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 0/2:31:99:10,1,20,0 chr1 112005451 . C A 703.32 PASS AC=2;AF=0.6;AN=2;DP=982;MQ=60;set=variant3-variant4-variant6-variant11-variant13-variant15-variant16-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1855,173,0:0,0,21,37 chr1 112005509 . G T 332.59 PASS AC=1;AF=0.536;AN=2;DP=240;FractionInformativeReads=1;MQ=60;set=variant3-variant11-variant13-variant16-variant19-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:372,0,458:1,11,2,10 chr1 112018657 . G A 1626.91 PASS AC=1;AF=0.5;AN=2;DP=1773;MQ=60;set=variant3-variant11-variant13-variant16-variant19-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,44:101:99:973,0,1365:29,28,23,21 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 1/1:0,13:13:39:447,39,0:0,0,4,9 chr1 112020453 . C G 1092.58 PASS AC=1;AF=0.591;AN=2;DP=1124;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant15-variant21-variant23-variant25-variant26-variant30-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,48:84:99:1121,0,896:17,19,21,27 chr1 112021029 . A G 422.15 PASS AC=2;AF=0.625;AN=2;DP=948;MQ=60;set=variant3-variant4-variant6-variant11-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:984,96,0:0,0,12,20 chr1 112028344 . T C 170.49 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1064;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:66,14:80:99:206,0,3419:10,56,14,0 chr1 112028577 . A T 822.33 PASS AC=2;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 1/1:0,64:64:99:2223,191,0:0,0,13,51 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 0/1:26,26:52:99:607,0,619:11,15,13,13 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 0/1:57,49:106:99:1075,0,1365:28,29,25,24 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 0/1:43,23:66:99:483,0,1005:20,23,8,15 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 0/1:37,30:67:99:806,0,1073:13,24,10,20 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 0/1:21,12:33:99:419,0,958:6,15,1,11 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 0/1:19,10:29:99:387,0,961:5,14,1,9 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 0/1:29,30:59:99:695,0,666:16,13,18,12 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 0/1:32,31:63:99:731,0,779:17,15,18,13 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 0/1:32,25:57:99:610,0,772:14,18,12,13 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 0/1:24,24:48:99:641,0,629:10,14,10,14 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 0/1:18,19:37:99:521,0,552:11,7,11,8 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 0/1:57,58:115:99:1624,0,1420:25,32,23,35 chr1 112045632 . G A 927 PASS AC=1;AF=0.5;AN=2;DP=196;MQ=60;set=variant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:44,61:105:99:1443,0,1013:26,18,35,26 chr1 112106342 . C T 1524.77 PASS AC=1;AF=0.653;AN=2;DP=2374;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,35:69:99:891,0,950:22,12,22,13 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 1/1:0,126:126:99:3862,378,0:0,0,59,67 chr1 112162448 . C T 245.84 PASS AC=1;AF=0.5;AN=2;DP=17;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.342;QD=14.46;ReadPosRankSum=0.732;SOR=0.495;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:7,10:17:99:274,0,218:4,3,5,5 chr1 112234068 . T A 1299.53 PASS AC=2;AF=0.563;AN=2;DP=685;MQ=60;set=variant-variant12-variant17-variant23-variant31-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:1,86:87:99:2411,215,0:0,1,37,49 chr1 112251902 . C T 1205.62 PASS AC=2;AF=0.563;AN=2;DP=760;FractionInformativeReads=1;MQ=60;set=variant-variant12-variant17-variant23-variant31-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2511,258,0:0,0,44,42 chr1 112258545 . G T 6213.02 PASS AC=2;AF=0.619;AN=2;DP=3294;MQ=60;set=variant-variant3-variant6-variant11-variant12-variant14-variant16-variant17-variant19-variant23-variant26-variant28-variant31-variant32-variant34-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,145:145:99:4408,434,0:0,0,69,76 chr1 112259306 . A T 220.13 PASS AC=1;AF=0.5;AN=2;DP=25;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant39 GT:AD:DP:GQ:PL:SB 0/1:4,8:12:99:248,0,105:1,3,3,5 chr1 112269510 . C T 1191.32 PASS AC=1;AF=0.5;AN=2;DP=306;FractionInformativeReads=1;MQ=60;set=variant-variant23-variant31 GT:AD:DP:GQ:PL:SB 0/1:53,43:96:99:1021,0,1444:32,21,24,19 chr1 112298378 . T C 2886.01 PASS AC=1;AF=0.5;AN=2;DP=1681;MQ=60;set=variant-variant12-variant17-variant23-variant31-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:119,99:218:99:2443,0,2918:61,58,47,52 chr1 112298582 . A G 2687.6 PASS AC=1;AF=0.528;AN=2;DP=2733;MQ=60;set=variant3-variant7-variant9-variant11-variant14-variant15-variant16-variant18-variant19-variant23-variant30-variant31-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,68:149:99:1670,0,2037:36,45,29,39 chr1 112298829 . T C 67.47 PASS AC=2;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 1/1:0,25:25:75:795,75,0:0,0,6,19 chr1 112302208 . G T 1267.52 PASS AC=1;AF=0.5;AN=2;DP=905;MQ=60;set=variant-variant12-variant17-variant23-variant31-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:63,50:113:99:1342,0,1641:26,37,20,30 chr1 112302219 . G A 1159.46 PASS AC=2;AF=0.591;AN=2;DP=1362;FractionInformativeReads=1;MQ=60;set=variant-variant12-variant15-variant16-variant17-variant18-variant19-variant23-variant31-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3292,309,0:0,0,39,64 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 1/1:0,69:69:99:2451,207,0:0,0,26,43 chr1 112304137 . A G 988.96 PASS AC=1;AF=0.5;AN=2;DP=497;FractionInformativeReads=1;MQ=60;set=variant-variant12-variant17-variant23-variant31-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:35,25:60:99:766,0,909:13,22,8,17 chr1 112304184 . C G 754.28 PASS AC=1;AF=0.5;AN=2;DP=338;FractionInformativeReads=1;MQ=60;set=variant-variant12-variant17-variant23-variant31-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:22,17:39:99:550,0,610:6,16,8,9 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 0/1:92,27:119:99:179,0,1738:49,43,9,18 chr1 112308953 . T C 1492.65 PASS AC=2;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 1/1:0,74:74:99:2369,222,0:0,0,40,34 chr1 112308972 . G A 1438.6 PASS AC=2;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 1/1:0,79:79:99:2584,237,0:0,0,42,37 chr1 112313430 . GT G 2960.16 PASS AC=2;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 1/1:8,300:308:99:8010,720,0:5,3,161,139 chr1 112315450 . A C 3835.19 PASS AC=2;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 1/1:0,170:170:99:5751,510,0:0,0,59,111 chr1 112316030 . CT CTT,C 2124.21 PASS AC=2,0;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 1/1:164:99:0,1,45,118 chr1 112316047 . C CT,CTT 1770.97 PASS AC=2,0;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 1/1:83:53:0,8,20,55 chr1 112317135 . T C 200.88 PASS AC=2;AF=0.591;AN=2;DP=342;MQ=60;set=variant-variant12-variant15-variant16-variant17-variant18-variant19-variant23-variant31-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:990,102,0:0,0,17,17 chr1 112317196 . G C 270.54 PASS AC=2;AF=0.577;AN=2;DP=428;FractionInformativeReads=1;MQ=60;set=variant-variant12-variant15-variant16-variant17-variant18-variant19-variant23-variant31-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1011,96,0:0,0,17,15 chr1 112317512 . C A 818.86 PASS AC=2;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 1/1:0,67:67:99:2061,201,0:0,0,38,29 chr1 112320846 . T G 111.22 PASS AC=1;AF=0.6;AN=2;DP=76;FractionInformativeReads=1;MQ=60;set=variant14-variant15-variant16-variant18-variant19-variant22-variant23-variant31-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:29:104,0,29:2,0,2,2 chr1 112321032 . T A 1421.8 PASS AC=1;AF=0.533;AN=2;DP=965;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant9-variant11-variant14-variant15-variant16-variant18-variant19-variant23-variant30-variant31-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,26:47:99:642,0,471:14,7,15,11 chr1 112329551 . G T 562.62 PASS AC=1;AF=0.5;AN=2;DP=433;MQ=60;set=variant-variant12-variant22-variant23-variant27-variant29-variant31-variant32-variant39 GT:AD:DP:GQ:PL:SB 0/1:20,17:37:99:422,0,544:14,6,12,5 chr1 112329838 . G T 246.76 PASS AC=1;AF=0.5;AN=2;DP=334;MQ=60;set=variant-variant12-variant22-variant23-variant27-variant29-variant31-variant32-variant39 GT:AD:DP:GQ:PL:SB 0/1:14,22:36:99:595,0,346:4,10,8,14 chr1 112533728 . G A 1868.07 PASS AC=1;AF=0.536;AN=2;DP=1907;MQ=60;set=variant3-variant5-variant16-variant19-variant23-variant25-variant26-variant27-variant30-variant31-variant33-variant34-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:87,51:138:99:1071,0,2294:48,39,25,26 chr1 112534017 . T TG 389.02 PASS AC=1;AF=0.571;AN=2;DP=192;MQ=60;set=variant3-variant5-variant16-variant19-variant23-variant25-variant26-variant27-variant31-variant33-variant34-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:117,0,193:0,3,1,2 chr1 112534023 . C T 367.58 PASS AC=1;AF=0.538;AN=2;DP=166;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant16-variant19-variant23-variant25-variant26-variant27-variant31-variant33-variant34-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:117,0,193:0,3,1,2 chr1 112954766 . G C 3396.6 PASS AC=2;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 1/1:0,95:95:99:2897,284,0:0,0,60,35 chr1 112954964 . G A 2074.52 PASS AC=2;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 1/1:0,76:76:99:2475,228,0:0,0,24,52 chr1 112954994 . A G 1009.99 PASS AC=2;AF=0.92;AN=2;DP=2140;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1897,167,0:0,0,14,42 chr1 112991698 . T C 2594.14 PASS AC=2;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 1/1:0,80:80:99:2425,240,0:0,0,40,40 chr1 112999227 . G A 809.01 PASS AC=2;AF=0.92;AN=2;DP=5547;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:2986,284,0:0,0,48,47 chr1 113000946 . GGTCA G 4509.33 PASS AC=2;AF=0.909;AN=2;DP=8715;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,156:156:99:7012,471,0:0,0,80,76 chr1 113002127 . TA T 8573.62 PASS AC=2;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 1/1:1,222:223:99:7883,636,0:1,0,129,93 chr1 113009044 . T TA 81.06 PASS AC=1;AF=0.5;AN=2;DP=46;MQ=60;set=variant2-variant3-variant23-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:171,0,107:2,2,3,3 chr1 113051730 . C G 5458.37 PASS AC=1;AF=0.595;AN=2;DP=2638;MQ=60;set=variant3-variant4-variant5-variant6-variant8-variant9-variant14-variant15-variant17-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant32-variant34-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:68,69:137:99:1554,0,1705:41,27,34,35 chr1 113052155 . C G 2265.32 PASS AC=1;AF=0.595;AN=2;DP=1154;MQ=60;set=variant3-variant4-variant5-variant6-variant8-variant9-variant14-variant15-variant17-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant32-variant34-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,20:39:99:519,0,501:9,10,9,11 chr1 113052186 . G C 1988.53 PASS AC=1;AF=0.595;AN=2;DP=893;MQ=60;set=variant3-variant4-variant5-variant6-variant8-variant9-variant14-variant15-variant17-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant32-variant34-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,15:29:99:410,0,404:6,8,6,9 chr1 113059220 . T A 226.96 PASS AC=2;AF=0.786;AN=2;DP=228;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant15-variant16-variant19-variant20-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:407,33,0:0,0,2,9 chr1 113063933 . CTTTT CT,CTTTTT,CTTT,CTT,CTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTT,C 1535.24 PASS AC=0,0,1,0,0,0,0,0;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 0/3:116:99:22,53,15,26 chr1 113064350 . A G 393.24 PASS AC=1;AF=0.5;AN=2;DP=360;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant13-variant23-variant24-variant26-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:17,28:45:99:849,0,476:11,6,20,8 chr1 113068722 . G C 1434.73 PASS AC=1;AF=0.5;AN=2;DP=226;FractionInformativeReads=1;MQ=60;set=variant2-variant23 GT:AD:DP:GQ:PL:SB 0/1:56,60:116:99:1480,0,1496:24,32,26,34 chr1 113084805 . A G 182.45 PASS AC=1;AF=0.5;AN=2;DP=34;FractionInformativeReads=1;MQ=60;set=variant2-variant23 GT:AD:DP:GQ:PL:SB 0/1:7,10:17:99:372,0,227:1,6,0,10 chr1 113113938 . G A 863.06 PASS AC=1;AF=0.5;AN=2;DP=688;MQ=60;set=variant2-variant7-variant13-variant23-variant24-variant26-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:39,35:74:99:792,0,915:18,21,13,22 chr1 113196196 . TAA TA,T 41.97 PASS AC=2,0;AF=0.6,0.05;AN=2;DP=136;set=variant8-variant9-variant13-variant14-variant23-variant27-variant28-variant32-variant37-variant40 GT:DP:GQ:SB 1/1:7:21:0,0,7,0 chr1 113197203 . A G 929.89 PASS AC=1;AF=0.5;AN=2;DP=511;MQ=60;set=variant2-variant7-variant13-variant23-variant24-variant26-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:21,28:49:99:661,0,498:14,7,16,12 chr1 113202417 . G A 1003.72 PASS AC=2;AF=0.671;AN=2;DP=2600;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1258,134,0:0,0,27,18 chr1 113212984 . CTTTTTTTT CTTTTTTTTTTTT,CTTTTTTTTTT,C,CTTTTTTTTTTT,CTTTTTTT,CTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTTTTTT 1051.6 PASS AC=0,1,0,0,0,0,0,0,0,0;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 0/2:93:99:9,25,21,38 chr1 113234456 . G A 1771.32 PASS AC=2;AF=0.671;AN=2;DP=6295;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,153:154:99:4625,434,0:0,1,70,83 chr1 113238201 . T C 708.78 PASS AC=1;AF=0.5;AN=2;DP=531;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant13-variant23-variant24-variant26-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:23,32:55:99:760,0,614:9,14,11,21 chr1 113239478 . T C 661.87 PASS AC=2;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 1/1:0,89:89:99:2881,267,0:0,0,39,50 chr1 113242488 . C T 1449.51 PASS AC=2;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 1/1:1,136:137:99:4167,400,0:1,0,63,73 chr1 113244401 . CA C 459.5 PASS AC=1;AF=0.5;AN=2;DP=36;FS=3.296;FractionInformativeReads=1;MQ=60;MQRankSum=0.353;QD=12.76;ReadPosRankSum=0.995;SOR=1.387;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:21,15:36:99:497,0,716:7,14,3,12 chr1 113244433 . T C 288.36 PASS AC=2;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 1/1:0,23:23:69:825,69,0:0,0,6,17 chr1 113245532 . A C 49.21 PASS AC=1;AF=0.5;AN=2;DP=410;MQ=60;set=filterInvariant3-variant4-variant5-variant9-variant14-filterInvariant19-variant21-variant23-variant24-variant29-variant32-variant34-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:13,11:24:99:218,0,592:4,9,11,0 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 0/1:13,9:22:99:218,0,592:4,9,9,0 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 0/1:25,19:44:99:580,0,714:22,3,19,0 chr1 113248365 . A G 1217.7 PASS AC=2;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 1/1:0,128:128:99:4142,384,0:0,0,56,72 chr1 113249851 . C A 89.16 PASS AC=1;AF=0.5;AN=2;DP=28;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant23 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:197,0,129:3,1,4,3 chr1 113252614 . C A 929.41 PASS AC=2;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 1/1:0,68:68:99:2263,204,0:0,0,45,23 chr1 113254226 . G A 242.92 PASS AC=1;AF=0.5;AN=2;DP=97;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant23 GT:AD:DP:GQ:PL:SB 0/1:18,16:34:99:389,0,479:6,12,7,9 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 1/1:0,24:24:72:797,72,0:0,0,9,15 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 1/1:0,19:19:57:658,57,0:0,0,12,7 chr1 113254828 . C G 1746.64 PASS AC=1;AF=0.5;AN=2;DP=119;FS=1.502;FractionInformativeReads=1;MQ=60;MQRankSum=-1.151;QD=14.68;ReadPosRankSum=-0.745;SOR=0.548;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:48,71:119:99:1775,0,1240:29,19,40,31 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 1/1:0,14:14:42:387,42,0:0,0,7,7 chr1 113255686 . TTGTGTG TTGTGTGTG,TTGTGTGTGTG,TTGTG,T,TTG,TTGTGTGTGTGTG 80.4 PASS AC=1,0,0,0,0,0;AF=0.485,0.015,0.044,0.015,0.015,0.015;AN=2;DP=565;set=variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:6:72:1,2,0,3 chr1 113454424 . T C 735.91 PASS AC=1;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 0/1:17,16:33:99:484,0,531:15,2,12,4 chr1 113454571 . A G 2571.54 PASS AC=1;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 0/1:110,103:213:99:2310,0,2648:57,53,56,47 chr1 113455099 . G A 4658.17 PASS AC=1;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 0/1:137,124:261:99:3002,0,3583:70,67,53,71 chr1 113456368 . A C 6102.31 PASS AC=1;AF=0.5;AN=2;DP=884;FractionInformativeReads=1;MQ=60;set=variant2-variant23 GT:AD:DP:GQ:PL:SB 0/1:241,194:435:99:4437,0,5707:116,125,86,108 chr1 113456546 . A T 2615.55 PASS AC=1;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 0/1:57,49:106:99:1099,0,1489:28,29,19,30 chr1 113471629 . C CT 216.78 PASS AC=1;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 0/1:27,27:54:99:458,0,480:17,10,16,11 chr1 113498283 . A C 1339.42 PASS AC=1;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 0/1:30,30:60:99:1166,0,1725:14,16,13,17 chr1 113498284 . G A 1339.42 PASS AC=1;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 0/1:31,30:61:99:1166,0,1725:14,17,13,17 chr1 113616382 . G GA 459.36 PASS AC=2;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 1/1:0,20:20:60:712,60,0:0,0,4,16 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 1/1:0,11:11:33:373,33,0:0,0,8,3 chr1 113642815 . G C 613.46 PASS AC=1;AF=0.5;AN=2;DP=211;FractionInformativeReads=1;MQ=60;set=variant20-variant23-variant24-variant30-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,19:40:99:438,0,564:14,7,11,8 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 1/1:0,122:122:99:3799,364,0:0,0,75,47 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 1/1:0,95:95:99:3162,284,0:0,0,50,45 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 1/1:0,95:95:99:4192,286,0:0,0,40,55 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 1/1:0,7:7:21:196,21,0:0,0,6,1 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 1/1:1,18:19:45:483,45,0:0,1,14,4 chr1 114137013 . C CAT 496.09 PASS AC=1;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 0/1:8,3:11:99:102,0,314:8,0,3,0 chr1 114161116 . C A 236.23 PASS AC=1;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 0/1:15,7:22:99:165,0,347:6,9,2,5 chr1 114196364 . T G 337.67 PASS AC=1;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 0/1:28,39:67:99:918,0,624:16,12,22,17 chr1 114196495 . A G 788.41 PASS AC=1;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 0/1:42,47:89:99:1173,0,972:21,21,23,24 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 0/1:44:99:18,8,13,5 chr1 114240319 . T TA 2043.5 PASS AC=1;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 0/1:54,55:109:99:1714,0,1654:19,35,22,33 chr1 114242122 . T C 169.61 PASS AC=1;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 0/1:10,10:20:99:285,0,333:8,2,6,4 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 0/1:57,28:85:99:516,0,1443:30,27,16,12 chr1 114246453 . C T 223.27 PASS AC=1;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 0/1:13,3:16:79:79,0,371:9,4,2,1 chr1 114249382 . C T 878.68 PASS AC=1;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 0/1:18,15:33:99:443,0,510:5,13,4,11 chr1 114267347 . C T 867.58 PASS AC=1;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 0/1:20,18:38:99:435,0,583:11,9,12,6 chr1 114280717 . A C 163.58 PASS AC=1;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 0/1:27,19:46:99:535,0,843:20,7,13,6 chr1 114301335 . C T 864.14 PASS AC=1;AF=0.5;AN=2;DP=1219;MQ=60;set=variant-variant4-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:33,40:73:99:1037,0,824:22,11,22,18 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 1/1:0,17:17:51:765,51,0:0,0,5,12 chr1 114306368 . TA T 3115.24 PASS AC=1;AF=0.533;AN=2;DP=3675;MQ=60;set=variant-variant4-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:119,110:229:99:3075,0,3258:58,61,54,56 chr1 114307292 . GA G 1612.69 PASS AC=1;AF=0.533;AN=2;DP=3151;MQ=60;set=variant-variant4-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:87,87:174:99:1926,0,1777:49,38,43,44 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 1/1:0,18:18:54:746,54,0:0,0,2,16 chr1 114339956 . C CTAAA 436.29 PASS AC=1;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 0/1:17,12:29:99:484,0,1003:12,5,8,4 chr1 114357211 . G A 2103.48 PASS AC=1;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 0/1:38,51:89:99:1549,0,957:22,16,26,25 chr1 114372332 . TA T 608.67 PASS AC=1;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 0/1:20,19:39:99:394,0,419:8,12,10,9 chr1 114377093 . A G 1549.49 PASS AC=1;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 0/1:21,26:47:99:621,0,465:8,13,11,15 chr1 114377568 . A G 3643.61 PASS AC=1;AF=0.92;AN=2;DP=4977;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:51,55:106:99:1217,0,1009:23,28,26,29 chr1 114400195 . G GA 35.14 PASS AC=1;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 0/1:1,6:7:7:148,0,7:0,1,4,2 chr1 114401231 . A G 411.31 PASS AC=1;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 0/1:17,11:28:99:326,0,470:5,12,4,7 chr1 114401904 . T G 580.95 PASS AC=1;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 0/1:13,8:21:99:238,0,488:12,1,6,2 chr1 114406750 . C G 158.29 PASS AC=1;AF=0.5;AN=2;DP=21;FS=2.128;FractionInformativeReads=1;MQ=60;MQRankSum=0.634;QD=7.54;ReadPosRankSum=-1.828;SOR=1.688;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:14,7:21:99:187,0,443:9,5,6,1 chr1 114423544 . AC A 3598.73 PASS AC=1;AF=0.609;AN=2;DP=5327;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant10-variant12-variant15-variant17-variant18-variant19-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:126,79:205:99:2494,0,4258:63,63,43,36 chr1 114423653 . C T 2228.45 PASS AC=1;AF=0.587;AN=2;DP=3749;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant10-variant12-variant15-variant17-variant18-variant19-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:103,77:180:99:1795,0,2580:44,59,34,43 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 1/1:0,60:60:99:1892,179,0:0,0,23,37 chr1 114429340 . T C 1180.81 PASS AC=1;AF=0.625;AN=2;DP=1825;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant12-variant15-variant17-variant18-variant19-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,25:51:99:731,0,673:11,15,8,17 chr1 114429461 . G A 34.46 PASS AC=1;AF=0.591;AN=2;DP=107;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant11-variant13-variant16-variant19-variant20-variant21-variant22-variant23-variant36 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:159,0,116:0,3,0,4 chr1 114438951 . A G 1051.39 PASS AC=1;AF=0.625;AN=2;DP=2445;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant12-variant15-variant17-variant18-variant19-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,39:76:99:1011,0,889:21,16,20,19 chr1 114440258 . C G 43.27 PASS AC=2;AF=0.75;AN=2;DP=319;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-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:184,15,0:0,0,4,1 chr1 114443035 . C G 183.29 PASS AC=1;AF=0.58;AN=2;DP=663;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant11-variant13-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant31-variant32-variant34-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,8:25:99:160,0,508:5,12,3,5 chr1 114444444 . T G 983.63 PASS AC=1;AF=0.5;AN=2;DP=493;MQ=60;set=variant2-variant12-variant15-variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:37,45:82:99:1109,0,931:16,21,27,18 chr1 114447034 . G C 207.79 PASS AC=1;AF=0.58;AN=2;DP=890;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant11-variant13-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant31-variant32-variant34-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,24:49:99:593,0,612:16,9,16,8 chr1 114447565 . G A 1886.34 PASS AC=1;AF=0.609;AN=2;DP=3719;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant12-variant15-variant17-variant18-variant19-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:73,67:140:99:1535,0,1750:36,37,35,32 chr1 114447776 . C G 1393.15 PASS AC=2;AF=0.72;AN=2;DP=7147;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-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,154:154:99:4558,461,0:0,0,71,83 chr1 114447914 . G T 1449.15 PASS AC=1;AF=0.625;AN=2;DP=3025;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant12-variant15-variant17-variant18-variant19-variant22-variant23-variant25-variant26-variant28-variant30-variant31-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,48:90:99:1227,0,1019:21,21,24,24 chr1 114448389 . C T 753.22 PASS AC=1;AF=0.545;AN=2;DP=1060;MQ=60;set=variant-variant4-variant11-variant13-variant16-variant19-variant20-variant21-variant22-variant23-variant36 GT:AD:DP:GQ:PL:SB 0/1:42,50:92:99:1202,0,919:18,24,19,31 chr1 114449662 . T C 1373.15 PASS AC=1;AF=0.545;AN=2;DP=1380;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant11-variant13-variant16-variant19-variant20-variant21-variant22-variant23-variant36 GT:AD:DP:GQ:PL:SB 0/1:58,42:100:99:997,0,1269:32,26,26,16 chr1 114455801 . C A 269.07 PASS AC=1;AF=0.5;AN=2;DP=179;FractionInformativeReads=1;MQ=60;set=variant2-variant12-variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:19,18:37:99:443,0,522:7,12,6,12 chr1 114455907 . G A 527.76 PASS AC=1;AF=0.55;AN=2;DP=816;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant11-variant13-variant16-variant18-variant23-variant24-variant26-variant27-variant29-variant31-variant34-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,16:28:99:471,0,284:6,6,5,11 chr1 114456389 . TC T 347.95 PASS AC=1;AF=0.529;AN=2;DP=540;MQ=60;set=variant4-variant6-variant11-variant16-variant18-variant23-variant24-variant26-variant27-variant29-variant31-variant34-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,7:27:99:234,0,1273:12,8,5,2 chr1 114456398 . C A 361.65 PASS AC=1;AF=0.559;AN=2;DP=579;MQ=60;set=variant4-variant6-variant11-variant13-filterInvariant16-variant18-variant23-variant24-variant26-variant29-variant31-variant34-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,9:31:99:271,0,1310:13,9,6,3 chr1 114472218 . A G 337.51 PASS AC=2;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 1/1:0,31:31:93:1055,93,0:0,0,11,20 chr1 114472321 . C A 238.53 PASS AC=1;AF=0.611;AN=2;DP=498;MQ=60;set=variant-variant2-variant4-variant5-variant12-variant14-variant15-variant19-variant22-variant23-variant24-variant26-variant28-variant32-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:19,10:29:99:128,0,453:11,8,4,6 chr1 114472650 . C T 750.26 PASS AC=1;AF=0.5;AN=2;DP=832;MQ=60;set=variant4-variant6-variant8-variant11-variant16-variant18-variant23-variant24-variant26-variant27-variant29-variant31-variant34-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,14:41:99:259,0,636:12,15,5,9 chr1 114496607 . A G 159.61 PASS AC=1;AF=0.5;AN=2;DP=132;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant8-variant11-variant16-variant18-variant23-variant24-variant27-variant31-variant34-variant36-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:73:73,0,107:2,2,1,2 chr1 114504860 . G A 437.23 PASS AC=1;AF=0.5;AN=2;DP=600;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant8-variant11-variant16-variant18-variant23-variant24-variant26-variant27-variant31-variant34-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,9:34:99:173,0,650:16,9,5,4 chr1 114505000 . G A 1288.78 PASS AC=1;AF=0.5;AN=2;DP=2085;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant8-variant11-variant16-variant18-variant23-variant24-variant26-variant27-variant31-variant34-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,41:84:99:884,0,1128:23,20,22,19 chr1 114512939 . A T 1923.76 PASS AC=2;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 1/1:0,39:39:99:1276,117,0:0,0,12,27 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 0/1:78,68:146:99:1669,0,1949:40,38,39,29 chr1 114516330 . C T 1903.13 PASS AC=1;AF=0.5;AN=2;DP=2898;MQ=60;set=variant4-variant6-variant8-variant11-variant16-variant18-variant23-variant24-variant26-variant27-variant31-variant32-variant34-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,76:140:99:1965,0,1717:39,25,42,34 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 0/1:12,24:36:99:633,0,377:8,4,11,13 chr1 114521883 . C G 130.3 PASS AC=2;AF=0.763;AN=2;DP=258;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-variant31-variant32-variant34-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:131,12,0:0,0,3,1 chr1 114523465 . A G 1433.91 PASS AC=1;AF=0.611;AN=2;DP=1020;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant36-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,12:25:99:368,0,339:10,3,10,2 chr1 114524661 . C A 549.68 PASS AC=1;AF=0.556;AN=2;DP=756;MQ=60;set=variant4-variant6-variant11-variant12-variant16-variant18-variant23-variant24-variant26-variant27-variant31-variant32-variant34-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,13:30:99:272,0,364:7,10,6,7 chr1 114524980 . TG T 34.17 PASS AC=2;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 1/1:0,3:3:9:107,9,0:0,0,1,2 chr1 114631980 . C T 128.82 PASS AC=2;AF=0.625;AN=2;DP=364;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant16-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:144,15,0:0,0,3,2 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 0/1:11,5:16:99:110,0,278:6,5,3,2 chr1 114634228 . C T 749.23 PASS AC=1;AF=0.571;AN=2;DP=1031;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:24,23:47:99:561,0,686:15,9,13,10 chr1 114634367 . C CT 3534.96 PASS AC=2;AF=0.864;AN=2;DP=7284;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:7,145:152:99:3633,276,0:4,3,76,69 chr1 114634485 . T C 1961.46 PASS AC=1;AF=0.571;AN=2;DP=2936;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant12-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:57,63:120:99:1810,0,1435:27,30,24,39 chr1 114640807 . G A 52.74 PASS AC=1;AF=0.591;AN=2;DP=207;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant7-variant8-variant12-variant14-variant15-variant23-variant24-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,2:8:66:66,0,173:1,5,0,2 chr1 114641685 . A G 2527.95 PASS AC=2;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 1/1:0,71:71:99:2100,213,0:0,0,44,27 chr1 114680540 . C T 1340.48 PASS AC=1;AF=0.575;AN=2;DP=5040;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant10-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant28-variant34-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:116,99:215:99:2344,0,2999:55,61,40,59 chr1 114682028 . G A 500.67 PASS AC=1;AF=0.55;AN=2;DP=622;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant10-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant28-variant34-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:6,17:23:99:496,0,122:3,3,11,6 chr1 114682780 . G C 201.22 PASS AC=1;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 0/1:1,5:6:28:140,0,28:0,1,1,4 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 0/1:37,61:98:99:1718,0,858:16,21,23,38 chr1 114938090 . A AT 2931.84 PASS AC=2;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 1/1:0,154:154:99:4622,463,0:0,0,91,63 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 0/1:53,60:113:99:1556,0,1502:19,34,28,32 chr1 114939730 . G GA 4816.92 PASS AC=1;AF=0.5;AN=2;DP=2372;MQ=60;set=variant4-variant23-variant27-variant36-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:148,157:305:99:4035,0,3672:77,71,86,71 chr1 114940211 . GT GTT,G 255.92 PASS AC=1,0;AF=0.462,0.038;AN=2;DP=761;set=variant-variant2-variant4-variant6-variant7-filterInvariant8-filterInvariant15-variant22-filterInvariant23-variant36-variant37-variant41-variant42 GT:DP:GQ:SB 0/1:45:99:9,25,4,7 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 0/1:21,33:54:99:866,0,608:6,15,9,24 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 0/1:37:99:7,10,5,15 chr1 114942296 . T C 229.81 PASS AC=1;AF=0.5;AN=2;DP=59;FS=0;FractionInformativeReads=1;MQ=60;set=variant4-variant23-variant27-variant36-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:156,0,159:0,4,0,4 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 1/1:0,187:187:99:5766,561,0:0,0,92,95 chr1 114949820 . T C 125.97 PASS AC=1;AF=0.5;AN=2;DP=49;FS=0;FractionInformativeReads=1;MQ=60;set=variant4-variant23-variant27-variant36-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:75:75,0,108:0,3,0,2 chr1 114951220 . C T 271.93 PASS AC=2;AF=0.679;AN=2;DP=92;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant8-variant13-variant14-variant16-variant20-variant23-variant27-variant28-variant31-variant32-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:214,15,0:0,0,5,0 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 0/1:26,30:56:99:649,0,586:13,13,15,15 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 0/1:33,43:76:99:1111,0,796:12,21,20,23 chr1 114973429 . T C 1872.89 PASS AC=2;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 1/1:0,124:124:99:3729,371,0:0,0,65,59 chr1 115006230 . TAA TA,T 231.02 PASS AC=2,0;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 1/1:11:33:0,0,1,10 chr1 115110683 . A C 4517.22 PASS AC=2;AF=0.662;AN=2;DP=9866;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,258:258:99:7670,773,0:0,0,117,141 chr1 115110989 . C CT 206.56 PASS AC=1;AF=0.607;AN=2;DP=916;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-filterInvariant11-variant13-variant14-variant15-variant17-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant34-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,14:16:2:271,0,2:0,2,4,10 chr1 115126114 . AAC A,AACAC,AACACAC,AACACACAC 60.97 PASS AC=1,0,0,0;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 0/1:57:99:14,33,2,8 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 0/1:34:49:5,2,24,3 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 1/1:0,93:93:99:2936,279,0:0,0,52,41 chr1 115144304 . C T 40.7 PASS AC=2;AF=0.571;AN=2;DP=215;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant11-variant12-variant13-variant14-variant17-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant34-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:217,21,0:0,0,2,5 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 1/1:0,116:116:99:3645,348,0:0,0,59,57 chr1 115161140 . C T 336.48 PASS AC=2;AF=0.545;AN=2;DP=319;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant11-variant12-variant13-variant14-variant17-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant34-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:420,39,0:0,0,4,9 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 1/1:0,12:12:36:534,36,0:0,0,12,0 chr1 115166350 . ATTGT A 277.87 PASS AC=2;AF=0.943;AN=2;DP=256;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-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:225,15,0:0,0,0,5 chr1 115168600 . A T 2912.08 PASS AC=2;AF=0.545;AN=2;DP=4766;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant11-variant12-variant13-variant14-variant17-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant34-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:2,209:211:99:6359,582,0:1,1,105,104 chr1 115168822 . C T 1669.89 PASS AC=2;AF=0.545;AN=2;DP=2219;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant11-variant12-variant13-variant14-variant17-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant34-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2635,231,0:0,0,22,55 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 0/1:58,78:136:99:1133,0,721:22,36,34,44 chr1 115220419 . C CTT 38.19 PASS AC=2;AF=0.667;AN=2;DP=90;set=variant4-variant17-variant21-variant23-variant28-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:20:232,20,0:0,0,2,5 chr1 115220420 . CTCCTTCCTTCCTTCCT CTCCTTCCTTCCT,CTCCTTCCTTCCTTCCTTCCTTCCTTCCT,CCTTCCTTCCTTCCTTCCT,CTCCTTCCTTCCTTCCTTCCT,CTCCT,CTCCTTCCTTCCTTCCTTCCTTCCT,CCTTCCTTCCTTCCTTCCTTCCT,CCTTCCTTCCTTCCTTCCTTCCTTCCT,CTCCTTCCT,C 188.27 PASS AC=0,0,1,0,0,0,0,1,0,0;AF=0.208,0.111,0.056,0.097,0.056,0.111,0.042,0.014,0.083,0.014;AN=2;DP=542;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant10-variant40-variant-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 3/8:7:86:0,0,1,6 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 1/1:0,9:9:27:358,27,0:0,0,1,8 chr1 115238016 . CAA CA,CAAA,C 708.48 PASS AC=1,0,0;AF=0.636,0.057,0.045;AN=2;DP=2106;set=Intersection GT:DP:GQ:SB 0/1:53:17:4,3,34,12 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 0/1:105,88:193:99:2447,0,2832:42,63,40,48 chr1 115256669 . G A 566.72 PASS AC=1;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 0/1:21,18:39:99:471,0,683:4,17,4,14 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 0/1:17:90:9,3,4,1 chr1 115279360 . T G 892.27 PASS AC=1;AF=0.5;AN=2;DP=61;FS=0.968;FractionInformativeReads=1;MQ=60;MQRankSum=2.737;QD=14.63;ReadPosRankSum=-0.878;SOR=0.859;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:27,34:61:99:921,0,570:13,14,15,19 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 0/1:35,27:62:99:584,0,1037:24,11,15,12 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 0/1:13,19:32:99:488,0,357:3,10,6,13 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 0/1:56,47:103:99:1925,0,3213:40,16,31,16 chr1 115313051 . T C 3091.49 PASS AC=1;AF=0.5;AN=2;DP=2982;MQ=60;set=variant-variant2-variant4-variant5-variant11-variant12-variant13-variant17-variant23-variant24-variant25-variant27-variant31-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:89,82:171:99:2858,0,4094:62,27,57,25 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 0/1:3,7:10:57:180,0,57:1,2,4,3 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 1/1:0,28:28:84:864,84,0:0,0,17,11 chr1 115399757 . CA C,CAA,CAAA,CAAAA 50.05 PASS AC=0,2,0,0;AF=0.056,0.278,0.278,0.111;AN=2;DP=73;MQ=60;set=variant2-variant7-variant12-variant21-variant23-variant28-variant38-variant42-variant43 GT:DP:GQ:SB 2/2:8:25:0,0,5,3 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 0/1:37,20:57:99:453,0,841:19,18,8,12 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 1/1:0,33:33:99:1133,99,0:0,0,24,9 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 0/1:10,20:30:99:506,0,283:2,8,7,13 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 0/1:30,16:46:99:271,0,788:17,13,10,6 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 0/1:1,5:6:28:158,0,28:1,0,4,1 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 0/1:10,8:18:99:262,0,277:3,7,2,6 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 0/1:85,67:152:99:1623,0,1974:45,40,32,35 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 1/1:0,164:164:99:5049,491,0:0,0,93,71 chr1 115576175 . G A 1794.33 PASS AC=1;AF=0.5;AN=2;DP=1442;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant12-variant13-variant16-variant23-variant25-variant33-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:50,41:91:99:1034,0,1540:14,36,16,25 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 0/1:28:99:7,13,2,6 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 0/1:34,19:53:99:426,0,722:17,17,11,8 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 0/1:42,39:81:99:801,0,1590:22,20,20,19 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 0/1:39,41:80:99:819,0,1505:20,19,21,20 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 0/1:40,32:72:99:865,0,1047:25,15,21,11 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 0/1:211,177:388:99:6680,0,8113:106,105,95,82 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 0/1:88,90:178:99:2362,0,2467:42,46,45,45 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 1/1:0,41:41:99:1330,122,0:0,0,11,30 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 1/1:0,138:138:99:4138,412,0:0,0,76,62 chr1 116206407 . C T 2986.48 PASS AC=1;AF=0.5;AN=2;DP=473;FractionInformativeReads=1;MQ=60;set=variant23-variant43 GT:AD:DP:GQ:PL:SB 0/1:117,123:240:99:3015,0,2879:62,55,69,54 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 1/1:0,31:31:92:1040,92,0:0,0,22,9 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 1/1:1,36:37:99:1195,101,0:1,0,25,11 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 1/1:0,25:25:75:1020,75,0:0,0,3,22 chr1 116228220 . C T 186.16 PASS AC=2;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 1/1:0,30:30:90:1004,90,0:0,0,9,21 chr1 116234313 . A G 625.63 PASS AC=1;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 0/1:36,26:62:99:724,0,1015:17,19,10,16 chr1 116234505 . A G 773.41 PASS AC=1;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 0/1:28,24:52:99:661,0,780:11,17,12,12 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 0/1:132,123:255:99:2966,0,3271:67,65,54,69 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 0/1:131,127:258:99:3045,0,3038:73,58,61,66 chr1 116243230 . C G 2248.67 PASS AC=1;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 0/1:53,71:124:99:1646,0,1176:30,23,41,30 chr1 116243380 . G A 979.63 PASS AC=1;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 0/1:31,32:63:99:809,0,794:11,20,10,22 chr1 116245809 . C T 289.6 PASS AC=1;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 0/1:14,13:27:99:301,0,408:3,11,5,8 chr1 116247790 . G A 779.38 PASS AC=1;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 0/1:33,26:59:99:662,0,828:21,12,16,10 chr1 116260532 . A T 912.98 PASS AC=1;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 0/1:32,30:62:99:701,0,886:14,18,13,17 chr1 116260604 . G A 451.95 PASS AC=1;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 0/1:18,15:33:99:447,0,499:7,11,3,12 chr1 116268178 . GAAAA GAA,GA,GAAA,G,GAAAAA 187.7 PASS AC=1,0,0,0,0;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 0/1:27:99:3,10,5,9 chr1 116268283 . C T 324.84 PASS AC=1;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 0/1:13,6:19:99:132,0,397:3,10,4,2 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 1/1:0,67:67:99:1985,201,0:0,0,36,31 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 1/1:0,29:29:87:952,87,0:0,0,10,19 chr1 116287634 . A G 1135.48 PASS AC=1;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 0/1:20,23:43:99:629,0,646:4,16,7,16 chr1 116287651 . G A 795.79 PASS AC=1;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 0/1:15,15:30:99:422,0,391:4,11,3,12 chr1 116287682 . T C 860.7 PASS AC=1;AF=0.621;AN=2;DP=568;MQ=60;set=variant-variant3-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:250,0,351:2,9,3,6 chr1 116310818 . G C 282.99 PASS AC=1;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 0/1:7,9:16:99:269,0,222:6,1,7,2 chr1 116310967 . T C 5107.94 PASS AC=1;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 0/1:64,90:154:99:2139,0,1436:34,30,51,39 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 1/1:0,41:41:99:1371,123,0:0,0,22,19 chr1 116311366 . GCACACA GCACACACACACACA,GCACACACACACA,G 318.35 PASS AC=1,0,0;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 0/1:9:99:1,4,0,4 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 0/1:40,46:86:99:1179,0,995:14,26,17,29 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 0/1:24,25:49:99:613,0,660:14,10,13,12 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 1/1:0,72:72:99:2306,215,0:0,0,37,35 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 1/1:0,60:60:99:1961,180,0:0,0,31,29 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 1/1:0,96:96:99:3035,288,0:0,0,46,50 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 1/1:0,104:104:99:3631,311,0:0,0,28,76 chr1 116383364 . AT ATTT,A,ATT,ATTTT 512.1 PASS AC=1,0,1,0;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 3/1:34:99:0,2,11,21 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 1/1:0,149:149:99:4842,446,0:0,0,78,71 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 0/1:142,118:260:99:3097,0,3689:60,82,40,78 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 0/1:52,44:96:99:971,0,1271:26,26,21,23 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 0/1:21,24:45:99:666,0,554:9,12,11,13 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 0/1:19,26:45:99:582,0,538:8,11,12,14 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 0/1:15,17:32:99:497,0,377:7,8,9,8 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 0/1:22,12:34:99:310,0,589:11,11,6,6 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 0/1:21,16:37:99:446,0,586:12,9,8,8 chr1 116385721 . T C 198.61 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2441;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:51,21:72:99:260,0,1140:4,47,21,0 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 1/1:1,76:77:99:2385,220,0:1,0,32,44 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 0/1:95,91:186:99:2254,0,2228:56,39,57,34 chr1 116386543 . G A 355.22 PASS AC=1;AF=0.667;AN=2;DP=114;FS=0;MQ=60;set=variant4-variant14-variant23-variant39-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:252,0,298:0,8,0,7 chr1 116534852 . C T 2165.52 PASS AC=2;AF=0.773;AN=2;DP=3592;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:2783,281,0:0,0,45,49 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 1/1:0,33:33:99:1068,99,0:0,0,21,12 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 1/1:0,48:48:99:1587,144,0:0,0,21,27 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 1/1:0,28:28:84:999,84,0:0,0,6,22 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 1/1:0,19:19:57:836,57,0:0,0,1,18 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 1/1:0,85:85:99:2929,256,0:0,0,52,33 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 1/1:0,262:262:99:7852,784,0:0,0,108,154 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 1/1:0,67:67:99:2140,201,0:0,0,37,30 chr1 116610599 . G GA 7231.31 PASS AC=2;AF=0.75;AN=2;DP=7786;MQ=60;set=variant-variant2-variant4-variant6-variant10-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:4,231:235:99:6634,594,0:1,3,118,113 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 1/1:0,173:173:99:5268,518,0:0,0,86,87 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 1/1:0,81:81:99:2722,243,0:0,0,28,53 chr1 116677253 . C T 400.3 PASS AC=1;AF=0.5;AN=2;DP=185;FractionInformativeReads=1;MQ=60;set=variant23-variant24-variant32-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,17:38:99:429,0,549:11,10,8,9 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 1/1:0,12:12:36:493,36,0:0,0,2,10 chr1 116940481 . CT C,CTT 65.51 PASS AC=0,1;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 0/2:96:85:45,34,10,7 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 1/1:0,42:42:99:1341,126,0:0,0,16,26 chr1 117078462 . CAAA CA,CAA,C 85.62 PASS AC=0,1,0;AF=0.333,0.083,0.083;AN=2;DP=67;set=variant2-variant3-variant15-variant23-variant24-variant33 GT:DP:GQ:SB 0/2:10:41:1,3,6,0 chr1 117121865 . G A 412.2 PASS AC=1;AF=0.632;AN=2;DP=359;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant10-variant11-variant13-filterInvariant18-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant34-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:368,0,333:10,1,10,2 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 0/1:109,78:187:99:2842,0,6530:59,50,44,34 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 0/1:114,107:221:99:3955,0,6478:62,52,57,50 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 0/1:15,17:32:99:515,0,400:10,5,13,4 chr1 117142583 . T A 305.71 PASS AC=1;AF=0.5;AN=2;DP=873;set=variant4-filterInvariant13-variant14-variant18-variant19-filterInvariant21-filterInvariant23-variant26-filterInvariant28-filterInvariant37-filterInvariant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:60,9:69:99:103,0,1695:35,25,8,1 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 0/1:81,31:112:99:645,0,2262:47,34,23,8 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 0/1:97,57:154:99:1252,0,2591:54,43,39,18 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 0/1:138,97:235:99:2154,0,3537:74,64,61,36 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 0/1:152,115:267:99:2449,0,3556:79,73,66,49 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 0/1:119,108:227:99:2529,0,2981:51,68,48,60 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 0/1:116,95:211:99:3624,0,5701:50,66,41,54 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 0/1:116,95:211:99:3624,0,5701:50,66,41,54 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 0/2:117:99:39,47,9,22 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 0/1:10,7:17:99:161,0,270:7,3,5,2 chr1 117146423 . C T 35.27 PASS AC=1;AF=0.5;AN=2;DP=1569;FractionInformativeReads=1;set=filterInvariant4-variant8-filterInvariant19-filterInvariant23-filterInvariant34-filterInvariant36-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:177,26:203:99:201,0,4839:105,72,20,6 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 0/1:291,116:407:99:1619,0,7194:142,149,60,56 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 0/1:237,95:332:99:3013,0,9443:99,138,41,54 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 0/1:221,82:303:99:2812,0,9061:88,133,33,49 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 0/1:188,69:257:99:2343,0,8083:73,115,25,44 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 0/1:174,65:239:99:2200,0,7174:62,112,23,42 chr1 117146629 . T C 217.21 PASS AC=1;AF=0.5;AN=2;DP=1982;set=filterInvariant3-filterInvariant5-variant8-filterInvariant9-filterInvariant12-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant23-variant27-filterInvariant33-filterInvariant34-filterInvariant37-filterInvariant39-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:98,15:113:99:121,0,2847:32,66,1,14 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 0/1:35,24:59:99:857,0,1638:12,23,8,16 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 0/1:32,22:54:99:860,0,1599:12,20,7,15 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 0/1:22,11:33:99:226,0,591:7,15,4,7 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 0/1:4,3:7:99:103,0,211:1,3,1,2 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 0/1:3,3:6:99:103,0,211:1,2,1,2 chr1 117156326 . C T 220.39 PASS AC=1;AF=0.5;AN=2;DP=3001;FractionInformativeReads=1;set=variant-filterInvariant2-variant3-variant4-filterInvariant5-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-variant20-variant22-filterInvariant23-filterInvariant24-variant26-variant27-filterInvariant28-variant29-variant31-variant32-filterInvariant33-variant34-filterInvariant36-variant37-variant39-variant41-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,10:92:99:170,0,3435:44,38,9,1 chr1 117156333 . T C 290.13 PASS AC=1;AF=0.5;AN=2;DP=3612;FractionInformativeReads=1;set=variant-filterInvariant2-variant3-variant4-filterInvariant5-filterInvariant6-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant15-filterInvariant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-filterInvariant25-variant26-variant27-filterInvariant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-filterInvariant36-variant37-variant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,11:98:99:237,0,3637:49,38,9,2 chr1 117156340 . C T 350.62 PASS AC=1;AF=0.5;AN=2;DP=3992;set=variant-filterInvariant2-variant3-variant4-filterInvariant5-filterInvariant6-variant8-variant9-variant10-variant11-variant12-variant13-filterInvariant15-filterInvariant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-filterInvariant25-variant26-variant27-filterInvariant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-filterInvariant36-variant37-variant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:90,18:108:99:359,0,3661:50,40,13,5 chr1 117156418 . G A 450.95 PASS AC=1;AF=0.5;AN=2;DP=1728;set=filterInvariant3-filterInvariant11-variant21-filterInvariant23-filterInvariant24-variant25-variant27-variant29-filterInvariant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:140,23:163:99:116,0,3682:69,71,12,11 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 0/1:97,64:161:99:1136,0,2527:51,46,34,30 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 0/1:91,53:144:99:1052,0,2425:50,41,28,25 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 0/1:132,30:162:99:856,0,8257:70,62,11,19 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 0/1:132,30:162:99:851,0,8286:69,63,11,19 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 0/1:129,26:155:99:695,0,8027:65,64,10,16 chr1 117158898 . C T 62.52 PASS AC=1;AF=0.5;AN=2;DP=664;set=filterInvariant8-filterInvariant9-filterInvariant11-variant12-filterInvariant15-filterInvariant18-variant23-filterInvariant24-filterInvariant27-filterInvariant29-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:39,12:51:99:162,0,1060:16,23,8,4 chr1 117158909 . C T 100.49 PASS AC=1;AF=0.5;AN=2;DP=696;set=filterInvariant8-variant9-filterInvariant11-variant12-filterInvariant15-filterInvariant17-variant18-variant23-filterInvariant24-filterInvariant27-filterInvariant29-variant40-variant41-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:33,13:46:99:197,0,913:14,19,8,5 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 0/1:28,15:43:99:246,0,785:11,17,8,7 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 0/1:20,16:36:99:288,0,440:7,13,8,8 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 0/1:9,6:15:99:120,0,240:2,7,1,5 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 1/1:0,55:55:99:1853,165,0:0,0,15,40 chr1 117297734 . A G 3266.44 PASS AC=1;AF=0.595;AN=2;DP=1485;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant17-variant19-variant20-variant23-variant25-variant26-variant27-variant30-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,34:78:99:1003,0,1288:10,34,7,27 chr1 117297784 . A G 721.35 PASS AC=2;AF=0.64;AN=2;DP=684;MQ=60;set=variant-variant7-variant8-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1214,87,0:0,0,1,28 chr1 117487270 . G A 876.64 PASS AC=1;AF=0.625;AN=2;DP=550;MQ=60;set=variant-variant5-variant9-variant11-variant12-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant31-variant32-variant33-variant34-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:14,5:19:99:124,0,365:6,8,4,1 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 1/1:0,98:98:99:4348,295,0:0,0,39,59 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 1/1:0,96:96:99:4348,295,0:0,0,38,58 chr1 117487884 . G A 838.55 PASS AC=1;AF=0.756;AN=2;DP=798;FractionInformativeReads=1;MQ=60;set=variant-variant2-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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,10:13:68:271,0,68:0,3,4,6 chr1 117509981 . G A 5716.6 PASS AC=1;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 0/1:31,41:72:99:1563,0,1280:14,17,15,26 chr1 117509987 . C T 5750.85 PASS AC=1;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 0/1:31,39:70:99:1536,0,1280:14,17,14,25 chr1 117510061 . C T 2192.17 PASS AC=1;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 0/1:9,18:27:99:561,0,218:3,6,4,14 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 1/1:0,66:66:99:2962,199,0:0,0,23,43 chr1 117529458 . G A 535.38 PASS AC=1;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 0/1:55,64:119:99:1419,0,1269:30,25,38,26 chr1 117529965 . A G 986.17 PASS AC=1;AF=0.5;AN=2;DP=306;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant12-variant23-variant28 GT:AD:DP:GQ:PL:SB 0/1:22,28:50:99:722,0,639:13,9,12,16 chr1 117530193 . CTTTTT CTTT,CTT,C,CT,CTTTT 213.95 PASS AC=0,2,0,0,0;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 2/2:18:42:0,1,5,12 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 1/1:0,14:14:42:522,42,0:0,0,8,6 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 1/1:0,31:31:93:949,93,0:0,0,14,17 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 1/1:0,31:31:93:1395,93,0:0,0,16,15 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 1/1:0,31:31:93:1395,93,0:0,0,16,15 chr1 117531122 . A G 653.66 PASS AC=1;AF=0.5;AN=2;DP=260;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant12-variant23-variant28 GT:AD:DP:GQ:PL:SB 0/1:24,17:41:99:364,0,651:10,14,7,10 chr1 117531620 . G A 256.59 PASS AC=1;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 0/1:9,11:20:99:305,0,345:4,5,7,4 chr1 117531627 . A G 540.99 PASS AC=1;AF=0.5;AN=2;DP=137;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant12-variant23-variant28 GT:AD:DP:GQ:PL:SB 0/1:12,9:21:99:236,0,469:8,4,5,4 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 1/1:0,53:53:99:1630,159,0:0,0,28,25 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 1/1:0,43:43:99:1396,129,0:0,0,18,25 chr1 117532035 . G A 706.47 PASS AC=1;AF=0.5;AN=2;DP=70;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.591;QD=10.09;ReadPosRankSum=-1.076;SOR=0.73;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:39,31:70:99:735,0,961:21,18,17,14 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 1/1:0,213:213:99:6351,641,0:0,0,102,111 chr1 117532509 . C A 1102.49 PASS AC=1;AF=0.5;AN=2;DP=412;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant12-variant23-variant28 GT:AD:DP:GQ:PL:SB 0/1:39,61:100:99:1581,0,998:14,25,25,36 chr1 117532790 . C T 5244.14 PASS AC=1;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 0/1:125,128:253:99:3334,0,3113:73,52,80,48 chr1 117532891 . T C 4451.49 PASS AC=1;AF=0.5;AN=2;DP=1440;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant12-variant23-variant28 GT:AD:DP:GQ:PL:SB 0/1:153,153:306:99:3491,0,3609:69,84,69,84 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 1/1:0,99:99:99:4447,298,0:0,0,32,67 chr1 117552560 . T C 1280.94 PASS AC=1;AF=0.5;AN=2;DP=727;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant12-variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:74,55:129:99:1276,0,1783:36,38,30,25 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 1/1:0,31:31:93:1067,93,0:0,0,24,7 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 1/1:0,94:94:99:2876,281,0:0,0,56,38 chr1 117560058 . C G 676.25 PASS AC=1;AF=0.5;AN=2;DP=229;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant12-variant23 GT:AD:DP:GQ:PL:SB 0/1:22,24:46:99:647,0,625:6,16,10,14 chr1 117560818 . A G 698.89 PASS AC=1;AF=0.553;AN=2;DP=1583;MQ=60;set=variant-variant2-variant4-variant8-variant9-variant10-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,35:67:99:905,0,746:21,11,24,11 chr1 117560929 . C A 2103.4 PASS AC=1;AF=0.5;AN=2;DP=3498;MQ=60;set=variant-variant2-variant4-variant8-variant9-variant10-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant43 GT:AD:DP:GQ:PL:SB 0/1:80,52:132:99:1217,0,2095:41,39,25,27 chr1 117576522 . A T 1582.15 PASS AC=1;AF=0.5;AN=2;DP=777;MQ=60;set=variant7-variant22-variant23-variant29-variant31-variant34 GT:AD:DP:GQ:PL:SB 0/1:52,80:132:99:1913,0,1080:31,21,42,38 chr1 117602960 . C A 8260.14 PASS AC=1;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 0/1:117,104:221:99:2530,0,3082:72,45,60,44 chr1 117603188 . G T 1494.82 PASS AC=1;AF=0.729;AN=2;DP=2689;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,35:64:99:1016,0,813:7,22,8,27 chr1 117617705 . A G 1376.46 PASS AC=1;AF=0.719;AN=2;DP=3102;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,36:79:99:969,0,1085:24,19,21,15 chr1 117618067 . C T 1046.48 PASS AC=1;AF=0.719;AN=2;DP=2445;MQ=60;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,28:66:99:664,0,933:19,19,13,15 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 1/1:0,24:24:72:786,72,0:0,0,17,7 chr1 117622286 . A G 2124.53 PASS AC=2;AF=0.743;AN=2;DP=4364;MQ=60;set=variant3-variant4-variant5-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-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:3508,344,0:0,0,42,73 chr1 117631391 . T C 2219.07 PASS AC=1;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 0/1:25,29:54:99:775,0,684:17,8,20,9 chr1 117659352 . C T 3687.64 PASS AC=1;AF=0.563;AN=2;DP=758;MQ=60;set=variant4-variant5-variant12-variant13-variant14-variant23-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,47:91:99:1121,0,1210:26,18,25,22 chr1 117660608 . C T 862.64 PASS AC=1;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 0/1:17,17:34:99:445,0,453:12,5,12,5 chr1 117663913 . C T 1508.46 PASS AC=2;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 1/1:0,65:65:99:1955,194,0:0,0,38,27 chr1 117664046 . C T 2059.09 PASS AC=2;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 1/1:0,111:111:99:3443,332,0:0,0,46,65 chr1 117686492 . C A 155.91 PASS AC=2;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 1/1:0,11:11:33:414,33,0:0,0,3,8 chr1 117686827 . C T 670.3 PASS AC=2;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 1/1:0,60:60:99:1911,180,0:0,0,37,23 chr1 117686914 . C T 894.97 PASS AC=2;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 1/1:0,90:90:99:2860,270,0:0,0,47,43 chr1 117687125 . A T 1650.93 PASS AC=2;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 1/1:0,121:121:99:3842,360,0:0,0,76,45 chr1 117690272 . G A 558.31 PASS AC=2;AF=0.864;AN=2;DP=3044;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1788,159,0:0,0,34,19 chr1 117714953 . G A 632.18 PASS AC=1;AF=0.5;AN=2;DP=81;FractionInformativeReads=1;MQ=60;set=variant23-variant31 GT:AD:DP:GQ:PL:SB 0/1:13,24:37:99:660,0,320:8,5,17,7 chr1 117715026 . C T 1188.03 PASS AC=2;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 1/1:0,72:72:99:2190,215,0:0,0,43,29 chr1 117715987 . AACAC AACACACAC,AACACAC,A,AACACACACAC,AACACACACACACAC 523.65 PASS AC=0,2,0,0,0;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 2/2:15:45:0,0,5,10 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 1/1:0,132:132:99:3867,394,0:0,0,73,59 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 1/1:0,18:18:54:750,54,0:0,0,17,1 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 0/1:36,20:56:99:506,0,844:14,22,6,14 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 0/1:6,12:18:99:356,0,178:5,1,9,3 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 0/1:4,3:7:71:71,0,100:0,4,0,3 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 0/1:44,39:83:99:894,0,1055:26,18,22,17 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 0/1:3,2:5:72:72,0,114:3,0,2,0 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 0/1:80,59:139:99:1425,0,2301:37,43,30,29 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 0/1:25,32:57:99:1075,0,659:12,13,20,12 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 0/1:6,4:10:99:150,0,231:6,0,4,0 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 0/1:59,44:103:99:1194,0,1583:30,29,21,23 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 0/1:52,51:103:99:1497,0,1336:23,29,24,27 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 0/1:59,71:130:99:2106,0,1503:16,43,15,56 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 1/1:0,4:4:12:177,12,0:0,0,3,1 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 0/1:40,32:72:99:1202,0,1650:29,11,28,4 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 0/1:198,228:426:99:5199,0,4608:79,119,100,128 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 1/1:0,38:38:99:1166,114,0:0,0,10,28 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 0/1:9,24:33:99:739,0,253:7,2,19,5 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 0/1:131:99:32,36,32,31 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 0/1:80,63:143:99:1612,0,2099:41,39,29,34 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 0/1:102,74:176:99:1807,0,2681:53,49,37,37 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 0/1:18,17:35:99:521,0,560:7,11,8,9 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 0/2:25:99:10,4,4,7 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 0/1:11,10:21:99:343,0,390:4,7,5,5 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 0/1:87,89:176:99:2104,0,2139:53,34,48,41 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 0/1:16,20:36:99:570,0,435:9,7,8,12 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 0/1:21,17:38:99:520,0,672:14,7,8,9 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 0/1:18,20:38:99:582,0,438:8,10,14,6 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 0/1:26,27:53:99:677,0,679:13,13,14,13 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 0/1:72:99:14,6,30,22 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 0/1:30,34:64:99:1309,0,1661:5,25,7,27 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 1/1:0,24:24:72:740,72,0:0,0,17,7 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 1/1:1,47:48:99:1457,133,0:1,0,26,21 chr1 118419782 . C T 281.64 PASS AC=1;AF=0.5;AN=2;DP=32;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant33 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:310,0,234:6,1,8,1 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 0/1:94,86:180:99:1781,0,2055:46,48,44,42 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 1/1:0,56:56:99:1651,168,0:0,0,32,24 chr1 118502732 . CGTGTGTGT CGTGT,CGTGTGT,CGTGTGTGTGTGT,CGTGTGTGTGT,CGT,C 705.63 PASS AC=0,0,2,0,0,0;AF=0.317,0.037,0.183,0.244,0.049,0.012;AN=2;DP=1464;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-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 3/3:6:22:0,0,2,4 chr1 118526592 . G A 761.44 PASS AC=2;AF=0.929;AN=2;DP=814;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-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:530,45,0:0,0,3,12 chr1 118565953 . G A 164.41 PASS AC=1;AF=0.589;AN=2;DP=923;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant29-variant33-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,7:28:99:184,0,581:15,6,6,1 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 0/1:2,6:8:43:163,0,43:2,0,4,2 chr1 118583408 . G A 2434.18 PASS AC=1;AF=0.589;AN=2;DP=4995;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant29-variant33-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,61:142:99:1251,0,1989:33,48,30,31 chr1 118596790 . A G 37.5 PASS AC=1;AF=0.5;AN=2;DP=7;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.198;QD=5.36;ReadPosRankSum=-1.495;SOR=0.892;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:5,2:7:66:66,0,166:1,4,0,2 chr1 118617274 . C T 1496.74 PASS AC=1;AF=0.597;AN=2;DP=5134;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,47:121:99:1084,0,1637:35,39,18,29 chr1 118623681 . TACACAC T,TAC,TACACACAC 590.68 PASS AC=1,0,0;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 0/1:21:99:8,2,8,3 chr1 118644430 . A G 1206.57 PASS AC=1;AF=0.645;AN=2;DP=3190;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-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,40:77:99:976,0,807:23,14,20,20 chr1 118644524 . T A 972.49 PASS AC=1;AF=0.563;AN=2;DP=1586;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant10-variant14-variant18-variant20-variant21-variant22-variant23-variant26-variant29-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,29:68:99:705,0,944:19,20,13,16 chr1 118693016 . T G 110.06 PASS AC=1;AF=0.529;AN=2;DP=317;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant10-variant14-variant18-variant20-variant21-variant22-variant23-variant26-variant29-variant33-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,7:17:99:142,0,296:7,3,4,3 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 0/1:110:99:31,39,22,18 chr1 119427454 . G A 2295.22 PASS AC=1;AF=0.5;AN=2;DP=1798;FractionInformativeReads=1;MQ=60;set=variant9-variant11-variant20-variant21-variant23-variant33-variant36-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:85,71:156:99:1831,0,2173:47,38,34,37 chr1 119466275 . A G 1502.29 PASS AC=1;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 0/1:27,27:54:99:608,0,729:8,19,12,15 chr1 119469188 . G T 1078.6 PASS AC=1;AF=0.571;AN=2;DP=1809;MQ=60;set=variant9-variant15-variant19-variant20-variant21-variant23-variant26-variant30-variant34-variant36-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:58,61:119:99:1392,0,1305:23,35,29,32 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 0/1:70,67:137:99:1560,0,1736:46,24,39,28 chr1 119574074 . G C 2435.36 PASS AC=2;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 1/1:0,107:107:99:3792,321,0:0,0,56,51 chr1 119574587 . C T 3279.49 PASS AC=2;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 1/1:0,249:249:99:7818,746,0:0,0,145,104 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 0/1:145,122:267:99:3274,0,3777:67,78,53,69 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 0/1:114,115:229:99:3162,0,2936:51,63,53,62 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 0/1:46,37:83:99:787,0,1112:22,24,21,16 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 0/1:11,11:22:99:291,0,382:1,10,3,8 chr1 119923531 . A C 750.39 PASS AC=1;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 0/1:33,39:72:99:1000,0,831:13,20,20,19 chr1 119927680 . A G 1360.93 PASS AC=1;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 0/1:61,75:136:99:1923,0,1546:26,35,33,42 chr1 119965339 . C G 507.8 PASS AC=1;AF=0.5;AN=2;DP=80;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:24,18:42:99:536,0,707:15,9,12,6 chr1 119965445 . A G 1840.44 PASS AC=1;AF=0.5;AN=2;DP=297;FractionInformativeReads=1;MQ=60;set=variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:84,74:158:99:1869,0,2196:53,31,47,27 chr1 119965519 . C T 2730.49 PASS AC=1;AF=0.5;AN=2;DP=4213;set=variant-variant2-variant3-variant5-variant10-variant13-variant23-variant29-variant34-variant36-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:163,136:299:99:3220,0,3929:93,70,73,63 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 1/1:1,207:208:99:6800,614,0:0,1,65,142 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 1/1:0,49:49:99:1907,146,0:0,0,4,45 chr1 120254506 . A G 470.4 PASS AC=1;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 0/1:25,34:59:99:936,0,695:16,9,18,16 chr1 120254545 . G C 720.98 PASS AC=1;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 0/1:35,42:77:99:1138,0,911:21,14,23,19 chr1 120263643 . T C 1597.28 PASS AC=1;AF=0.6;AN=2;DP=2082;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant8-variant10-variant11-variant13-variant14-variant18-variant21-variant22-variant23-variant24-variant26-variant29-variant32-variant33-variant34-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,49:91:99:1344,0,1054:23,19,26,23 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 0/3:14:92:7,1,5,1 chr1 120267505 . C G 1559.47 PASS AC=1;AF=0.589;AN=2;DP=3418;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant23-variant25-variant26-variant27-variant28-variant30-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,49:116:99:1058,0,1695:27,40,22,27 chr1 120285546 . G A 2743.54 PASS AC=1;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 0/1:56,33:89:99:737,0,1328:28,28,19,14 chr1 120286941 . G A,C 509.8 PASS AC=0,1;AF=0.24,0.3;AN=2;DP=562;MQ=60;set=variant3-variant5-variant7-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant32-variant33-variant38-variant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/2:23:99:3,12,0,8 chr1 120293352 . T C 1211.67 PASS AC=1;AF=0.526;AN=2;DP=2057;MQ=60;set=variant2-variant5-variant8-variant10-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant28-variant31-variant33-variant34-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,47:82:99:1210,0,850:21,14,30,17 chr1 120293367 . T C 3991.38 PASS AC=1;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 0/1:40,56:96:99:1299,0,1032:25,15,35,21 chr1 120293568 . G A 807.42 PASS AC=1;AF=0.526;AN=2;DP=1259;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant8-variant10-variant13-variant14-variant15-variant16-variant20-variant21-variant22-variant23-variant28-variant31-variant33-variant34-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,28:61:99:716,0,835:14,19,10,18 chr1 120293748 . T G 295.68 PASS AC=1;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 0/1:6,10:16:99:244,0,129:2,4,3,7 chr1 120336785 . C T 2189.46 PASS AC=1;AF=0.786;AN=2;DP=3284;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,37:81:99:907,0,1163:29,15,20,17 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 0/1:48,54:102:99:2081,0,1810:22,26,23,31 chr1 120336876 . T G 1494.09 PASS AC=1;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 0/1:51,54:105:99:2131,0,1850:23,28,26,28 chr1 120337384 . T C 665.91 PASS AC=1;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 0/1:13,18:31:99:556,0,390:2,11,3,15 chr1 120337403 . A G 440.92 PASS AC=1;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 0/1:9,8:17:99:285,0,260:1,8,0,8 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 0/1:5,8:13:99:266,0,144:2,3,1,7 chr1 120344044 . G A 1105.29 PASS AC=1;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 0/1:59,55:114:99:1337,0,1371:28,31,23,32 chr1 120344091 . C G 357.44 PASS AC=1;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 0/1:52,39:91:99:1099,0,1347:25,27,16,23 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 1/1:0,86:86:99:2803,257,0:0,0,36,50 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 1/1:0,79:79:99:2651,237,0:0,0,33,46 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 1/1:0,79:79:99:2567,236,0:0,0,36,43 chr1 120344239 . T A 328.51 PASS AC=1;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 0/1:25,31:56:99:772,0,665:12,13,13,18 chr1 120344398 . C T 430.57 PASS AC=1;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 0/1:22,24:46:99:604,0,626:10,12,14,10 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 1/1:0,51:51:99:1606,153,0:0,0,26,25 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 1/1:0,38:38:99:1258,114,0:0,0,20,18 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 1/1:0,38:38:99:1169,114,0:0,0,19,19 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 1/1:0,108:108:99:3231,323,0:0,0,63,45 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 1/1:0,39:39:99:1149,116,0:0,0,18,21 chr1 120384205 . A G 1874.33 PASS AC=2;AF=0.795;AN=2;DP=5089;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3144,326,0:0,0,51,58 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 1/1:1,37:38:78:1323,78,0:1,0,10,27 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 1/1:0,19:19:57:577,57,0:0,0,9,10 chr1 120461956 . A T 154.32 PASS AC=1;AF=0.5;AN=2;DP=1821;FractionInformativeReads=1;set=variant-variant5-variant8-variant11-variant12-variant15-variant17-variant21-variant22-variant23-variant25-filterInvariant27-variant28-variant29-variant30-variant31-variant34-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:80,12:92:99:302,0,4020:48,32,7,5 chr1 120461959 . T G 232.28 PASS AC=1;AF=0.5;AN=2;DP=1900;FractionInformativeReads=1;set=variant-variant5-variant8-variant11-variant12-variant15-variant17-variant21-variant22-variant23-variant25-filterInvariant27-variant28-variant29-variant30-variant31-variant34-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:84,13:97:99:290,0,4188:51,33,8,5 chr1 120461962 . C A 313.25 PASS AC=1;AF=0.5;AN=2;DP=1972;FractionInformativeReads=1;set=variant-variant5-variant8-variant11-variant12-variant15-variant17-variant21-variant22-variant23-variant25-filterInvariant27-variant28-variant29-variant30-variant31-variant34-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:86,13:99:99:371,0,4224:53,33,8,5 chr1 120461965 . T A 310.24 PASS AC=1;AF=0.5;AN=2;DP=2026;FractionInformativeReads=1;set=variant-variant5-variant8-variant11-variant12-variant15-variant17-variant21-variant22-variant23-variant25-filterInvariant27-variant28-variant29-variant30-variant31-variant34-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:85,15:100:99:536,0,4254:52,33,10,5 chr1 120461974 . G A 304.22 PASS AC=1;AF=0.5;AN=2;DP=2215;FractionInformativeReads=1;set=variant-variant5-variant8-variant11-variant12-variant15-variant17-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant34-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:88,22:110:99:659,0,4287:54,34,12,10 chr1 120461977 . T A 336.43 PASS AC=1;AF=0.5;AN=2;DP=2268;FractionInformativeReads=1;set=variant-variant5-variant8-variant11-variant12-variant15-variant17-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant34-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:91,24:115:99:722,0,4331:56,35,14,10 chr1 120461980 . A G 368.49 PASS AC=1;AF=0.5;AN=2;DP=2308;set=variant-variant5-variant8-variant11-variant12-variant15-variant17-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant34-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:91,25:116:99:720,0,4405:56,35,14,11 chr1 120462019 . T A 522.09 PASS AC=1;AF=0.5;AN=2;DP=6309;set=variant-variant2-variant3-variant4-variant5-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-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:116,35:151:99:533,0,2791:59,57,16,19 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 0/1:108,40:148:99:1390,0,5094:52,56,19,21 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 0/1:111,42:153:99:1492,0,5166:54,57,20,22 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 0/1:117,46:163:99:1507,0,5350:57,60,22,24 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 0/1:115,46:161:99:832,0,3037:56,59,21,25 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 0/1:93,45:138:99:1641,0,21335:44,49,18,27 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 0/1:93,46:139:99:1641,0,21335:44,49,18,28 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 0/1:88,38:126:99:1538,0,22344:43,45,12,26 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 0/1:84,35:119:99:1295,0,22373:40,44,9,26 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 0/1:82,30:112:99:1052,0,22137:37,45,8,22 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 0/1:88,30:118:99:992,0,23631:41,47,9,21 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 0/1:84,23:107:99:701,0,23384:37,47,6,17 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 0/1:77,17:94:99:479,0,20494:38,39,4,13 chr1 120462181 . A G 256.06 PASS AC=1;AF=0.5;AN=2;DP=3577;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-filterInvariant28-variant29-variant30-variant31-filterInvariant32-variant33-filterInvariant34-variant36-filterInvariant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:76,14:90:99:353,0,19013:38,38,2,12 chr1 120462184 . C T 223.1 PASS AC=1;AF=0.5;AN=2;DP=3458;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant27-filterInvariant28-variant29-variant30-variant31-filterInvariant32-filterInvariant33-variant36-filterInvariant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:79,12:91:99:299,0,19217:40,39,1,11 chr1 120462186 . A G 223.1 PASS AC=1;AF=0.5;AN=2;DP=3435;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant15-variant16-variant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant27-filterInvariant28-variant29-variant30-variant31-filterInvariant32-filterInvariant33-variant36-filterInvariant37-variant38-variant39-variant40-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:80,10:90:99:260,0,19000:41,39,1,9 chr1 120466388 . C T 57.25 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=454;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:126,11:137:58:58,0,5447:60,66,7,4 chr1 120466390 . G A 63.27 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=456;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:126,11:137:70:70,0,5279:60,66,7,4 chr1 120466420 . G T 132.36 PASS AC=1;AF=0.5;AN=2;DP=2492;set=filterInvariant2-variant3-filterInvariant5-filterInvariant7-filterInvariant9-variant10-filterInvariant12-filterInvariant16-filterInvariant20-filterInvariant23-filterInvariant24-filterInvariant27-filterInvariant32-filterInvariant39-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:118,14:132:99:218,0,5021:60,58,9,5 chr1 120466430 . G T 147.23 PASS AC=1;AF=0.5;AN=2;DP=2785;FractionInformativeReads=1;set=filterInvariant2-variant3-filterInvariant4-filterInvariant5-variant7-filterInvariant9-variant10-filterInvariant12-filterInvariant16-filterInvariant20-variant23-filterInvariant24-filterInvariant27-filterInvariant32-filterInvariant39-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:119,16:135:99:344,0,5073:60,59,9,7 chr1 120466435 . C A 129.17 PASS AC=1;AF=0.5;AN=2;DP=2788;FractionInformativeReads=1;set=filterInvariant2-variant3-filterInvariant4-filterInvariant5-variant7-filterInvariant9-variant10-filterInvariant12-filterInvariant16-variant20-variant23-filterInvariant24-filterInvariant27-variant32-filterInvariant39-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:123,17:140:99:377,0,5237:64,59,10,7 chr1 120466442 . G A 102.07 PASS AC=1;AF=0.5;AN=2;DP=4079;FractionInformativeReads=1;set=filterInvariant2-variant3-filterInvariant4-filterInvariant5-variant7-filterInvariant8-filterInvariant9-variant10-variant12-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant19-variant20-variant23-filterInvariant24-filterInvariant27-filterInvariant31-variant32-filterInvariant37-filterInvariant39-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:119,17:136:99:332,0,5282:62,57,10,7 chr1 120466448 . T C 96.05 PASS AC=1;AF=0.5;AN=2;DP=4650;FractionInformativeReads=1;set=filterInvariant2-variant3-filterInvariant4-filterInvariant5-filterInvariant6-variant7-filterInvariant8-filterInvariant9-variant10-filterInvariant11-variant12-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant19-variant20-filterInvariant21-variant23-filterInvariant24-variant27-filterInvariant31-variant32-filterInvariant37-variant39-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:119,18:137:99:392,0,5027:63,56,11,7 chr1 120466457 . T G 183.04 PASS AC=1;AF=0.5;AN=2;DP=5297;FractionInformativeReads=1;set=filterInvariant2-variant3-filterInvariant4-variant5-filterInvariant6-variant7-filterInvariant8-filterInvariant9-variant10-filterInvariant11-variant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant19-variant20-filterInvariant21-filterInvariant22-variant23-filterInvariant24-variant27-filterInvariant31-variant32-filterInvariant36-filterInvariant37-filterInvariant38-variant39-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:118,21:139:99:506,0,5186:62,56,14,7 chr1 120466462 . T G 174.01 PASS AC=1;AF=0.5;AN=2;DP=5287;FractionInformativeReads=1;set=filterInvariant2-variant3-filterInvariant4-variant5-filterInvariant6-variant7-filterInvariant8-filterInvariant9-variant10-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-variant20-filterInvariant21-filterInvariant22-variant23-filterInvariant24-variant27-filterInvariant31-variant32-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:122,21:143:99:541,0,5266:62,60,15,6 chr1 120466463 . C G 177.02 PASS AC=1;AF=0.5;AN=2;DP=5305;FractionInformativeReads=1;set=filterInvariant2-variant3-filterInvariant4-variant5-filterInvariant6-variant7-filterInvariant8-filterInvariant9-variant10-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-filterInvariant18-filterInvariant19-variant20-filterInvariant21-filterInvariant22-variant23-filterInvariant24-variant27-filterInvariant31-variant32-filterInvariant37-filterInvariant38-variant39-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:122,21:143:99:541,0,5266:63,59,15,6 chr1 120466465 . A G 219.01 PASS AC=1;AF=0.5;AN=2;DP=5934;FractionInformativeReads=1;set=filterInvariant2-variant3-variant4-variant5-filterInvariant6-variant7-filterInvariant8-variant9-variant10-filterInvariant11-variant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-filterInvariant18-filterInvariant19-variant20-filterInvariant21-filterInvariant22-variant23-filterInvariant24-variant27-filterInvariant31-variant32-filterInvariant33-filterInvariant34-filterInvariant36-filterInvariant37-filterInvariant38-variant39-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:121,22:143:99:718,0,5128:61,60,15,7 chr1 120466466 . T C 222.02 PASS AC=1;AF=0.5;AN=2;DP=5950;FractionInformativeReads=1;set=filterInvariant2-variant3-variant4-variant5-filterInvariant6-variant7-filterInvariant8-filterInvariant9-variant10-filterInvariant11-variant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-filterInvariant18-filterInvariant19-variant20-filterInvariant21-filterInvariant22-variant23-variant24-variant27-filterInvariant31-variant32-filterInvariant33-filterInvariant34-filterInvariant36-filterInvariant37-filterInvariant38-variant39-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:120,22:142:99:715,0,5170:61,59,15,7 chr1 120466475 . A G 87.79 PASS AC=1;AF=0.5;AN=2;DP=6284;FractionInformativeReads=1;set=filterInvariant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-filterInvariant8-variant9-variant10-filterInvariant11-variant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-filterInvariant18-filterInvariant19-variant20-filterInvariant21-filterInvariant22-variant23-filterInvariant24-variant27-filterInvariant31-variant32-filterInvariant33-filterInvariant34-filterInvariant36-variant37-filterInvariant38-variant39-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:128,27:155:99:816,0,5371:62,66,18,9 chr1 120466484 . A G 92.52 PASS AC=1;AF=0.5;AN=2;DP=6588;set=filterInvariant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-filterInvariant8-variant9-variant10-filterInvariant11-variant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-variant20-filterInvariant21-filterInvariant22-variant23-variant24-filterInvariant25-variant27-filterInvariant31-variant32-filterInvariant33-filterInvariant34-filterInvariant36-variant37-filterInvariant38-variant39-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:124,30:154:99:830,0,5202:62,62,19,11 chr1 120466487 . T C 95.52 PASS AC=1;AF=0.5;AN=2;DP=6393;set=filterInvariant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-filterInvariant8-variant9-variant10-filterInvariant11-variant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant19-variant20-filterInvariant21-filterInvariant22-variant23-variant24-filterInvariant25-variant27-filterInvariant31-variant32-filterInvariant33-filterInvariant34-filterInvariant36-variant37-filterInvariant38-variant39-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:124,30:154:99:833,0,5150:63,61,19,11 chr1 120466502 . A T 281.52 PASS AC=1;AF=0.5;AN=2;DP=7234;set=variant-filterInvariant2-variant3-variant4-variant5-filterInvariant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-filterInvariant13-filterInvariant14-variant15-filterInvariant16-variant17-filterInvariant18-filterInvariant19-variant20-filterInvariant21-filterInvariant22-variant23-variant24-filterInvariant25-variant27-filterInvariant31-variant32-filterInvariant33-filterInvariant34-filterInvariant36-variant37-variant38-variant39-filterInvariant40-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:142,32:174:99:835,0,5672:76,66,20,12 chr1 120466511 . A C 303.99 PASS AC=1;AF=0.5;AN=2;DP=7555;MQ=60;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-variant10-variant11-variant12-filterInvariant13-filterInvariant14-variant15-filterInvariant16-variant17-filterInvariant18-variant19-variant20-variant21-filterInvariant22-variant23-variant24-filterInvariant25-variant27-filterInvariant28-filterInvariant31-variant32-filterInvariant33-filterInvariant34-variant36-variant37-variant38-variant39-filterInvariant40-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:144,37:181:99:920,0,5745:76,68,22,15 chr1 120466535 . A G 112.47 PASS AC=1;AF=0.5;AN=2;DP=5504;MQ=60;set=filterInvariant-variant2-variant3-variant4-variant5-variant7-filterInvariant8-variant10-filterInvariant11-filterInvariant12-filterInvariant17-filterInvariant19-filterInvariant20-variant21-variant23-variant24-filterInvariant25-filterInvariant27-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:148,36:184:99:494,0,3850:75,73,21,15 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 0/1:154,41:195:99:1339,0,6368:73,81,22,19 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 0/1:154,43:197:99:1379,0,6384:73,81,23,20 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 0/1:155,45:200:99:1353,0,6428:73,82,23,22 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 0/1:146,41:187:99:616,0,3740:68,78,19,22 chr1 120466610 . AG A 231.12 PASS AC=1;AF=0.5;AN=2;DP=2668;set=variant-variant3-variant5-filterInvariant6-filterInvariant9-filterInvariant10-variant11-variant12-filterInvariant16-filterInvariant22-variant23-variant24-filterInvariant33-filterInvariant36-filterInvariant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:127,29:156:99:602,0,5139:55,72,9,20 chr1 120466614 . A T 237.14 PASS AC=1;AF=0.5;AN=2;DP=2435;MQ=60;set=variant-variant3-variant5-variant6-filterInvariant9-variant10-variant11-variant12-filterInvariant16-filterInvariant22-variant23-variant24-filterInvariant33-filterInvariant36-filterInvariant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:121,21:142:99:602,0,5139:52,69,1,20 chr1 120466619 . GAAGC G 163.8 PASS AC=1;AF=0.5;AN=2;DP=2119;FractionInformativeReads=1;MQ=60;set=filterInvariant-variant3-variant5-filterInvariant6-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant16-variant23-filterInvariant24-filterInvariant33-filterInvariant37-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:118,20:138:99:448,0,5105:50,68,1,19 chr1 120466628 . A AAGGG 150.85 PASS AC=1;AF=0.5;AN=2;DP=1836;FractionInformativeReads=1;MQ=60;set=filterInvariant-variant3-variant5-filterInvariant6-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant22-variant23-filterInvariant24-filterInvariant37-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:113,18:131:99:410,0,4775:48,65,0,18 chr1 120466634 . C G 93.96 PASS AC=1;AF=0.5;AN=2;DP=1594;FractionInformativeReads=1;MQ=60;set=filterInvariant-variant3-filterInvariant5-filterInvariant6-filterInvariant9-filterInvariant10-variant11-variant12-variant23-filterInvariant24-filterInvariant37-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:108,16:124:99:377,0,4652:45,63,0,16 chr1 120466638 . A G 54.98 PASS AC=1;AF=0.5;AN=2;DP=1628;FractionInformativeReads=1;MQ=60;set=filterInvariant-variant3-filterInvariant5-filterInvariant6-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-variant23-filterInvariant24-filterInvariant36-filterInvariant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:106,16:122:99:347,0,4487:43,63,0,16 chr1 120466646 . G A 411.06 PASS AC=1;AF=0.5;AN=2;DP=1254;FractionInformativeReads=1;MQ=60;set=variant3-filterInvariant5-filterInvariant6-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-variant23-filterInvariant24-variant40 GT:AD:DP:GQ:PL:SB 0/1:96,15:111:99:332,0,4112:35,61,0,15 chr1 120466648 . T A 414.07 PASS AC=1;AF=0.5;AN=2;DP=1225;FractionInformativeReads=1;MQ=60;set=variant3-filterInvariant5-filterInvariant6-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-variant23-filterInvariant24-variant40 GT:AD:DP:GQ:PL:SB 0/1:96,14:110:99:341,0,3986:35,61,0,14 chr1 120466651 . G C 423.1 PASS AC=1;AF=0.5;AN=2;DP=1079;FractionInformativeReads=1;MQ=60;set=variant3-filterInvariant5-filterInvariant6-filterInvariant10-filterInvariant11-filterInvariant12-variant23-filterInvariant24-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:92,14:106:99:299,0,3989:31,61,0,14 chr1 120466653 . C T 402.18 PASS AC=1;AF=0.5;AN=2;DP=1055;FractionInformativeReads=1;MQ=60;set=variant3-filterInvariant5-filterInvariant6-filterInvariant10-filterInvariant11-filterInvariant12-variant23-filterInvariant24-variant40 GT:AD:DP:GQ:PL:SB 0/1:90,13:103:99:311,0,3821:30,60,0,13 chr1 120466657 . A G 420.24 PASS AC=1;AF=0.5;AN=2;DP=1118;FractionInformativeReads=1;MQ=60;set=variant3-filterInvariant5-filterInvariant6-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant20-variant23-filterInvariant24-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:85,11:96:99:278,0,3698:29,56,0,11 chr1 120466658 . G A 423.25 PASS AC=1;AF=0.5;AN=2;DP=995;FractionInformativeReads=1;MQ=60;set=variant3-filterInvariant5-filterInvariant6-filterInvariant10-filterInvariant11-filterInvariant12-variant23-filterInvariant24-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:84,11:95:99:239,0,3659:29,55,0,11 chr1 120467899 . T C 241.01 PASS AC=1;AF=0.5;AN=2;DP=1907;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-filterInvariant7-variant10-filterInvariant11-filterInvariant13-filterInvariant16-variant17-filterInvariant20-filterInvariant22-filterInvariant23-variant24-filterInvariant29-variant31-filterInvariant32-filterInvariant33 GT:AD:DP:GQ:PL:SB 0/1:84,8:92:99:122,0,3522:52,32,7,1 chr1 120467902 . A G 345.9 PASS AC=1;AF=0.5;AN=2;DP=2181;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-filterInvariant7-variant10-filterInvariant11-filterInvariant13-filterInvariant16-variant17-filterInvariant20-filterInvariant22-filterInvariant23-variant24-filterInvariant29-variant31-filterInvariant32-filterInvariant33-filterInvariant38-filterInvariant39 GT:AD:DP:GQ:PL:SB 0/1:85,9:94:99:119,0,3584:52,33,7,2 chr1 120467903 . G GC 330.85 PASS AC=1;AF=0.5;AN=2;DP=2339;FractionInformativeReads=1;set=variant-filterInvariant2-variant3-variant4-variant5-filterInvariant7-variant10-filterInvariant11-filterInvariant13-filterInvariant16-variant17-filterInvariant20-filterInvariant22-filterInvariant23-variant24-filterInvariant29-variant31-filterInvariant32-filterInvariant33-filterInvariant38-filterInvariant39 GT:AD:DP:GQ:PL:SB 0/1:86,9:95:99:110,0,3710:52,34,7,2 chr1 120467905 . T G 327.84 PASS AC=1;AF=0.5;AN=2;DP=2514;FractionInformativeReads=1;set=variant-filterInvariant2-variant3-variant4-variant5-filterInvariant7-filterInvariant8-variant10-filterInvariant11-filterInvariant13-variant16-variant17-filterInvariant20-filterInvariant22-filterInvariant23-variant24-filterInvariant29-variant31-filterInvariant32-filterInvariant33-filterInvariant38-filterInvariant39 GT:AD:DP:GQ:PL:SB 0/1:89,8:97:99:107,0,3752:54,35,6,2 chr1 120467914 . C G 318.66 PASS AC=1;AF=0.5;AN=2;DP=2864;FractionInformativeReads=1;set=variant-filterInvariant2-variant3-variant4-variant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-variant10-filterInvariant11-filterInvariant13-filterInvariant16-variant17-filterInvariant20-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant29-variant31-filterInvariant32-filterInvariant33-filterInvariant39 GT:AD:DP:GQ:PL:SB 0/1:95,8:103:99:134,0,3959:55,40,6,2 chr1 120467916 . T TCC 333.55 PASS AC=1;AF=0.5;AN=2;DP=3175;FractionInformativeReads=1;set=variant-filterInvariant2-variant3-variant4-variant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-variant10-filterInvariant11-filterInvariant13-filterInvariant16-variant17-filterInvariant20-filterInvariant22-filterInvariant23-variant24-filterInvariant27-filterInvariant29-variant31-filterInvariant32-filterInvariant33-filterInvariant39-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:95,10:105:99:128,0,4043:55,40,8,2 chr1 120467918 . A G 336.58 PASS AC=1;AF=0.5;AN=2;DP=3260;FractionInformativeReads=1;set=variant-filterInvariant2-variant3-variant4-variant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-variant10-filterInvariant11-filterInvariant13-filterInvariant16-variant17-filterInvariant20-filterInvariant22-filterInvariant23-variant24-filterInvariant27-variant29-variant31-filterInvariant32-filterInvariant33-filterInvariant39-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:97,10:107:99:122,0,4120:56,41,8,2 chr1 120467922 . C T 356.56 PASS AC=1;AF=0.5;AN=2;DP=4119;FractionInformativeReads=1;set=variant-filterInvariant2-variant3-variant4-variant5-filterInvariant6-variant7-filterInvariant8-variant9-variant10-variant11-variant13-filterInvariant15-variant16-variant17-filterInvariant18-variant20-filterInvariant22-filterInvariant23-variant24-variant27-filterInvariant28-variant29-filterInvariant30-variant31-variant32-filterInvariant33-filterInvariant38-filterInvariant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:101,10:111:99:116,0,4175:59,42,8,2 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 0/1:112,21:133:99:575,0,4784:65,47,11,10 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 0/1:125,22:147:99:545,0,5204:74,51,11,11 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 0/1:123,22:145:99:551,0,5120:71,52,11,11 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 0/1:147,29:176:99:763,0,6233:79,68,16,13 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 0/1:149,29:178:99:763,0,6233:80,69,16,13 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 0/1:149,29:178:99:763,0,6233:79,70,16,13 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 0/1:155,34:189:99:994,0,6344:85,70,17,17 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 1/1:0,4:4:12:180,12,0:0,0,4,0 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 1/1:1,65:66:99:2060,152,0:0,1,20,45 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 1/1:0,8:8:24:290,24,0:0,0,7,1 chr1 120505996 . G C 1197.82 PASS AC=2;AF=0.795;AN=2;DP=1366;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:873,84,0:0,0,19,9 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 1/1:0,40:40:99:1452,120,0:0,0,30,10 chr1 120539213 . G T 1018.35 PASS AC=1;AF=0.5;AN=2;DP=1465;set=variant4-variant8-variant9-variant13-variant14-filterInvariant19-variant20-filterInvariant21-variant23-variant25-variant26-variant27-variant30-variant33-filterInvariant36-variant37-variant39-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:60,16:76:99:363,0,1944:47,13,15,1 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 0/1:163,144:307:99:3308,0,4144:91,72,72,72 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 0/1:1,2:3:24:68,0,24:1,0,2,0 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 0/1:199,87:286:99:1589,0,5067:89,110,47,40 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 0/1:146,104:250:99:2382,0,3692:64,82,57,47 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 0/1:109,110:219:99:2645,0,2798:51,58,66,44 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 0/1:118,162:280:99:3949,0,2804:61,57,89,73 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 0/1:199,224:423:99:5054,0,4573:110,89,110,114 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 0/1:392:99:50,53,133,156 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 0/1:172,25:197:99:513,0,7976:78,94,11,14 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 0/1:166,25:191:99:519,0,7992:78,88,11,14 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 0/1:140,51:191:99:795,0,3959:69,71,21,30 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 0/1:76,14:90:99:297,0,2005:28,48,1,13 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 1/1:0,46:46:99:1749,138,0:0,0,24,22 chr1 120905120 . A C 379.95 PASS AC=1;AF=0.529;AN=2;DP=1991;set=variant-variant4-variant5-variant8-variant13-variant14-variant19-variant20-variant21-variant23-variant27-variant32-variant33-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:61,39:100:99:1229,0,1702:20,41,7,32 chr1 120906101 . C A 3921.72 PASS AC=1;AF=0.529;AN=2;DP=4798;FractionInformativeReads=1;set=variant-variant4-variant5-variant8-variant13-variant14-variant19-variant20-variant21-variant23-variant27-variant32-variant33-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:148,134:282:99:5133,0,7586:80,68,75,59 chr1 120906102 . G A 3921.72 PASS AC=1;AF=0.529;AN=2;DP=4826;FractionInformativeReads=1;set=variant-variant4-variant5-variant8-variant13-variant14-variant19-variant20-variant21-variant23-variant27-variant32-variant33-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:150,133:283:99:5133,0,7586:81,69,74,59 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 1/1:0,41:41:99:1263,123,0:0,0,13,28 chr1 120927081 . C T 64.76 PASS AC=1;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 0/1:3,12:15:44:328,0,44:3,0,11,1 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 0/1:40,8:48:99:110,0,1381:39,1,7,1 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 0/1:50,23:73:99:551,0,1421:41,9,23,0 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 0/1:103,51:154:99:784,0,2684:66,37,27,24 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 0/1:138,66:204:99:2338,0,5615:75,63,43,23 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 0/1:143,71:214:99:2439,0,5714:78,65,48,23 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 0/1:201,43:244:99:505,0,5273:104,97,15,28 chr1 121116933 . T C 1061.74 PASS AC=1;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 0/1:27,27:54:99:723,0,764:7,20,8,19 chr1 121116953 . A G 984.23 PASS AC=1;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 0/1:17,21:38:99:638,0,534:3,14,5,16 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 0/1:7,3:10:64:64,0,181:4,3,1,2 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 0/1:2,8:10:60:330,0,60:2,0,7,1 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 0/1:2,8:10:54:414,0,54:2,0,7,1 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 0/1:2,8:10:54:414,0,54:2,0,7,1 chr1 142542720 . TGTGGAGTGGAGTGGA T,TAGTGGAGTGGA 259.98 PASS AC=1,0;AF=0.263,0.237;AN=2;DP=663;set=variant6-variant13-variant16-variant17-filterInvariant21-variant23-filterInvariant24-filterInvariant26-variant28-variant30-filterInvariant32-variant33-variant34-variant36-variant38-variant40-filterInvariant41-variant43-variant44 GT:DP:GQ:SB 0/1:14:99:3,1,8,2 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 0/1:28,9:37:99:294,0,1149:19,9,7,2 chr1 142542779 . G T 385.13 PASS AC=1;AF=0.5;AN=2;DP=672;set=variant6-filterInvariant9-variant23-variant24-variant25-filterInvariant30-variant32-variant37-variant38-variant39-variant40-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:39,10:49:99:303,0,1191:25,14,8,2 chr1 142542800 . G C,A 56.16 PASS AC=1,0;AF=0.375,0.125;AN=2;DP=250;set=filterInvariant6-filterInvariant17-filterInvariant23-variant38 GT:DP:GQ:SB 0/1:62:80:35,21,5,1 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 0/1:54,21:75:99:409,0,1405:35,19,13,8 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 0/1:68,10:78:99:207,0,2696:34,34,5,5 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 0/1:68,10:78:99:207,0,2696:34,34,5,5 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 1/1:0,43:43:99:1416,129,0:0,0,13,30 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 0/1:7,4:11:96:96,0,163:4,3,2,2 chr1 142690721 . C A 59.03 PASS AC=1;AF=0.571;AN=2;DP=86;FS=0;FractionInformativeReads=1;set=variant4-variant6-filterInvariant10-variant11-variant19-variant20-filterInvariant23-variant24-variant26-variant27-variant31-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:30:120,0,30:0,1,0,4 chr1 142690739 . G A 102.04 PASS AC=1;AF=0.571;AN=2;DP=114;FS=0;FractionInformativeReads=1;set=filterInvariant-filterInvariant3-variant5-variant7-variant9-filterInvariant10-filterInvariant13-filterInvariant14-variant15-variant17-filterInvariant19-filterInvariant20-variant21-filterInvariant23-variant24-variant25-variant26-variant30-variant40-filterInvariant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:72:72,0,162:0,4,0,2 chr1 142690740 . G A 102.04 PASS AC=1;AF=0.571;AN=2;DP=114;FS=0;FractionInformativeReads=1;set=filterInvariant-filterInvariant3-variant5-variant7-variant9-filterInvariant10-filterInvariant13-filterInvariant14-variant15-variant17-filterInvariant19-filterInvariant20-variant21-filterInvariant23-variant24-variant25-variant26-variant30-variant40-filterInvariant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:72:72,0,162:0,4,0,2 chr1 142813098 . T C 49.04 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1261;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:20,6:26:99:113,0,542:15,5,5,1 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 0/1:66,11:77:99:136,0,1863:45,21,10,1 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 0/1:179,24:203:99:263,0,6907:99,80,14,10 chr1 142826369 . C A 2438.06 PASS AC=1;AF=0.614;AN=2;DP=8960;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:115,99:214:99:2518,0,2925:66,49,52,47 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 1/1:0,68:68:99:2527,204,0:0,0,25,43 chr1 142849522 . A C 59.99 DRAGENHardSNP AC=2;AF=1;AN=2;DP=51;FS=0;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:210,21,0:0,0,1,6 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 0/1:16,6:22:99:114,0,411:7,9,4,2 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 0/1:13,13:26:99:341,0,269:5,8,9,4 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 0/1:20,11:31:99:190,0,489:7,13,5,6 chr1 143187297 . G C 356.2 PASS AC=1;AF=0.618;AN=2;DP=530;set=variant-variant4-variant5-variant10-variant13-variant14-variant19-variant21-variant23-variant24-variant27-variant33-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,15:35:99:403,0,432:9,11,7,8 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 0/1:68:88:25,33,5,5 chr1 143376703 . A T 61.77 PASS AC=1;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 0/1:2,2:4:78:78,0,87:1,1,1,1 chr1 143376705 . A C 61.77 PASS AC=1;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 0/1:2,2:4:78:78,0,87:1,1,1,1 chr1 143400907 . A G 153.92 PASS AC=1;AF=0.717;AN=2;DP=200;FractionInformativeReads=1;set=filterInvariant2-variant4-variant5-filterInvariant6-variant11-filterInvariant12-variant13-variant14-filterInvariant15-filterInvariant17-variant18-variant20-filterInvariant21-variant23-variant24-variant25-filterInvariant26-variant27-filterInvariant28-filterInvariant29-variant33-filterInvariant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,10:14:91:213,0,91:3,1,4,6 chr1 143424027 . A C 41.5 PASS AC=1;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 0/1:3,3:6:99:114,0,119:3,0,3,0 chr1 143767312 . G T 242.84 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1726;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:26,12:38:99:224,0,611:24,2,12,0 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 0/1:318,154:472:99:5362,0,12618:138,180,60,94 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 0/1:307,148:455:99:5296,0,12452:134,173,55,93 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 0/1:285,115:400:99:1967,0,6803:134,151,38,77 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 0/1:208,24:232:99:124,0,5761:109,99,3,21 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 0/1:94,54:148:99:1276,0,2304:52,42,36,18 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 0/1:102,56:158:99:1323,0,2504:53,49,36,20 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 0/1:81,15:96:99:164,0,2207:35,46,6,9 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 0/1:34,43:77:99:1110,0,879:12,22,16,27 chr1 144052641 . CAAAAA CAAA,CAA,CA,C,CAAAAAA,CAAAA 221.22 PASS AC=0,0,1,0,0,0;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 0/3:33:99:9,13,11,0 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 0/1:41,26:67:99:600,0,991:26,15,18,8 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 0/1:60,62:122:99:2422,0,2409:24,36,30,32 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 0/1:70,12:82:99:263,0,1905:42,28,11,1 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 0/1:67,50:117:99:1151,0,1725:26,41,22,28 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 0/1:58,7:65:99:119,0,2414:37,21,5,2 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 0/1:58,7:65:99:206,0,2402:37,21,5,2 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 0/1:70,22:92:99:497,0,1769:43,27,14,8 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 0/1:162,43:205:99:596,0,3603:87,75,24,19 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 1/1:0,183:183:99:4962,547,0:0,0,84,99 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 0/1:57,13:70:99:116,0,1498:23,34,0,13 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 0/1:62,21:83:99:481,0,1802:42,20,17,4 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 0/1:84,48:132:99:1151,0,2156:50,34,33,15 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 0/1:95,66:161:99:2518,0,4228:51,44,43,23 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 0/1:97,72:169:99:2577,0,4285:51,46,44,28 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 0/1:50,94:144:99:2370,0,1021:18,32,38,56 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 0/1:71,15:86:99:174,0,1752:43,28,4,11 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 0/1:14,5:19:85:85,0,522:14,0,5,0 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 0/1:22,8:30:99:264,0,977:22,0,8,0 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 0/1:24,11:35:99:359,0,968:24,0,11,0 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 1/1:0,41:41:99:1760,123,0:0,0,41,0 chr1 144811924 . T G 4451.43 PASS AC=2;AF=0.989;AN=2;DP=6738;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,150:150:99:4348,449,0:0,0,86,64 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 0/1:118,38:156:99:484,0,2834:52,66,16,22 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 0/1:88,21:109:99:317,0,2445:30,58,2,19 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 0/1:71,11:82:99:248,0,2931:24,47,0,11 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 0/1:71,11:82:99:248,0,2931:24,47,0,11 chr1 144813718 . A G 794.4 PASS AC=1;AF=0.726;AN=2;DP=1733;set=variant2-variant5-filterInvariant6-variant7-variant8-filterInvariant9-variant10-variant12-filterInvariant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,17:79:99:418,0,1596:32,30,16,1 chr1 144816086 . C G 640.14 PASS AC=1;AF=0.571;AN=2;DP=439;FractionInformativeReads=1;set=variant23-variant32-variant34-variant35-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,27:39:99:668,0,260:7,5,13,14 chr1 144824146 . A C 102.96 PASS AC=2;AF=1;AN=2;DP=99;FS=0;FractionInformativeReads=1;set=filterInvariant-filterInvariant3-filterInvariant4-filterInvariant6-variant8-filterInvariant11-filterInvariant13-filterInvariant14-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant27-filterInvariant29-filterInvariant31-filterInvariant32-filterInvariant34-filterInvariant37-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:92,9,0:0,0,0,3 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 1/1:0,3:3:9:98,9,0:0,0,1,2 chr1 144825577 . G A 399.21 PASS AC=1;AF=0.5;AN=2;DP=2042;FractionInformativeReads=1;set=variant2-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-variant33-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,18:59:99:416,0,1080:16,25,5,13 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 0/1:10,17:27:99:524,0,369:9,1,15,2 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 0/1:22,10:32:99:263,0,823:18,4,9,1 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 0/1:17,34:51:99:968,0,482:13,4,29,5 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 0/1:59,11:70:99:242,0,2478:46,13,9,2 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 0/1:79,12:91:99:212,0,3021:59,20,8,4 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 0/1:176,19:195:99:268,0,7194:66,110,11,8 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 0/1:174,19:193:99:268,0,7194:64,110,11,8 chr1 144828845 . A T 1049.62 PASS AC=1;AF=0.5;AN=2;DP=3145;set=variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant33-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,24:67:99:607,0,1154:17,26,5,19 chr1 144828857 . C G 843.64 PASS AC=1;AF=0.5;AN=2;DP=2623;set=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-variant33-variant37-variant39-variant40-filterInvariant41-filterInvariant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,19:55:99:494,0,955:13,23,3,16 chr1 144828910 . A T 183.07 PASS AC=1;AF=0.5;AN=2;DP=1207;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:16,4:20:99:117,0,507:2,14,0,4 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 0/1:26,8:34:99:157,0,1007:15,11,5,3 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 0/1:17,20:37:99:451,0,533:9,8,12,8 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 0/1:19,28:47:99:628,0,440:10,9,14,14 chr1 144852476 . T C 275.96 PASS AC=1;AF=0.5;AN=2;DP=1842;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:12,18:30:99:524,0,252:6,6,5,13 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 0/1:19,3:22:66:66,0,810:8,11,0,3 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 0/1:20,3:23:66:66,0,810:8,12,0,3 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 0/1:12,7:19:99:177,0,346:3,9,2,5 chr1 144854180 . T C 2026.92 PASS AC=1;AF=0.5;AN=2;DP=7056;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:84,31:115:99:697,0,2361:56,28,24,7 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 0/1:209,69:278:99:1240,0,5219:124,85,39,30 chr1 144854277 . A G 5887.67 PASS AC=1;AF=0.511;AN=2;DP=19169;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:68,257:325:99:6415,0,993:37,31,133,124 chr1 144854351 . A C 5707 PASS AC=2;AF=0.784;AN=2;DP=13823;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,243:243:99:9535,731,0:0,0,95,148 chr1 144854380 . T C 4238.04 PASS AC=1;AF=0.5;AN=2;DP=10209;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:105,79:184:99:2244,0,2761:38,67,27,52 chr1 144854397 . T C 5409.55 PASS AC=2;AF=0.807;AN=2;DP=7614;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:6424,433,0:0,0,46,96 chr1 144854412 . A C 2069.17 PASS AC=1;AF=0.5;AN=2;DP=6201;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:63,51:114:99:1545,0,1709:20,43,20,31 chr1 144854452 . T A 758.2 PASS AC=1;AF=0.5;AN=2;DP=1075;set=variant4-filterInvariant6-filterInvariant8-variant23-variant26-variant29-variant30-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,21:74:99:620,0,2093:27,26,6,15 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 0/1:46,22:68:99:756,0,1725:26,20,6,16 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 0/1:70,35:105:99:1275,0,2855:37,33,21,14 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 0/1:73,40:113:99:1393,0,2870:39,34,23,17 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 0/1:114,33:147:99:985,0,4704:66,48,17,16 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 0/1:125,37:162:99:1027,0,4871:68,57,18,19 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 0/1:158,37:195:99:465,0,4160:81,77,18,19 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 0/1:150,39:189:99:1133,0,6948:74,76,16,23 chr1 144854597 . T C 4504.87 PASS AC=1;AF=0.5;AN=2;DP=8847;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:71,118:189:99:4736,0,3101:33,38,55,63 chr1 144854598 . C T 2548.15 PASS AC=1;AF=0.5;AN=2;DP=8801;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:109,80:189:99:3008,0,4870:48,61,39,41 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 0/1:25,11:36:99:284,0,925:2,23,2,9 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 0/1:7,7:14:99:151,0,151:3,4,4,3 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 0/1:5,3:8:85:93,0,85:2,3,1,2 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 0/1:2,2:4:58:75,0,58:1,1,1,1 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 0/1:5,4:9:99:144,0,192:0,5,0,4 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 1/1:0,18:18:54:658,54,0:0,0,14,4 chr1 144860026 . G C 91.69 PASS AC=1;AF=0.5;AN=2;DP=1359;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:13,14:27:99:418,0,377:4,9,5,9 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 0/1:40,6:46:99:122,0,2357:22,18,4,2 chr1 144863208 . A G 580.29 PASS AC=1;AF=0.511;AN=2;DP=2538;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:23,25:48:99:818,0,559:12,11,14,11 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 0/1:47,36:83:99:917,0,1136:21,26,16,20 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 0/1:10,11:21:99:398,0,296:2,8,0,11 chr1 144864454 . G A 112.19 PASS AC=1;AF=0.5;AN=2;DP=1150;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:4,17:21:99:536,0,102:0,4,3,14 chr1 144865850 . G T 2165.41 PASS AC=1;AF=0.5;AN=2;DP=8448;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:78,76:154:99:1730,0,1826:34,44,36,40 chr1 144866509 . G A 184.38 PASS AC=1;AF=0.5;AN=2;DP=2643;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:19,24:43:99:641,0,598:15,4,16,8 chr1 144866643 . G A 134.98 PASS AC=1;AF=0.5;AN=2;DP=8379;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:94,77:171:99:1590,0,2167:49,45,38,39 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 0/1:91,82:173:99:1756,0,2147:43,48,39,43 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 0/1:27,25:52:99:663,0,674:10,17,8,17 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 0/1:18,18:36:99:490,0,504:3,15,6,12 chr1 144871738 . C A 451.41 PASS AC=1;AF=0.5;AN=2;DP=2588;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:31,24:55:99:886,0,1645:21,10,18,6 chr1 144871755 . A T 611.68 PASS AC=1;AF=0.5;AN=2;DP=3227;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:37,35:72:99:1157,0,1715:25,12,22,13 chr1 144871782 . A G 659.76 PASS AC=1;AF=0.5;AN=2;DP=4281;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:39,40:79:99:1025,0,942:25,14,22,18 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 0/1:52,74:126:99:1848,0,1254:25,27,32,42 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 0/1:83,77:160:99:1793,0,2171:55,28,51,26 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 0/1:110,99:209:99:2343,0,2840:69,41,61,38 chr1 144873840 . A G 2374.63 PASS AC=1;AF=0.5;AN=2;DP=12461;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:127,118:245:99:2704,0,3230:78,49,68,50 chr1 144873887 . C T 2787.42 PASS AC=1;AF=0.5;AN=2;DP=15002;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:161,135:296:99:2845,0,4035:86,75,67,68 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 0/1:234,67:301:99:1787,0,8397:107,127,29,38 chr1 144874038 . T C 2554.08 PASS AC=1;AF=0.5;AN=2;DP=10333;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:115,81:196:99:1856,0,2772:43,72,32,49 chr1 144874070 . C T 1978.37 PASS AC=1;AF=0.5;AN=2;DP=6686;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:72,54:126:99:1404,0,1870:27,45,20,34 chr1 144874088 . G C 1643.95 PASS AC=1;AF=0.5;AN=2;DP=4965;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:56,41:97:99:1021,0,1587:17,39,12,29 chr1 144874641 . G C 355.59 PASS AC=1;AF=0.5;AN=2;DP=5382;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:63,44:107:99:1084,0,1634:38,25,30,14 chr1 144874760 . T C 1179.62 PASS AC=1;AF=0.5;AN=2;DP=10355;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:127,95:222:99:2028,0,2990:60,67,47,48 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 0/1:134,28:162:99:444,0,3634:52,82,12,16 chr1 144875799 . G A 1527.03 PASS AC=1;AF=0.5;AN=2;DP=4598;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:33,41:74:99:957,0,921:25,8,25,16 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 0/1:126,64:190:99:1202,0,3310:51,75,29,35 chr1 144877176 . C T 1129.88 PASS AC=1;AF=0.5;AN=2;DP=4453;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:42,38:80:99:1046,0,1086:29,13,28,10 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 0/1:57,55:112:99:1410,0,1466:20,37,19,36 chr1 144877390 . G A 945.15 PASS AC=1;AF=0.5;AN=2;DP=3645;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:35,41:76:99:1137,0,1102:8,27,12,29 chr1 144878928 . G T 2504.06 PASS AC=1;AF=0.5;AN=2;DP=10003;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:107,115:222:99:2850,0,2749:70,37,75,40 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 0/1:6,22:28:99:704,0,116:2,4,10,12 chr1 144879375 . T C 691.25 PASS AC=1;AF=0.5;AN=2;DP=4941;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:54,30:84:99:685,0,1513:36,18,21,9 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 0/1:27,8:35:99:214,0,850:6,21,3,5 chr1 144882581 . A G 1908.64 PASS AC=1;AF=0.5;AN=2;DP=4418;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:43,37:80:99:1187,0,1509:27,16,22,15 chr1 144882823 . C T 5139.25 PASS AC=1;AF=0.5;AN=2;DP=19290;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:176,186:362:99:4701,0,4526:71,105,69,117 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 0/1:75,26:101:99:677,0,2556:14,61,4,22 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 0/1:32,42:74:99:1047,0,768:20,12,26,16 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 0/1:51,63:114:99:1601,0,1233:33,18,40,23 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 0/1:68,90:158:99:2179,0,1364:33,35,46,44 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 0/1:51,24:75:99:550,0,1389:17,34,10,14 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 0/1:4,26:30:89:871,0,89:0,4,3,23 chr1 144890833 . T C 302.34 PASS AC=1;AF=0.5;AN=2;DP=1166;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:12,5:17:99:133,0,401:10,2,3,2 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 0/1:13,5:18:99:144,0,472:5,8,1,4 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 0/1:34,23:57:99:627,0,920:23,11,16,7 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 0/1:70,50:120:99:1157,0,1668:39,31,27,23 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 0/1:72,21:93:99:306,0,2131:40,32,11,10 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 0/1:53,22:75:99:453,0,1486:15,38,7,15 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 0/1:233,125:358:99:3571,0,5735:118,115,75,50 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 0/1:295,56:351:99:571,0,12953:151,144,33,23 chr1 144910082 . A G 820.94 PASS AC=1;AF=0.727;AN=2;DP=3090;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:16,48:64:99:1106,0,288:6,10,21,27 chr1 144911702 . C A 415.59 PASS AC=1;AF=0.5;AN=2;DP=920;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:13,8:21:99:294,0,778:9,4,6,2 chr1 144911704 . G C 415.59 PASS AC=1;AF=0.5;AN=2;DP=950;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:14,8:22:99:294,0,778:10,4,6,2 chr1 144912153 . A G 161.01 PASS AC=1;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 0/1:2,9:11:49:267,0,49:0,2,5,4 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 0/1:8,10:18:99:219,0,225:4,4,4,6 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 0/1:87,34:121:99:631,0,2275:55,32,21,13 chr1 144915561 . G A 1600.31 PASS AC=1;AF=0.5;AN=2;DP=6400;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:64,75:139:99:1722,0,1512:24,40,31,44 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 0/1:36,13:49:99:336,0,1220:8,28,3,10 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 0/1:37,12:49:99:224,0,1166:8,29,3,9 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 0/1:120,32:152:99:483,0,2963:61,59,16,16 chr1 144916748 . C G 1631.42 PASS AC=1;AF=0.5;AN=2;DP=5632;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:61,52:113:99:1265,0,1394:28,33,21,31 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 0/1:61,71:132:99:1688,0,1381:30,31,37,34 chr1 144917809 . T C 184.35 PASS AC=1;AF=0.5;AN=2;DP=133;FractionInformativeReads=1;set=variant7-variant22-variant23-variant26-variant32 GT:AD:DP:GQ:PL:SB 0/1:19,10:29:99:238,0,635:12,7,7,3 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 0/1:21,12:33:99:351,0,658:12,9,9,3 chr1 144917841 . T C 590.47 PASS AC=1;AF=0.5;AN=2;DP=1594;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:18,19:37:99:573,0,456:9,9,14,5 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 0/1:6,3:9:88:88,0,201:1,5,0,3 chr1 144918957 . T A 1270.16 PASS AC=1;AF=0.5;AN=2;DP=3877;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:39,39:78:99:961,0,894:17,22,23,16 chr1 144919008 . AC A 716.79 PASS AC=1;AF=0.5;AN=2;DP=2546;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-filterInvariant38-variant39-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,16:62:99:390,0,1481:19,27,8,8 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 0/1:8,18:26:99:625,0,234:2,6,5,13 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 0/1:156,54:210:99:909,0,4385:90,66,29,25 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 0/1:123,95:218:99:2363,0,3048:64,59,44,51 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 0/1:124,91:215:99:2207,0,3180:58,66,40,51 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 0/1:91,33:124:99:608,0,2436:50,41,17,16 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 0/1:76,47:123:99:1038,0,1884:35,41,19,28 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 0/1:136,23:159:99:383,0,4595:71,65,13,10 chr1 144923823 . TAGGAAGAAACGGCA T 2299.16 PASS AC=1;AF=0.761;AN=2;DP=6057;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:36,57:93:99:2243,0,1738:15,21,15,42 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 0/1:27,35:62:99:919,0,657:19,8,22,13 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 0/1:33,45:78:99:1068,0,747:20,13,26,19 chr1 144930940 . T C 3408.15 PASS AC=1;AF=0.5;AN=2;DP=10589;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:117,102:219:99:2694,0,2967:55,62,44,58 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 0/1:142,148:290:99:3611,0,3749:76,66,69,79 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 0/1:133,116:249:99:2683,0,3393:66,67,50,66 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 0/1:154,41:195:99:539,0,4176:76,78,20,21 chr1 144931873 . C G 2611.39 PASS AC=1;AF=0.5;AN=2;DP=5542;MQ=60;set=variant-variant4-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant17-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:151,37:188:99:719,0,4017:81,70,24,13 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 0/1:122,102:224:99:2433,0,3012:58,64,47,55 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 0/1:160,31:191:99:409,0,4607:76,84,15,16 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 0/1:102,80:182:99:3099,0,4119:57,45,43,37 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 0/1:94,83:177:99:3168,0,3862:55,39,43,40 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 0/1:94,83:177:99:3136,0,3606:55,39,43,40 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 0/1:185,139:324:99:3372,0,4442:101,84,73,66 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 0/1:261,55:316:99:738,0,6789:126,135,24,31 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 0/1:174,132:306:99:4930,0,7774:81,93,63,69 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 0/1:174,129:303:99:4930,0,7774:81,93,61,68 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 1/1:0,22:22:66:725,66,0:0,0,16,6 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 0/1:206,137:343:99:2989,0,4914:104,102,70,67 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 0/1:77,33:110:99:714,0,2385:36,41,13,20 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 0/1:76,74:150:99:1840,0,1944:40,36,41,33 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 1/1:0,198:198:99:6041,593,0:0,0,100,98 chr1 144946768 . G A 1506.56 PASS AC=1;AF=0.5;AN=2;DP=4629;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:49,33:82:99:890,0,1250:16,33,12,21 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 0/1:11,6:17:99:215,0,938:1,10,0,6 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 0/1:98,13:111:99:102,0,2614:61,37,10,3 chr1 144951973 . T C 4189.54 PASS AC=1;AF=0.5;AN=2;DP=8820;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:63,72:135:99:1798,0,1501:38,25,47,25 chr1 144952078 . C A 2498.81 PASS AC=1;AF=0.5;AN=2;DP=11632;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:158,56:214:99:909,0,3965:77,81,29,27 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 0/1:94,16:110:99:107,0,2620:27,67,7,9 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 0/1:60,31:91:99:590,0,1630:14,46,12,19 chr1 144994658 . C A 4865.19 PASS AC=1;AF=0.5;AN=2;DP=20914;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:226,220:446:99:5243,0,5962:136,90,132,88 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 1/1:0,608:608:99:18687,1815,0:0,0,280,328 chr1 144994902 . G A 1990.56 PASS AC=1;AF=0.5;AN=2;DP=15939;MQ=60;set=variant2-filterInvariant7-filterInvariant9-filterInvariant10-variant12-filterInvariant13-filterInvariant14-filterInvariant15-variant16-filterInvariant18-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant25-filterInvariant26-filterInvariant28-variant29-variant30-filterInvariant32-variant33-filterInvariant37-filterInvariant39-filterInvariant40-filterInvariant41-filterInvariant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:483,87:570:99:1019,0,13840:216,267,38,49 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 0/1:40,6:46:71:71,0,1434:7,33,2,4 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 1/1:0,44:44:99:1464,132,0:0,0,31,13 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 0/1:148,48:196:99:803,0,3763:71,77,24,24 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 0/1:92,58:150:99:1597,0,2457:46,46,23,35 chr1 145014186 . GAA G,GA,GAAA 1305.56 PASS AC=0,0,1;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 0/3:76:99:32,22,14,8 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 0/1:82,12:94:72:72,0,3202:48,34,7,5 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 0/1:82,12:94:69:69,0,3224:48,34,7,5 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 0/1:90,14:104:99:112,0,3008:52,38,9,5 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 0/1:76,68:144:99:1531,0,1912:36,40,33,35 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 0/1:29,22:51:99:816,0,1752:5,24,6,16 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 0/1:22,18:40:99:753,0,1514:4,18,5,13 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 1/1:2,129:131:99:3820,343,0:1,1,49,80 chr1 145016032 . C CA 264.95 PASS AC=1;AF=0.5;AN=2;DP=3889;MQ=60;set=variant-variant2-variant4-variant5-variant6-filterInvariant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant15-filterInvariant16-variant18-variant19-variant20-variant21-filterInvariant22-variant23-variant24-variant25-variant26-variant27-variant28-filterInvariant29-variant30-variant31-variant32-variant33-variant36-variant37-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,34:88:99:603,0,1250:19,35,14,20 chr1 145017784 . CTT CT,C 159.27 PASS AC=1,0;AF=0.636,0.091;AN=2;DP=1028;set=Intersection GT:DP:GQ:SB 0/1:17:28:1,2,4,10 chr1 145017822 . C CTCCTTCCTTCCCTCCCCTCCCCTCCCTTCCTTCCTTCCT,CTCCTTCCTTCCCTCCCCTCCCCTCCCTTCCTTCCT,CTCCTTCCTTCCCTCCCCTCCCCTCCCTTCCT,CTCCTTCCTTCCCTCCCCCCCCCTCCCTCCCTTCCTTCCT,CTCCTTCCTTCCCTCCCCTCCCCTCCCTCCCTTCCTTCCT,CTCCTTCCTTCCCTCCCCTCCCCTCCCCTCCCTTCCTTCCT 396.15 PASS AC=0,0,0,1,0,0;AF=0.063,0.344,0.031,0.031,0.094,0.031;AN=2;DP=224;set=variant-variant2-variant5-variant7-variant10-variant12-variant15-variant17-variant23-variant26-variant28-variant29-variant32-variant41-variant43-variant44 GT:DP:GQ:SB 0/4:7:99:0,5,1,1 chr1 145017851 . T C 171.25 PASS AC=1;AF=0.5;AN=2;DP=1046;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant11-variant12-variant13-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,11:46:99:233,0,1219:19,16,4,7 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 0/1:74,48:122:99:1119,0,1909:29,45,22,26 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 0/1:37,6:43:99:140,0,1673:16,21,1,5 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 0/1:38,21:59:99:732,0,1148:26,12,17,4 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 0/1:46,17:63:99:402,0,2235:33,13,12,5 chr1 145021089 . G A 66.5 PASS AC=1;AF=0.5;AN=2;DP=7472;MQ=60;set=filterInvariant-variant4-variant5-filterInvariant6-variant7-filterInvariant8-variant9-filterInvariant10-variant11-filterInvariant12-variant13-variant14-filterInvariant15-variant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-filterInvariant40-filterInvariant41-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:109,75:184:99:1794,0,3138:77,32,50,25 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 0/1:143,55:198:99:1235,0,3921:47,96,20,35 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 0/1:13,6:19:99:186,0,469:12,1,5,1 chr1 145038736 . C G 476.74 PASS AC=1;AF=0.5;AN=2;DP=1898;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:14,24:38:99:658,0,314:10,4,16,8 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 1/1:0,105:105:99:3406,323,0:0,0,64,41 chr1 145038889 . G A 82.23 PASS AC=1;AF=0.5;AN=2;DP=1911;MQ=60;set=filterInvariant4-filterInvariant19-filterInvariant20-variant23-filterInvariant24-filterInvariant26-filterInvariant27-filterInvariant30-variant31-filterInvariant36-variant37-variant40-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:112,24:136:99:383,0,3331:55,57,14,10 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 0/1:100,121:221:99:3500,0,2808:44,56,57,64 chr1 145038954 . G T 181.18 PASS AC=1;AF=0.5;AN=2;DP=3204;MQ=60;set=filterInvariant4-filterInvariant11-variant13-filterInvariant19-filterInvariant20-variant23-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant30-variant31-filterInvariant34-variant37-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:188,37:225:99:488,0,6501:84,104,19,18 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 0/1:101,131:232:99:3369,0,2437:41,60,59,72 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 0/1:95,74:169:99:1754,0,2454:57,38,48,26 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 0/1:344,115:459:99:2085,0,12859:184,160,59,56 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 0/1:275,182:457:99:5743,0,7431:150,125,91,91 chr1 145039866 . A G 4713.77 PASS AC=1;AF=0.5;AN=2;DP=20613;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:223,212:435:99:5245,0,5452:118,105,101,111 chr1 145039922 . G C 109.48 PASS AC=1;AF=0.5;AN=2;DP=13546;MQ=60;set=filterInvariant2-variant5-variant7-variant8-variant9-variant10-variant12-filterInvariant13-variant14-filterInvariant15-filterInvariant16-variant17-variant19-variant20-filterInvariant21-variant22-filterInvariant23-variant25-filterInvariant26-variant28-filterInvariant29-variant30-filterInvariant31-filterInvariant32-variant33-filterInvariant36-variant38-variant39-filterInvariant40-filterInvariant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:381,58:439:99:418,0,10243:184,197,30,28 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 0/1:116,104:220:99:2586,0,3063:39,77,39,65 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 0/1:105,74:179:99:1864,0,3291:37,68,27,47 chr1 145040063 . CT C 1540.04 PASS AC=1;AF=0.5;AN=2;DP=5186;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant13-filterInvariant14-variant15-variant16-variant17-filterInvariant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-filterInvariant31-variant32-variant33-filterInvariant34-variant36-variant38-variant41-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:110,41:151:99:1151,0,4277:37,73,14,27 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 0/1:94,30:124:99:598,0,2673:63,31,18,12 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 0/1:154,94:248:99:2209,0,3960:97,57,54,40 chr1 145074975 . G A 261.58 PASS AC=1;AF=0.5;AN=2;DP=4849;MQ=60;set=filterInvariant-variant4-filterInvariant8-filterInvariant9-variant14-filterInvariant20-filterInvariant23-filterInvariant25-filterInvariant27-filterInvariant28-variant30-filterInvariant31-filterInvariant36-filterInvariant37-filterInvariant39 GT:AD:DP:GQ:PL:SB 0/1:264,35:299:99:137,0,7326:152,112,20,15 chr1 145075234 . C T 645.58 PASS AC=1;AF=0.5;AN=2;DP=1523;MQ=60;set=variant4-variant8-variant10-variant13-variant14-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant23-filterInvariant25-filterInvariant28-variant30-filterInvariant31-filterInvariant37-filterInvariant39-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:75,9:84:99:103,0,2351:22,53,1,8 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 0/1:31,9:40:99:123,0,927:22,9,5,4 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 0/1:191,105:296:99:1946,0,4745:109,82,60,45 chr1 145075775 . G A,T 2362.17 PASS AC=1,0;AF=0.464,0.036;AN=2;DP=7754;MQ=60;set=variant4-filterInvariant9-filterInvariant13-variant14-filterInvariant18-filterInvariant21-filterInvariant23-filterInvariant25-filterInvariant26-filterInvariant30-filterInvariant37-filterInvariant39-filterInvariant41-filterInvariant42 GT:DP:GQ:SB 0/1:524:99:248,212,38,26 chr1 145075854 . G C 6694.88 PASS AC=1;AF=0.5;AN=2;DP=26249;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:333,270:603:99:6000,0,8046:166,167,135,135 chr1 145076041 . C T 107.95 PASS AC=1;AF=0.5;AN=2;DP=8301;MQ=60;set=filterInvariant-variant4-filterInvariant9-variant10-variant13-variant14-filterInvariant19-filterInvariant23-filterInvariant25-filterInvariant26-filterInvariant28-filterInvariant30-filterInvariant31-filterInvariant33-filterInvariant36-filterInvariant37-filterInvariant39-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:365,42:407:99:132,0,10635:177,188,22,20 chr1 145076156 . C T 1088.84 PASS AC=1;AF=0.5;AN=2;DP=4848;MQ=60;set=variant4-filterInvariant9-filterInvariant10-variant13-variant14-filterInvariant21-filterInvariant23-filterInvariant25-filterInvariant26-filterInvariant30-filterInvariant31-filterInvariant33-filterInvariant36-filterInvariant37-filterInvariant39-variant41-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:204,24:228:95:95,0,6712:66,138,7,17 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 0/1:159,59:218:99:1216,0,4876:52,107,19,40 chr1 145076241 . C T 279.8 PASS AC=1;AF=0.5;AN=2;DP=3423;MQ=60;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-filterInvariant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-filterInvariant37-variant38-variant39-variant40-variant41-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,11:65:99:136,0,1908:8,46,3,8 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 0/1:6,20:26:99:782,0,151:3,3,2,18 chr1 145103844 . G A 617.51 PASS AC=1;AF=0.5;AN=2;DP=4769;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:66,22:88:99:579,0,2116:50,16,19,3 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 0/1:199,92:291:99:1578,0,4884:97,102,47,45 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 0/1:93,27:120:99:810,0,3723:34,59,10,17 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 0/1:49,8:57:99:104,0,1662:41,8,6,2 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 0/1:90,15:105:99:186,0,2976:64,26,11,4 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 0/1:17,109:126:99:3664,0,123:11,6,75,34 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 0/1:134,32:166:99:481,0,3962:89,45,18,14 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 0/1:206,78:284:99:1430,0,5219:109,97,43,35 chr1 145109583 . C A 4525.34 PASS AC=1;AF=0.5;AN=2;DP=15878;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:194,117:311:99:2666,0,5468:100,94,60,57 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 0/1:274,43:317:99:266,0,8849:135,139,21,22 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 0/1:13,7:20:99:237,0,453:1,12,0,7 chr1 145112284 . CCG C 232.12 PASS AC=1;AF=0.5;AN=2;DP=3146;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:54,7:61:99:165,0,2934:46,8,6,1 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 0/1:48,16:64:99:382,0,1601:40,8,13,3 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 0/1:57,8:65:99:165,0,2934:48,9,6,2 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 0/1:79,30:109:99:678,0,2415:61,18,22,8 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 0/1:243,72:315:99:2330,0,11527:128,115,37,35 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 0/1:255,75:330:99:2302,0,11889:135,120,39,36 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 0/1:217,66:283:99:1068,0,5718:99,118,29,37 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 0/1:53,20:73:99:681,0,2701:41,12,15,5 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 0/1:193,103:296:99:2657,0,4837:96,97,50,53 chr1 145115883 . G T 62.46 PASS AC=1;AF=0.5;AN=2;DP=946;MQ=60;set=filterInvariant7-filterInvariant23-filterInvariant37-variant39-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:155,26:181:99:263,0,4099:58,97,9,17 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 1/1:0,17:17:54:669,54,0:0,0,17,0 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 0/1:166,43:209:99:465,0,4059:94,72,20,23 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 1/1:128:99:1,1,77,49 chr1 145209846 . G A 610.05 PASS AC=1;AF=0.5;AN=2;DP=4257;set=variant-variant4-variant11-variant22-variant23-variant26-variant27-variant29-variant30-variant36-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:279,64:343:99:902,0,7523:144,135,28,36 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 0/1:320,26:346:99:146,0,13646:158,162,19,7 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 0/1:322,27:349:99:149,0,13624:160,162,20,7 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 0/1:497,169:666:99:3068,0,12364:303,194,100,69 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 0/1:659,210:869:99:3525,0,15904:341,318,105,105 chr1 145273431 . A G 2053.98 PASS AC=1;AF=0.5;AN=2;DP=14303;set=variant-variant4-filterInvariant11-filterInvariant13-filterInvariant14-filterInvariant18-filterInvariant22-variant23-filterInvariant26-filterInvariant27-variant29-variant30-filterInvariant32-filterInvariant33-variant34-filterInvariant36-filterInvariant37-variant41-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:422,173:595:99:3324,0,11217:151,271,65,108 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 0/1:262,98:360:99:2113,0,7464:77,185,28,70 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 0/1:106,21:127:99:362,0,3482:20,86,4,17 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 0/1:56,15:71:99:240,0,1693:52,4,13,2 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 0/1:736,73:809:99:253,0,24908:448,288,46,27 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 0/1:852,252:1104:99:3641,0,21214:471,381,137,115 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 0/1:524,236:760:99:4837,0,14430:213,311,97,139 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 0/1:364,132:496:99:4158,0,14588:137,227,55,77 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 0/1:315,121:436:99:4056,0,13156:108,207,55,66 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 0/1:304,75:379:99:1153,0,12025:114,190,32,43 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 0/1:98,47:145:99:1162,0,3044:49,49,15,32 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 0/1:100,43:143:99:1190,0,2987:60,40,25,18 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 0/1:111,25:136:99:444,0,3365:30,81,6,19 chr1 145290346 . A G 746.92 PASS AC=1;AF=0.5;AN=2;DP=1597;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:5,15:20:99:519,0,149:4,1,12,3 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 0/1:21,3:24:63:63,0,785:16,5,3,0 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 0/1:26,13:39:99:307,0,786:22,4,8,5 chr1 145290398 . G A 372.2 PASS AC=1;AF=0.5;AN=2;DP=2518;set=variant-variant2-variant4-variant5-variant6-variant8-filterInvariant9-variant11-variant13-variant15-variant16-filterInvariant18-filterInvariant19-variant20-filterInvariant21-filterInvariant22-variant23-variant24-filterInvariant25-variant26-variant27-variant28-filterInvariant29-variant32-variant33-variant36-filterInvariant39-variant40-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:38,19:57:99:456,0,1282:25,13,14,5 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 0/1:44,15:59:99:497,0,1848:33,11,8,7 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 0/1:45,15:60:99:494,0,1870:33,12,8,7 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 0/1:65,18:83:99:217,0,1788:33,32,8,10 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 0/1:52,11:63:99:132,0,1500:20,32,4,7 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 0/1:45,8:53:99:160,0,1576:15,30,3,5 chr1 145290553 . C T 229.88 PASS AC=1;AF=0.5;AN=2;DP=2348;set=variant-filterInvariant2-variant4-filterInvariant5-variant6-variant8-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-filterInvariant21-variant23-variant24-variant25-filterInvariant26-variant27-variant28-filterInvariant31-variant32-variant33-variant36-filterInvariant37-variant39-variant40-variant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:31,20:51:99:496,0,1052:10,21,6,14 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 0/1:41,6:47:99:129,0,1472:13,28,2,4 chr1 145290570 . G A 252.52 PASS AC=1;AF=0.5;AN=2;DP=1896;set=variant-filterInvariant2-variant4-filterInvariant5-variant6-filterInvariant7-variant8-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant25-filterInvariant26-variant27-variant28-filterInvariant31-variant32-variant33-variant36-variant37-variant39-variant40-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:25,18:43:99:457,0,793:7,18,5,13 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 0/1:50,10:60:97:97,0,1311:32,18,5,5 chr1 145293059 . A G 416.21 PASS AC=1;AF=0.5;AN=2;DP=3105;set=variant2-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-variant9-filterInvariant11-filterInvariant13-variant14-filterInvariant15-variant18-filterInvariant19-filterInvariant20-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-variant26-variant32-filterInvariant33-variant36-filterInvariant40-filterInvariant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,10:101:99:146,0,4078:49,42,7,3 chr1 145293069 . A T 479.37 PASS AC=1;AF=0.5;AN=2;DP=3441;set=variant2-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-variant9-filterInvariant11-filterInvariant13-variant14-filterInvariant15-variant18-filterInvariant19-filterInvariant20-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-variant26-variant32-filterInvariant33-variant36-filterInvariant40-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:100,13:113:99:228,0,4306:50,50,10,3 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 0/1:277,80:357:99:1336,0,7301:161,116,44,36 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 0/1:439,54:493:85:85,0,16954:230,209,26,28 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 0/1:393,122:515:99:4012,0,16107:197,196,61,61 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 0/1:384,123:507:99:4032,0,16042:188,196,62,61 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 0/1:377,124:501:99:3994,0,15706:173,204,59,65 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 0/1:350,141:491:99:2915,0,10857:157,193,65,76 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 0/1:289,104:393:99:1861,0,7338:128,161,45,59 chr1 145295539 . A G 204.12 PASS AC=2;AF=0.625;AN=2;DP=1077;FractionInformativeReads=1;set=variant7-filterInvariant8-variant10-variant13-filterInvariant14-filterInvariant15-variant18-filterInvariant22-filterInvariant23-variant26-filterInvariant28-filterInvariant29-variant30-filterInvariant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:720,75,0:0,0,10,15 chr1 145295541 . A G 70.62 PASS AC=1;AF=0.5;AN=2;DP=298;FractionInformativeReads=1;set=filterInvariant23-filterInvariant26-variant30-filterInvariant34 GT:AD:DP:GQ:PL:SB 0/1:21,5:26:99:99,0,448:11,10,0,5 chr1 145296268 . C T,G 1509.06 PASS AC=0,1;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 0/2:54:69:33,14,3,4 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 1/1:0,103:103:99:3029,308,0:0,0,51,52 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 1/1:0,46:46:99:1477,138,0:0,0,15,31 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 0/1:7,11:18:99:342,0,175:7,0,11,0 chr1 145297593 . T C 4299.76 PASS AC=1;AF=0.5;AN=2;DP=5725;set=variant-variant4-variant11-variant13-variant18-variant22-variant23-variant26-variant27-variant29-variant30-variant33-variant36-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:118,98:216:99:2272,0,2786:71,47,61,37 chr1 145297817 . G C 2392.12 PASS AC=2;AF=0.557;AN=2;DP=5067;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1919,162,0:0,0,10,44 chr1 145298186 . C G 367.26 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=3454;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:27,31:58:99:670,0,520:11,16,16,15 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 0/1:8,3:11:71:71,0,247:7,1,3,0 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 0/1:7,5:12:99:133,0,195:2,5,0,5 chr1 145299824 . C G 134.24 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1823;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:139,34:173:99:323,0,3335:81,58,17,17 chr1 145301587 . G T 296.19 DRAGENHardSNP AC=1;AF=0.512;AN=2;DP=1811;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:23,11:34:99:193,0,561:19,4,11,0 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 0/1:127,109:236:99:2042,0,2802:64,63,57,52 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 0/1:81,49:130:99:1599,0,3225:29,52,17,32 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 0/1:79,35:114:99:1314,0,3213:29,50,12,23 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 1/1:0,31:31:93:957,93,0:0,0,10,21 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 0/1:19,11:30:99:384,0,631:8,11,5,6 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 0/1:16,12:28:99:414,0,588:8,8,5,7 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 1/1:0,22:22:66:677,66,0:0,0,16,6 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 1/1:0,6:6:18:157,18,0:0,0,5,1 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 0/1:31,11:42:99:197,0,650:20,11,11,0 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 0/1:27,9:36:99:168,0,835:4,23,2,7 chr1 145310197 . C T 833.27 PASS AC=1;AF=0.5;AN=2;DP=3761;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:29,48:77:99:1027,0,736:9,20,21,27 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 0/1:19,6:25:99:118,0,535:18,1,6,0 chr1 145310983 . G C 1076.85 PASS AC=1;AF=0.591;AN=2;DP=3396;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:61,41:102:99:1011,0,1431:40,21,28,13 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 0/1:157,95:252:99:1847,0,3760:96,61,54,41 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 1/1:0,177:177:99:5200,530,0:0,0,104,73 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 0/1:19,24:43:99:564,0,452:17,2,22,2 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 0/1:261,41:302:99:236,0,6314:161,100,25,16 chr1 145323656 . A T 1282.53 PASS AC=1;AF=0.5;AN=2;DP=5674;set=variant4-filterInvariant5-filterInvariant12-filterInvariant13-filterInvariant22-variant23-filterInvariant25-filterInvariant32-filterInvariant33-variant34-filterInvariant38-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:305,116:421:99:1566,0,6439:156,149,57,59 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 0/1:20,144:164:99:3949,0,134:7,13,34,110 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 0/1:5,6:11:99:105,0,135:0,5,2,4 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 1/1:0,58:58:99:1651,173,0:0,0,10,48 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 0/1:11,3:14:80:80,0,343:7,4,3,0 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 0/1:21,7:28:99:171,0,494:10,11,5,2 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 0/1:20,7:27:99:173,0,471:10,10,5,2 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 0/1:13,10:23:99:250,0,435:3,10,3,7 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 0/1:6,5:11:99:143,0,193:1,5,1,4 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 0/1:312,207:519:99:4994,0,7577:194,118,130,77 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 0/1:516,99:615:99:925,0,14058:305,211,62,37 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 0/1:631,171:802:99:1873,0,16172:335,296,90,81 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 1/1:0,16:16:48:580,48,0:0,0,8,8 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 0/1:46,41:87:99:1077,0,1163:24,22,19,22 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 1/1:0,199:199:99:6005,595,0:0,0,101,98 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 1/1:0,149:149:99:5427,448,0:0,0,86,63 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 1/1:0,122:122:99:5338,370,0:0,0,42,80 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 1/1:0,106:106:99:4976,337,0:0,0,39,67 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 0/2:8:18:0,3,0,5 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 1/1:0,15:15:45:547,45,0:0,0,11,4 chr1 145472558 . GCCC G,GCC,GC 1437.38 PASS AC=0,0,1;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 0/3:46:99:14,1,16,15 chr1 145472582 . G C 847.2 PASS AC=1;AF=0.55;AN=2;DP=810;set=variant8-variant11-variant22-variant23-variant26-variant29-variant30-variant31-variant32-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,27:59:99:783,0,804:22,10,6,21 chr1 145475728 . T G 37.72 PASS AC=1;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 0/1:3,3:6:58:58,0,120:1,2,1,2 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 1/1:0,231:231:99:10494,728,0:0,0,141,90 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 0/1:50,49:99:99:1209,0,1324:20,30,25,24 chr1 145510376 . A G 546.92 DRAGENHardSNP AC=2;AF=0.955;AN=2;DP=1132;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:627,72,0:0,0,10,14 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 1/1:0,31:31:92:1031,92,0:0,0,23,8 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 0/1:79,76:155:99:1852,0,1961:34,45,34,42 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 1/1:0,70:70:99:2544,210,0:0,0,39,31 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 1/1:1,143:144:99:4456,422,0:1,0,78,65 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 0/1:20,42:62:99:1717,0,874:11,9,25,17 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 0/1:21,45:66:99:1754,0,923:12,9,26,19 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 0/1:42,33:75:99:936,0,1039:21,21,13,20 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 0/1:79,71:150:99:1674,0,1983:49,30,42,29 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 0/1:14,11:25:99:258,0,271:7,7,7,4 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 0/1:127,104:231:99:2546,0,3057:67,60,59,45 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 0/1:73,57:130:99:1513,0,1846:37,36,32,25 chr1 145555653 . C T 3351.89 PASS AC=2;AF=0.743;AN=2;DP=11105;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,265:266:99:7804,783,0:1,0,150,115 chr1 145556986 . C T 223.25 PASS AC=1;AF=0.615;AN=2;DP=949;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant12-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant28-variant31-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,23:35:99:672,0,357:11,1,17,6 chr1 145557362 . C A 362.64 PASS AC=1;AF=0.5;AN=2;DP=29;FS=0;FractionInformativeReads=1;MQ=60;set=variant8-variant23 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:144,0,283:2,7,2,4 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 1/1:0,77:77:99:2634,231,0:0,0,19,58 chr1 145558824 . A C 772.91 PASS AC=1;AF=0.641;AN=2;DP=2426;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,36:66:99:919,0,675:18,12,24,12 chr1 145560918 . G A 1613.06 PASS AC=1;AF=0.5;AN=2;DP=827;MQ=60;set=variant11-variant22-variant23-variant26-variant29-variant30-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,53:117:99:1242,0,1532:30,34,23,30 chr1 145561782 . G T 969.3 PASS AC=1;AF=0.5;AN=2;DP=91;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.603;QD=10.65;ReadPosRankSum=-1.035;SOR=0.767;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:55,36:91:99:998,0,1729:24,31,15,21 chr1 145562087 . G A 823.21 PASS AC=1;AF=0.533;AN=2;DP=1195;MQ=60;set=variant-variant11-variant13-variant16-variant21-variant22-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,35:59:99:1108,0,694:12,12,19,16 chr1 145562293 . G C 969.86 PASS AC=2;AF=0.763;AN=2;DP=6172;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,148:148:99:4629,444,0:0,0,69,79 chr1 145567008 . T G 790.03 PASS AC=1;AF=0.5;AN=2;DP=400;FractionInformativeReads=1;MQ=60;set=variant11-variant22-variant23-variant26-variant29-variant30-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,24:62:99:546,0,942:21,17,16,8 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 1/1:0,13:13:39:362,39,0:0,0,5,8 chr1 145568637 . C T 229.17 PASS AC=2;AF=0.825;AN=2;DP=102;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant12-variant13-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant31-variant32-variant36-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,0,2 chr1 145585317 . A G 2749.25 PASS AC=2;AF=0.989;AN=2;DP=5231;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,112:113:99:3410,300,0:1,0,65,47 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 1/1:0,36:36:99:1105,108,0:0,0,19,17 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 1/1:0,46:46:99:1403,138,0:0,0,23,23 chr1 145586780 . T C 3069.65 PASS AC=1;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 0/1:138,139:277:99:3148,0,3240:63,75,67,72 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 1/1:2,100:102:99:2939,255,0:1,1,56,44 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 1/1:1,86:87:99:2611,220,0:1,0,35,51 chr1 145589516 . G C 545.13 PASS AC=1;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 0/1:51,31:82:99:649,0,1476:19,32,14,17 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 1/1:0,6:6:18:262,18,0:0,0,0,6 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 1/1:0,6:6:18:189,18,0:0,0,4,2 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 1/1:0,95:95:99:2901,284,0:0,0,39,56 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 1/1:0,82:82:99:2597,246,0:0,0,42,40 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 1/1:0,100:100:99:3269,300,0:0,0,31,69 chr1 145687100 . A G 1445.97 PASS AC=1;AF=0.5;AN=2;DP=720;FractionInformativeReads=1;MQ=60;set=variant11-variant22-variant23-variant26-variant29-variant30-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,54:110:99:1351,0,1514:28,28,24,30 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 1/1:12,132:144:99:3128,175,0:6,6,73,59 chr1 145688893 . G A 574.75 PASS AC=1;AF=0.536;AN=2;DP=318;set=variant-variant6-variant11-variant13-variant17-variant21-variant22-variant23-variant26-variant29-variant30-variant32-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,18:22:99:635,0,103:0,4,2,16 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 1/1:0,19:19:57:669,57,0:0,0,14,5 chr1 145697315 . ATTT AT,A,ATT,ATTTT,ATTTTT 1326.8 PASS AC=0,1,1,0,0;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 2/3:122:99:23,20,35,44 chr1 145697799 . A G 7194.57 PASS AC=2;AF=0.989;AN=2;DP=7829;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,143:145:99:4582,387,0:1,1,48,95 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 0/1:41,37:78:99:546,0,657:15,26,10,27 chr1 145826770 . G A 4554.81 PASS AC=1;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 0/1:55,61:116:99:1607,0,1578:30,25,33,28 chr1 146013577 . A C 352.31 PASS AC=1;AF=0.534;AN=2;DP=2690;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:37,34:71:99:882,0,846:15,22,12,22 chr1 146215022 . T C 386.62 DRAGENHardSNP AC=2;AF=0.693;AN=2;DP=1403;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:323,33,0:0,0,11,0 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 1/1:0,114:114:99:5167,352,0:0,0,76,38 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 1/1:0,117:117:99:5167,352,0:0,0,77,40 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 1/1:0,146:146:99:4003,438,0:0,0,99,47 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 0/1:91,80:171:99:1562,0,1910:48,43,40,40 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 1/1:0,161:161:99:7011,478,0:0,0,69,92 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 1/1:1,156:157:99:6949,474,0:0,1,66,90 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 1/1:0,105:105:99:2949,315,0:0,0,37,68 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 1/1:0,21:21:63:616,63,0:0,0,5,16 chr1 146246193 . G A 462.95 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=283;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:51,41:92:99:785,0,1039:18,33,15,26 chr1 146246820 . C T 160.81 DRAGENHardSNP AC=1;AF=0.583;AN=2;DP=178;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:23,6:29:61:61,0,520:14,9,3,3 chr1 146250855 . C T 213.34 DRAGENHardSNP AC=2;AF=0.641;AN=2;DP=1946;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:148,18,0:0,0,3,3 chr1 146250905 . G C 248.36 DRAGENHardSNP AC=2;AF=0.621;AN=2;DP=2024;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:148,18,0:0,0,3,3 chr1 146317771 . C A 565.91 PASS AC=1;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 0/1:15,6:21:99:147,0,454:3,12,0,6 chr1 146395313 . A G 124.68 PASS AC=1;AF=0.5;AN=2;DP=88;FS=0;FractionInformativeReads=1;set=variant2-variant3-variant4-variant11-filterInvariant15-variant16-variant23-variant28-variant29-variant37-variant39-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:78:78,0,129:2,0,2,0 chr1 146395315 . T C 124.68 PASS AC=1;AF=0.5;AN=2;DP=91;FS=0;FractionInformativeReads=1;set=variant2-variant3-variant4-variant11-filterInvariant15-variant16-variant23-variant28-variant29-variant37-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:78:78,0,129:2,0,2,0 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 0/1:39,32:71:99:617,0,1075:29,10,17,15 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 0/1:56,26:82:99:532,0,1438:24,32,7,19 chr1 146397570 . A T 604.92 PASS AC=1;AF=0.5;AN=2;DP=31;FS=0;FractionInformativeReads=1;MQ=54.94;MQRankSum=-1.713;QD=19.51;ReadPosRankSum=-1.383;SOR=0.495;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:11,20:31:99:633,0,305:2,9,5,15 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 0/1:87:99:29,17,28,13 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 0/1:52,42:94:99:1593,0,2421:32,20,29,13 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 0/1:33,7:40:69:69,0,869:15,18,0,7 chr1 146399795 . C G 348.83 PASS AC=1;AF=0.5;AN=2;DP=29;FS=2.905;FractionInformativeReads=1;MQ=48.05;MQRankSum=0.472;QD=12.03;ReadPosRankSum=0.697;SOR=1.702;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:18,11:29:99:377,0,618:2,16,0,11 chr1 146403781 . G A 315.52 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=20;FS=0;FractionInformativeReads=1;MQ=28.66;MQRankSum=-0.047;QD=15.78;ReadPosRankSum=0.236;SOR=0.941;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:4,16:20:39:344,0,39:2,2,9,7 chr1 146409969 . A C 213.43 DRAGENHardSNP AC=1;AF=0.789;AN=2;DP=370;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:295,0,269:9,4,10,3 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 0/1:3,4:7:56:81,0,56:2,1,3,1 chr1 146466146 . G T 1634.11 PASS AC=1;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 0/1:39,36:75:99:976,0,1063:8,31,7,29 chr1 146491095 . A G 172.01 PASS AC=2;AF=0.941;AN=2;DP=419;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-filterInvariant20-variant21-filterInvariant23-variant24-variant25-variant26-filterInvariant27-variant28-filterInvariant29-filterInvariant31-variant33-variant34-filterInvariant37-variant38-variant39-variant40-variant41-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:173,18,0:0,0,3,3 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 1/1:0,9:9:27:405,27,0:0,0,8,1 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 1/1:0,9:9:27:405,27,0:0,0,8,1 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 1/1:0,7:7:21:274,21,0:0,0,5,2 chr1 146494511 . G A 106.77 PASS AC=1;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 0/1:3,4:7:73:89,0,73:2,1,3,1 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 1/1:0,7:7:21:271,21,0:0,0,5,2 chr1 146495752 . C T 78.16 PASS AC=1;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 0/1:12,5:17:99:111,0,287:5,7,2,3 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 0/1:70,80:150:99:1863,0,1693:44,26,47,33 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 0/1:143,123:266:99:2938,0,3527:74,69,64,59 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 1/1:0,86:86:99:2708,258,0:0,0,29,57 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 1/1:0,104:104:99:3321,311,0:0,0,56,48 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 1/1:0,18:18:54:655,54,0:0,0,2,16 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 1/1:0,40:40:99:1406,120,0:0,0,30,10 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 1/1:0,31:31:93:1053,93,0:0,0,12,19 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 1/1:0,16:16:48:707,48,0:0,0,16,0 chr1 146696955 . G C 629.27 PASS AC=2;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 1/1:0,57:57:99:1686,171,0:0,0,29,28 chr1 146714255 . A G 1383.97 PASS AC=2;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 1/1:0,100:100:99:3052,300,0:0,0,50,50 chr1 146714281 . C G 1160.21 PASS AC=2;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 1/1:0,101:101:99:3154,302,0:0,0,57,44 chr1 146714392 . G T,C 2135.73 PASS AC=0,2;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 2/2:175:99:0,0,101,74 chr1 146714588 . C T 678.67 PASS AC=2;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 1/1:0,55:55:99:1936,165,0:0,0,11,44 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 1/1:0,56:56:99:1845,168,0:0,0,23,33 chr1 146728149 . A G 1008.46 PASS AC=1;AF=0.583;AN=2;DP=1291;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant8-variant11-variant13-variant15-variant19-variant20-variant22-variant23-variant26-variant27-variant30-variant32-variant36-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,28:57:99:663,0,815:17,12,17,11 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 1/1:0,61:61:99:2309,187,0:0,0,36,25 chr1 146739068 . T C 452.48 PASS AC=1;AF=0.588;AN=2;DP=959;set=variant5-variant8-variant11-variant13-variant15-variant19-variant20-variant22-variant23-variant26-variant27-variant30-variant32-variant36-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,24:54:99:547,0,710:19,11,14,10 chr1 146739277 . T C 351.8 PASS AC=2;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 1/1:0,33:33:99:1131,99,0:0,0,9,24 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 1/1:0,201:201:99:6117,601,0:0,0,96,105 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 1/1:0,104:104:99:3330,311,0:0,0,39,65 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 0/1:5,18:23:99:565,0,112:1,4,4,14 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 0/1:12,9:21:99:321,0,477:4,8,2,7 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 1/1:0,12:12:36:415,36,0:0,0,3,9 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 1/1:0,98:98:99:3018,293,0:0,0,53,45 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 0/1:16,6:22:99:204,0,845:4,12,1,5 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 0/1:7,8:15:99:289,0,178:2,5,1,7 chr1 146762865 . A G 103.54 PASS AC=2;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 1/1:0,4:4:12:180,12,0:0,0,4,0 chr1 146762984 . A C 448.73 PASS AC=1;AF=0.588;AN=2;DP=532;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant11-variant13-variant15-variant19-variant20-variant22-variant23-variant26-variant27-variant30-variant32-variant36-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,7:19:99:258,0,637:7,5,4,3 chr1 146762985 . G A 448.73 PASS AC=1;AF=0.588;AN=2;DP=544;MQ=60;set=variant5-variant8-variant11-variant13-variant15-variant19-variant20-variant22-variant23-variant26-variant27-variant30-variant32-variant36-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,7:19:99:258,0,637:7,5,4,3 chr1 146763089 . G A 1432.49 PASS AC=2;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 1/1:0,75:75:99:2301,225,0:0,0,42,33 chr1 146763415 . T C 399.59 PASS AC=2;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 1/1:0,16:16:48:645,48,0:0,0,1,15 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 1/1:0,7:7:21:307,21,0:0,0,0,7 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 1/1:0,120:120:99:5520,373,0:0,0,77,43 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 1/1:0,50:50:99:1707,150,0:0,0,27,23 chr1 146767320 . A G 4136.4 PASS AC=2;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 1/1:0,208:208:99:6172,623,0:0,0,104,104 chr1 146767353 . G A 3239.8 PASS AC=1;AF=0.588;AN=2;DP=5376;MQ=60;set=variant5-variant8-variant11-variant13-variant15-variant19-variant20-variant22-variant23-variant26-variant27-variant30-variant32-variant36-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:117,119:236:99:2564,0,2848:53,64,59,60 chr1 146767486 . T C 2745.48 PASS AC=2;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 1/1:0,71:71:99:3138,217,0:0,0,22,49 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 1/1:0,68:68:99:3039,205,0:0,0,19,49 chr1 146767494 . C G 2562.17 PASS AC=2;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 1/1:0,64:64:99:3015,202,0:0,0,17,47 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 1/1:0,30:30:90:976,90,0:0,0,10,20 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 1/1:0,56:56:99:1731,168,0:0,0,19,37 chr1 147091689 . G A 1651.63 PASS AC=1;AF=0.5;AN=2;DP=949;FractionInformativeReads=1;MQ=60;set=variant23-variant26-variant29-variant30-variant32-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,70:140:99:1680,0,1798:38,32,39,31 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 1/1:0,113:113:99:3468,336,0:0,0,53,60 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 1/1:0,54:54:99:1624,162,0:0,0,26,28 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 1/1:0,46:46:99:1338,138,0:0,0,20,26 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 1/1:0,58:58:99:1834,173,0:0,0,29,29 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 1/1:0,80:80:99:2487,240,0:0,0,41,39 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 1/1:0,96:96:99:3060,288,0:0,0,64,32 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 1/1:0,78:78:99:2368,234,0:0,0,40,38 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 1/1:0,58:58:99:1832,174,0:0,0,34,24 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 1/1:0,87:87:99:2648,261,0:0,0,51,36 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 1/1:0,10:10:30:362,30,0:0,0,2,8 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 1/1:0,21:21:63:673,63,0:0,0,12,9 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 1/1:0,40:40:99:1253,120,0:0,0,21,19 chr1 147229628 . G GGGGCATTTGCCAGAGGTACATACCA 587.95 PASS AC=2;AF=0.683;AN=2;DP=1545;set=variant-variant2-variant3-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:83:1285,83,0:0,0,11,14 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 1/1:0,67:67:99:2304,201,0:0,0,45,22 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 1/1:0,12:12:36:460,36,0:0,0,1,11 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 1/1:0,17:17:51:543,51,0:0,0,12,5 chr1 147232740 . C T 226.59 PASS AC=2;AF=0.65;AN=2;DP=994;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:678,66,0:0,0,9,13 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 1/1:0,20:20:60:689,60,0:0,0,13,7 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 1/1:0,54:54:99:1650,162,0:0,0,24,30 chr1 147381397 . GA G,GAA 126.29 PASS AC=0,1;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 0/2:26:99:4,12,3,7 chr1 147381444 . A C 116.07 PASS AC=2;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 1/1:0,14:14:42:538,42,0:0,0,2,12 chr1 147597237 . G A 453.96 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=429;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:44,26:70:99:482,0,874:20,24,10,16 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 1/1:0,76:76:99:2462,227,0:0,0,48,28 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 1/1:0,24:24:72:989,72,0:0,0,6,18 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 1/1:0,18:18:63:898,63,0:0,0,4,14 chr1 148004440 . C A 361.53 PASS AC=1;AF=0.575;AN=2;DP=663;set=variant-variant4-variant8-variant9-variant13-variant14-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant30-variant33-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:22,17:39:99:541,0,637:19,3,15,2 chr1 148004472 . G A 52.13 PASS AC=1;AF=0.532;AN=2;DP=1511;set=filterInvariant-variant3-filterInvariant5-variant7-variant9-filterInvariant10-variant11-variant12-variant14-filterInvariant16-variant17-variant18-variant19-variant21-filterInvariant22-variant23-filterInvariant26-variant27-variant29-variant30-variant31-variant33-variant34-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,9:69:99:197,0,2746:46,14,9,0 chr1 148004475 . C G 40.13 PASS AC=1;AF=0.548;AN=2;DP=1618;set=filterInvariant-variant3-variant5-variant7-variant9-filterInvariant10-filterInvariant11-variant12-filterInvariant13-variant14-variant17-variant18-variant19-filterInvariant21-filterInvariant22-variant23-filterInvariant26-variant27-variant29-variant30-variant31-variant33-variant34-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,9:68:99:200,0,2724:45,14,9,0 chr1 148008380 . A T 70.79 PASS AC=1;AF=0.667;AN=2;DP=34;FractionInformativeReads=1;set=variant-variant21-variant23 GT:AD:DP:GQ:PL:SB 0/1:17,4:21:78:78,0,491:11,6,4,0 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 0/1:52,24:76:99:669,0,1742:27,25,17,7 chr1 148009768 . T A 700.48 PASS AC=1;AF=0.65;AN=2;DP=1184;set=variant-variant4-variant8-variant9-variant13-variant14-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant30-variant33-variant36-variant37-variant39-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:45,24:69:99:489,0,1165:24,21,13,11 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 0/1:39,18:57:99:501,0,1278:28,11,9,9 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 0/1:9,3:12:89:89,0,175:0,9,0,3 chr1 148010911 . G A 3363.42 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=20112;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:265,104:369:99:1405,0,6528:132,133,53,51 chr1 148010972 . A G 71.54 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2939;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:330,55:385:99:213,0,7014:154,176,26,29 chr1 148010987 . T C 189.76 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=963;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:313,66:379:99:473,0,6681:143,170,32,34 chr1 148011027 . C T 264.97 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=783;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:115,34:149:99:409,0,2537:36,79,9,25 chr1 148011047 . C T 39.83 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=88;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:22,7:29:81:81,0,514:2,20,0,7 chr1 148011763 . C T 76.69 PASS AC=1;AF=0.5;AN=2;DP=198;set=variant4-variant13-variant23-variant26-variant30-variant37 GT:AD:DP:GQ:PL:SB 0/1:25,4:29:90:90,0,694:7,18,0,4 chr1 148014718 . A T 756.02 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=924;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:43,9:52:99:102,0,1009:18,25,3,6 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 0/1:28,7:35:71:71,0,671:19,9,4,3 chr1 148015876 . C T 223.4 PASS AC=1;AF=0.647;AN=2;DP=244;FractionInformativeReads=1;set=variant4-variant8-variant9-variant13-variant14-variant18-variant19-variant20-variant23-variant25-variant26-variant27-variant33-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:257,0,223:4,6,4,8 chr1 148016252 . C G 61.73 PASS AC=1;AF=0.722;AN=2;DP=41;FS=0;FractionInformativeReads=1;set=filterInvariant-variant4-filterInvariant13-filterInvariant20-variant23-filterInvariant27-filterInvariant30-filterInvariant36-filterInvariant37 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:24:64,0,24:1,0,1,1 chr1 148017578 . C T 312.66 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=3757;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:160,31:191:99:301,0,3491:85,75,18,13 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 0/1:109,24:133:99:197,0,2558:50,59,9,15 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 0/1:58,16:74:99:181,0,1424:29,29,9,7 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 0/1:13,4:17:99:129,0,964:0,13,1,3 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 0/1:13,4:17:99:129,0,964:0,13,1,3 chr1 148023040 . G C 773.31 PASS AC=1;AF=0.5;AN=2;DP=3231;set=filterInvariant-filterInvariant4-filterInvariant8-filterInvariant9-variant13-filterInvariant14-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant23-variant25-filterInvariant26-filterInvariant27-filterInvariant30-filterInvariant33-filterInvariant36-filterInvariant37-filterInvariant39-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:82,39:121:99:905,0,1973:33,49,11,28 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 0/1:12,18:30:99:412,0,271:10,2,16,2 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 0/1:41,12:53:99:172,0,917:25,16,9,3 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 0/1:24,30:54:99:664,0,688:11,13,19,11 chr1 148023510 . C T 155.28 PASS AC=1;AF=0.5;AN=2;DP=1072;set=filterInvariant-variant4-filterInvariant8-filterInvariant9-filterInvariant13-filterInvariant14-variant18-filterInvariant19-variant20-filterInvariant21-filterInvariant23-filterInvariant25-variant26-filterInvariant27-filterInvariant30-variant33-filterInvariant36-filterInvariant37-filterInvariant39-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:45,10:55:85:85,0,1613:26,19,4,6 chr1 148024964 . A G 222.99 PASS AC=1;AF=0.688;AN=2;DP=1548;set=variant-filterInvariant4-variant8-variant9-filterInvariant10-filterInvariant13-filterInvariant14-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-filterInvariant30-filterInvariant31-variant33-variant36-filterInvariant37-filterInvariant39-filterInvariant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:48,20:68:99:349,0,1258:17,31,7,13 chr1 148025606 . C T 225.19 PASS AC=1;AF=0.643;AN=2;DP=902;set=variant-filterInvariant3-filterInvariant4-filterInvariant5-variant6-variant7-variant8-variant9-variant10-filterInvariant11-filterInvariant13-filterInvariant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-filterInvariant30-variant31-variant32-variant33-variant34-variant36-filterInvariant37-filterInvariant39-filterInvariant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,12:32:99:241,0,623:15,5,9,3 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 0/1:172,26:198:68:68,0,4468:64,108,14,12 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 0/1:3,2:5:63:64,0,63:2,1,0,2 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 0/1:82,28:110:99:912,0,4937:62,20,14,14 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 0/1:92,28:120:99:900,0,5048:67,25,14,14 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 0/1:34,11:45:99:190,0,1005:28,6,9,2 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 0/1:61,11:72:94:94,0,1857:48,13,9,2 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 0/1:89,42:131:99:832,0,2297:57,32,30,12 chr1 148344624 . T C,A 1879.8 PASS AC=0,1;AF=0.386,0.114;AN=2;DP=13312;set=Intersection GT:DP:GQ:SB 0/2:165:99:50,36,41,38 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 0/1:180,43:223:99:566,0,6697:92,88,23,20 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 0/1:140,20:160:99:177,0,3488:67,73,3,17 chr1 148588978 . C A 70.68 DRAGENHardSNP AC=1;AF=0.571;AN=2;DP=128;FS=0;FractionInformativeReads=1;SOR=0.693;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:2,6:8:25:124,0,25:1,1,3,3 chr1 148589042 . C A 52.7 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=14;FS=0;FractionInformativeReads=1;SOR=0.693;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:4,4:8:75:75,0,75:2,2,2,2 chr1 148644408 . A G 3296.68 DRAGENHardSNP AC=2;AF=0.86;AN=2;DP=2941;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1279,153,0:0,0,28,23 chr1 148754942 . A T 34.76 PASS AC=2;AF=0.875;AN=2;DP=58;FS=0;FractionInformativeReads=1;set=filterInvariant9-filterInvariant12-filterInvariant13-filterInvariant15-filterInvariant16-filterInvariant23-filterInvariant24-filterInvariant26-filterInvariant31-filterInvariant33-filterInvariant39-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:64,9,0:0,0,0,3 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 1/1:0,9:9:27:405,27,0:0,0,6,3 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 1/1:0,12:12:36:540,36,0:0,0,8,4 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 1/1:0,12:12:36:540,36,0:0,0,8,4 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 1/1:0,16:16:48:436,48,0:0,0,8,8 chr1 148756515 . A C 446.32 DRAGENHardSNP AC=2;AF=0.92;AN=2;DP=862;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,0,4 chr1 148756518 . C T 421.77 DRAGENHardSNP AC=2;AF=0.738;AN=2;DP=678;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,0,4 chr1 148873574 . G T 818.7 PASS AC=1;AF=0.5;AN=2;DP=4281;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:47,17:64:99:309,0,1230:13,34,5,12 chr1 148873588 . A T 87.81 PASS AC=1;AF=0.5;AN=2;DP=820;set=filterInvariant5-variant8-filterInvariant11-filterInvariant14-variant18-filterInvariant23-variant26-filterInvariant28-filterInvariant33-filterInvariant36-variant39-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:38,6:44:86:86,0,1102:10,28,1,5 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 0/1:24,20:44:99:396,0,542:9,15,9,11 chr1 148889543 . AT A 692.74 PASS AC=1;AF=0.5;AN=2;DP=3240;set=variant-variant2-filterInvariant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-filterInvariant15-variant16-variant17-variant18-variant19-variant20-variant21-filterInvariant22-filterInvariant23-variant24-variant25-filterInvariant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,12:71:99:104,0,1942:31,28,9,3 chr1 148889550 . TTA T 114.6 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=79;FS=6.112;FractionInformativeReads=0.949;MQ=48.77;MQRankSum=0.96;QD=1.45;ReadPosRankSum=2.669;SOR=0.915;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:60,15:75:99:152,0,1837:36,24,6,9 chr1 148889551 . T A 555.41 PASS AC=1;AF=0.5;AN=2;DP=234;set=variant6-variant23-variant43 GT:AD:DP:GQ:PL:SB 0/1:52,23:75:99:393,0,1263:30,22,12,11 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 0/1:39,22:61:99:528,0,956:15,24,6,16 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 0/1:13,7:20:99:184,0,384:1,12,1,6 chr1 148903047 . G A 391.27 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=18554;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:231,98:329:99:1486,0,5094:121,110,45,53 chr1 148903089 . G A 253.14 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=10999;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:198,32:230:99:178,0,5546:97,101,11,21 chr1 148903097 . C A 144.69 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=5364;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:200,37:237:99:369,0,5711:94,106,17,20 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 0/1:192,27:219:99:410,0,8096:101,91,9,18 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 0/1:187,20:207:99:274,0,7848:105,82,5,15 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 1/1:0,48:48:99:1725,144,0:0,0,6,42 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 0/1:14,11:25:99:224,0,287:8,6,6,5 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 0/1:14,11:25:99:226,0,287:8,6,6,5 chr1 149290401 . A G 86.89 PASS AC=1;AF=0.5;AN=2;DP=132;set=variant10-filterInvariant23-filterInvariant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:24,6:30:74:74,0,548:15,9,4,2 chr1 149290801 . C G 1078.67 PASS AC=2;AF=0.667;AN=2;DP=334;FractionInformativeReads=1;set=variant9-variant18-variant23 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1648,179,0:0,0,23,37 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 0/1:50,25:75:99:475,0,1023:26,24,9,16 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 1/1:0,8:8:24:246,24,0:0,0,2,6 chr1 149665167 . A G 5595.19 PASS AC=2;AF=0.977;AN=2;DP=9015;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,156:156:99:4651,468,0:0,0,83,73 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 0/1:105,95:200:99:2175,0,2423:56,49,52,43 chr1 149665383 . A G 1556.55 PASS AC=1;AF=0.523;AN=2;DP=6707;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:76,70:146:99:1597,0,1809:27,49,26,44 chr1 149665430 . T C 260.05 PASS AC=1;AF=0.5;AN=2;DP=602;set=variant4-variant8-variant10-variant20-variant23-variant33-variant38-variant39-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:42,19:61:99:320,0,1114:12,30,6,13 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 1/1:0,2:2:6:65,6,0:0,0,2,0 chr1 149676401 . A G 429.07 PASS AC=1;AF=0.5;AN=2;DP=8607;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:129,90:219:99:2261,0,3158:60,69,23,67 chr1 149764332 . G C 48.74 PASS AC=1;AF=0.5;AN=2;DP=92;FractionInformativeReads=1;set=filterInvariant23-variant30-variant32 GT:AD:DP:GQ:PL:SB 0/1:23,5:28:77:77,0,590:11,12,1,4 chr1 149764685 . G C 1745.92 PASS AC=1;AF=0.5;AN=2;DP=1233;set=variant13-variant15-variant19-variant21-variant23-variant25-variant30-variant32-variant34 GT:AD:DP:GQ:PL:SB 0/1:61,73:134:99:1782,0,1347:29,32,38,35 chr1 149783886 . C T 4015.95 PASS AC=1;AF=0.563;AN=2;DP=1909;set=variant15-variant19-variant21-variant23-variant25-variant30-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:123,123:246:99:2957,0,2909:52,71,49,74 chr1 149784689 . CCCA C 735.54 PASS AC=1;AF=0.563;AN=2;DP=255;set=variant15-variant19-variant21-variant23-variant25-variant30-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:345,0,520:10,1,8,1 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 0/1:139,31:170:99:880,0,30049:72,67,15,16 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 0/1:133,31:164:99:886,0,33034:65,68,15,16 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 0/1:139,31:170:99:862,0,36401:66,73,15,16 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 0/1:140,31:171:99:862,0,39083:70,70,15,16 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 0/1:149,25:174:99:622,0,44102:74,75,11,14 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 0/1:152,24:176:99:568,0,44866:78,74,11,13 chr1 149785183 . C G 104.62 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=383;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:167,16:183:99:196,0,46802:84,83,7,9 chr1 149785185 . T G 59.62 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=384;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:168,15:183:99:151,0,46783:84,84,6,9 chr1 149785192 . C T 41.56 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=396;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:172,14:186:94:94,0,47011:83,89,6,8 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 0/1:22,23:45:99:481,0,490:15,7,11,12 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 0/1:7,9:16:99:264,0,226:6,1,7,2 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 1/1:0,35:35:99:1311,105,0:0,0,25,10 chr1 149907919 . C T 1088.47 PASS AC=1;AF=0.5;AN=2;DP=97;FS=2.797;FractionInformativeReads=1;MQ=60;MQRankSum=-2.453;QD=11.22;ReadPosRankSum=-2.518;SOR=1.064;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:53,44:97:99:1117,0,1464:32,21,30,14 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 1/1:1,55:56:99:1610,155,0:1,0,24,31 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 1/1:0,165:165:99:4455,493,0:0,0,82,83 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 0/1:44,14:58:99:139,0,1808:15,29,14,0 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 1/1:0,78:78:99:2252,232,0:0,0,36,42 chr1 150055021 . G A 238.54 PASS AC=1;AF=0.5;AN=2;DP=119;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant17-variant23-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,14:19:99:508,0,162:0,5,1,13 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 1/1:0,100:100:99:3361,300,0:0,0,25,75 chr1 150121929 . C G 1297.49 PASS AC=1;AF=0.5;AN=2;DP=464;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant17-variant23-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,34:69:99:873,0,965:10,25,11,23 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 1/1:0,50:50:99:1497,150,0:0,0,19,31 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 1/1:0,29:29:87:991,87,0:0,0,9,20 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 1/1:0,38:38:99:1203,113,0:0,0,8,30 chr1 150192506 . CAAA CAA,C,CA,CAAAA 323.52 PASS AC=0,0,1,0;AF=0.136,0.091,0.303,0.015;AN=2;DP=4148;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant11-variant12-variant13-filterInvariant15-filterInvariant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:DP:GQ:SB 0/3:49:99:7,12,13,17 chr1 150199039 . CTCCTCT C 1169.6 PASS AC=1;AF=0.565;AN=2;DP=2575;MQ=60;set=variant2-variant3-variant6-variant7-variant9-variant10-variant12-variant15-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant34-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:59,40:99:99:1435,0,2456:25,34,13,27 chr1 150199123 . G T 2096.96 PASS AC=1;AF=0.721;AN=2;DP=2909;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,36:82:99:882,0,1235:19,27,13,23 chr1 150203082 . C CT 199.81 PASS AC=1;AF=0.615;AN=2;DP=230;set=variant2-variant3-variant7-variant9-filterInvariant15-variant17-variant20-variant22-variant23-variant24-variant27-variant29-variant40 GT:AD:DP:GQ:PL:SB 0/1:7,10:17:99:145,0,108:0,7,4,6 chr1 150203984 . AT A 106.65 PASS AC=1;AF=0.571;AN=2;DP=230;set=variant2-variant3-variant6-variant7-variant9-variant10-variant12-variant15-variant17-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant36-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:204,0,169:4,1,5,1 chr1 150234282 . T G 415.98 PASS AC=1;AF=0.625;AN=2;DP=273;MQ=60;set=variant2-variant3-variant7-variant9-variant10-variant12-variant13-variant15-variant17-variant22-variant23-variant24-variant26-variant29-variant31-variant36-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:115,0,155:3,1,1,3 chr1 150241230 . G T 2199.02 PASS AC=1;AF=0.563;AN=2;DP=1542;MQ=60;set=variant7-variant9-variant10-variant12-variant15-variant17-variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:91,74:165:99:1463,0,2278:42,49,32,42 chr1 150249101 . C A 583.17 PASS AC=2;AF=0.729;AN=2;DP=1925;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1508,126,0:0,0,8,34 chr1 150252329 . G A 395.02 PASS AC=2;AF=0.641;AN=2;DP=467;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:484,33,0:0,0,0,11 chr1 150252984 . T G 276.69 PASS AC=2;AF=0.769;AN=2;DP=451;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-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:416,39,0:0,0,7,6 chr1 150255587 . T C 2501.26 PASS AC=2;AF=0.756;AN=2;DP=2344;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-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1369,120,0:0,0,24,16 chr1 150258838 . C G 2945.71 PASS AC=2;AF=0.75;AN=2;DP=3634;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-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2496,234,0:0,0,51,27 chr1 150259400 . A C 1006.91 PASS AC=2;AF=0.633;AN=2;DP=2578;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2238,203,0:0,0,33,35 chr1 150266338 . T A 986.04 PASS AC=2;AF=0.613;AN=2;DP=2543;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2067,206,0:0,0,38,31 chr1 150276429 . G A 2649.53 PASS AC=2;AF=0.645;AN=2;DP=1764;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1684,150,0:0,0,13,37 chr1 150276461 . G A 690.23 PASS AC=2;AF=0.629;AN=2;DP=1174;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1330,114,0:0,0,9,29 chr1 150277387 . T C 402.01 PASS AC=2;AF=0.645;AN=2;DP=654;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:371,36,0:0,0,9,3 chr1 150281202 . A C 1765.6 PASS AC=2;AF=0.8;AN=2;DP=2317;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-variant30-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:2086,171,0:0,0,46,11 chr1 150281501 . A C 853.77 PASS AC=2;AF=0.788;AN=2;DP=763;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:831,57,0:0,0,0,19 chr1 150310549 . CA CAA,C 44.33 PASS AC=1,0;AF=0.107,0.411;AN=2;DP=1099;set=filterInvariant2-filterInvariant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant15-variant16-filterInvariant19-variant20-variant21-variant22-filterInvariant23-variant24-variant27-variant28-variant29-variant30-variant32-variant34-variant36-variant37-variant40-variant42-variant44 GT:DP:GQ:SB 0/1:38:72:21,9,7,1 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 0/2:88:99:28,27,13,20 chr1 150446673 . A G 4229.54 PASS AC=1;AF=0.542;AN=2;DP=3023;MQ=60;set=variant-variant4-variant14-variant19-variant23-variant25-variant26-variant30-variant33-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:105,97:202:99:2601,0,2908:48,57,43,54 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 1/1:1,222:223:99:6656,657,0:0,1,127,95 chr1 150469480 . C T 258.2 PASS AC=1;AF=0.55;AN=2;DP=465;MQ=60;set=variant5-variant6-variant7-variant9-variant10-variant12-variant17-variant23-variant32-variant42 GT:AD:DP:GQ:PL:SB 0/1:30,13:43:99:291,0,773:11,19,4,9 chr1 150482162 . A C 436.84 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2007;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:105,34:139:95:95,0,2099:33,72,34,0 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 1/1:0,15:15:45:569,45,0:0,0,12,3 chr1 150485984 . A C 175.1 PASS AC=1;AF=0.5;AN=2;DP=585;MQ=60;set=filterInvariant3-filterInvariant4-variant7-filterInvariant10-variant11-filterInvariant17-filterInvariant19-filterInvariant20-variant23-variant24-filterInvariant27-filterInvariant41-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:24,9:33:99:153,0,705:5,19,9,0 chr1 150485988 . T C 286.05 PASS AC=1;AF=0.5;AN=2;DP=483;MQ=60;set=filterInvariant3-filterInvariant4-filterInvariant9-filterInvariant10-variant11-filterInvariant17-variant19-filterInvariant20-filterInvariant23-filterInvariant24-filterInvariant29-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:25,5:30:75:75,0,1740:7,18,5,0 chr1 150485989 . G GC 37.35 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=31;FS=22.551;FractionInformativeReads=0.968;MQ=60;MQRankSum=0;QD=1.2;ReadPosRankSum=-1.669;SOR=3.588;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:25,5:30:75:75,0,1740:7,18,5,0 chr1 150485994 . A C 161.65 PASS AC=1;AF=0.5;AN=2;DP=405;MQ=60;set=variant3-variant4-variant9-variant19-filterInvariant23-variant24-filterInvariant29-filterInvariant37-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:25,5:30:72:72,0,1768:6,19,5,0 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 0/1:78,54:132:99:1141,0,1991:37,41,25,29 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 0/1:36,34:70:99:1319,0,1465:17,19,15,19 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 0/1:50:99:11,16,8,15 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 0/1:19,9:28:99:316,0,773:7,12,3,6 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 0/1:9,5:14:99:102,0,318:1,8,2,3 chr1 150529322 . T TAA 1986.04 PASS AC=1;AF=0.92;AN=2;DP=2499;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:15,21:36:99:834,0,635:9,6,8,13 chr1 150530265 . GGCT G 821.74 PASS AC=1;AF=0.5;AN=2;DP=109;MQ=60;set=variant9-variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,16:29:99:633,0,1547:5,8,7,9 chr1 150530270 . AGCC A 827.76 PASS AC=1;AF=0.5;AN=2;DP=106;FractionInformativeReads=1;MQ=60;set=variant9-variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,16:29:99:633,0,1612:5,8,7,9 chr1 150530274 . C A,T 845.74 PASS AC=1,0;AF=0.375,0.125;AN=2;DP=157;FractionInformativeReads=1;MQ=60;set=variant9-variant10-variant23-variant42 GT:DP:GQ:SB 0/1:29:99:5,8,7,9 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 1/1:0,165:165:99:4991,494,0:0,0,93,72 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 1/1:1,202:203:99:5901,595,0:1,0,109,93 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 1/1:0,211:211:99:6047,630,0:0,0,94,117 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 0/1:14,32:46:99:882,0,378:9,5,15,17 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 0/1:18,5:23:99:156,0,653:6,12,0,5 chr1 150548887 . C CCTAT 9352.87 PASS AC=2;AF=1;AN=2;DP=7788;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,159:159:99:7259,493,0:0,0,92,67 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 1/1:0,53:53:99:1979,159,0:0,0,15,38 chr1 150551295 . T C 996.19 PASS AC=1;AF=0.5;AN=2;DP=597;MQ=60;set=variant14-variant19-variant23-variant25-variant26-variant42 GT:AD:DP:GQ:PL:SB 0/1:52,60:112:99:1547,0,1256:29,23,32,28 chr1 150552202 . C T 227.59 PASS AC=1;AF=0.5;AN=2;DP=82;FractionInformativeReads=1;MQ=60;set=variant19-variant23-variant25-variant26-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,14:17:83:387,0,83:0,3,7,7 chr1 150595537 . G T 264 PASS AC=1;AF=0.536;AN=2;DP=325;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant8-variant9-variant15-variant23-variant25-variant27-variant29-variant30-variant33-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:273,0,186:3,4,2,7 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 0/1:8,8:16:99:150,0,192:3,5,4,4 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 0/1:86,97:183:99:2530,0,2185:46,40,52,45 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 1/1:0,228:228:99:7374,682,0:0,0,99,129 chr1 150619971 . GA GAA,G 40.66 PASS AC=1,0;AF=0.25,0.25;AN=2;DP=24;FS=0;MQ=60;set=variant23-variant32 GT:DP:GQ:SB 0/1:9:78:4,1,4,0 chr1 150620569 . C G 1623.04 PASS AC=1;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 0/1:76,81:157:99:1866,0,1956:29,47,36,45 chr1 150669414 . T G 353.06 PASS AC=1;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 0/1:9,14:23:99:351,0,227:6,3,10,4 chr1 150670484 . T G 1226 PASS AC=1;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 0/1:21,28:49:99:819,0,510:13,8,19,9 chr1 150670690 . T G 628.96 PASS AC=1;AF=0.5;AN=2;DP=53;FS=3.822;FractionInformativeReads=1;MQ=60;MQRankSum=1.399;QD=11.87;ReadPosRankSum=0.081;SOR=1.241;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:31,22:53:99:657,0,779:15,16,8,14 chr1 150671243 . AC A 1141.43 PASS AC=1;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 0/1:21,18:39:99:607,0,730:9,12,5,13 chr1 150676485 . T C 473.11 PASS AC=1;AF=0.66;AN=2;DP=319;FractionInformativeReads=1;set=variant-variant2-variant4-variant6-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant18-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant36-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,6:17:99:155,0,351:9,2,5,1 chr1 150676674 . TA T,TAA 112.02 PASS AC=0,1;AF=0.47,0.03;AN=2;DP=1334;MQ=60;set=variant-filterInvariant2-filterInvariant3-variant4-variant6-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant13-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-filterInvariant29-variant32-variant33-variant34-variant36-filterInvariant37-variant38-filterInvariant39 GT:DP:GQ:SB 0/2:35:99:10,14,5,6 chr1 150678910 . T C 265.32 PASS AC=1;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 0/1:4,10:14:99:375,0,99:3,1,10,0 chr1 150679033 . G A 1413.75 PASS AC=1;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 0/1:60,45:105:99:985,0,1373:31,29,23,22 chr1 150679358 . C T 646.57 PASS AC=1;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 0/1:12,20:32:99:545,0,365:8,4,13,7 chr1 150680988 . A T 80.01 PASS AC=1;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 0/1:5,4:9:99:153,0,193:0,5,0,4 chr1 150702663 . A C 1374.79 PASS AC=1;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 0/1:35,27:62:99:852,0,1037:27,8,23,4 chr1 150702717 . G C 1966.5 PASS AC=1;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 0/1:77,87:164:99:2299,0,1934:47,30,62,25 chr1 150703034 . CAGA C 614.49 PASS AC=1;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 0/1:14,12:26:99:454,0,668:8,6,6,6 chr1 150703366 . TAACA T 605.49 PASS AC=1;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 0/1:20,6:26:99:173,0,1176:5,15,0,6 chr1 150705755 . G A 207.15 PASS AC=1;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 0/1:7,5:12:99:189,0,242:1,6,0,5 chr1 150727539 . G A 1624.45 PASS AC=1;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 0/1:65,73:138:99:1797,0,1561:33,32,40,33 chr1 150730184 . C A 276.05 PASS AC=1;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 0/1:23,5:28:99:121,0,806:20,3,5,0 chr1 150730279 . A G 1512.13 PASS AC=1;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 0/1:72,46:118:99:1245,0,1778:34,38,35,11 chr1 150738197 . C T 1693.89 PASS AC=1;AF=0.672;AN=2;DP=1149;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant18-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant36-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,15:35:99:421,0,845:13,7,12,3 chr1 150738200 . A G 488.2 PASS AC=1;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 0/1:17,22:39:99:570,0,626:14,3,15,7 chr1 150738483 . CGGGA C 174.95 PASS AC=1;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 0/1:7,3:10:99:105,0,337:0,7,0,3 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 1/1:0,93:93:99:2767,279,0:0,0,48,45 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 1/1:0,113:113:99:3322,338,0:0,0,58,55 chr1 150782110 . CAAAAAAAAAAAAAA C,CAAAAAAAAAAAA,CAAAAAA,CAAAA,CAAAAAAAAAAAAA,CAAAAAAAAAAA,CAAAAAAAA,CAAAAAAAAAA 164.33 PASS AC=0,0,0,1,0,0,0,0;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 0/4:12:99:6,2,3,1 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 0/1:7,4:11:99:147,0,282:5,2,3,1 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 0/1:7,4:11:99:144,0,309:5,2,3,1 chr1 150782126 . A C 115.65 PASS AC=1;AF=0.5;AN=2;DP=12;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.468;QD=9.64;ReadPosRankSum=2.637;SOR=0.551;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:99:144,0,309:6,2,3,1 chr1 150782797 . C T 2343.52 PASS AC=1;AF=0.563;AN=2;DP=3188;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant9-variant15-variant23-variant25-variant27-variant29-variant30-variant33-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:106,98:204:99:2217,0,2667:53,53,48,50 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 0/1:65,26:91:99:255,0,1085:34,31,12,14 chr1 150783934 . GCACA GCACACACA,GCACACACACA,G,GCGCACACACA,GCACACACACACACACA,GCACACA,GCACACACACACA,GCACACACACACACA 1292.78 PASS AC=1,1,0,0,0,0,0,0;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 1/2:23:99:0,0,8,15 chr1 150783985 . T C 493.84 PASS AC=1;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 0/1:15,15:30:99:437,0,430:9,6,7,8 chr1 150789961 . A T 380.17 PASS AC=1;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 0/1:2,4:6:41:98,0,41:0,2,0,4 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 1/1:0,37:37:99:1103,111,0:0,0,24,13 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 0/2:24:80:8,9,2,5 chr1 150804429 . A C 273.78 PASS AC=1;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 0/1:14,11:25:99:281,0,389:6,8,3,8 chr1 150808889 . C G 754.71 PASS AC=1;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 0/1:43,22:65:99:424,0,1031:20,23,10,12 chr1 150811712 . T C 46.72 PASS AC=1;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 0/1:2,3:5:63:108,0,63:2,0,3,0 chr1 150811794 . T C 453.61 PASS AC=1;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 0/1:17,11:28:99:278,0,435:11,6,8,3 chr1 150815054 . GA G 207.21 PASS AC=1;AF=0.5;AN=2;DP=216;MQ=60;set=variant10-variant11-variant12-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant32-variant40 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:174,0,109:1,4,4,3 chr1 150825511 . C T 447.01 PASS AC=1;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 0/1:4,6:10:99:196,0,153:0,4,1,5 chr1 150849071 . ACC A,AC,ACCC 540.37 PASS AC=1,0,0;AF=0.239,0.67,0.045;AN=2;DP=1530;MQ=60;set=Intersection GT:DP:GQ:SB 0/1:21:89:2,3,10,6 chr1 150849103 . C A 334.37 PASS AC=1;AF=0.5;AN=2;DP=26;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.003;QD=12.86;ReadPosRankSum=1.312;SOR=0.73;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:363,0,345:8,6,7,5 chr1 150923099 . T C 1771.17 PASS AC=1;AF=0.5;AN=2;DP=1735;MQ=60;set=variant10-variant11-variant12-variant17-variant19-variant20-variant23-variant26-variant27-variant32-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:61,83:144:99:2081,0,1452:35,26,45,38 chr1 150923774 . T A 810.08 PASS AC=1;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 0/1:38,35:73:99:792,0,941:21,17,21,14 chr1 150935872 . A G 823.81 PASS AC=1;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 0/1:29,38:67:99:1017,0,725:16,13,25,13 chr1 150937594 . T C 1176.88 PASS AC=1;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 0/1:27,24:51:99:550,0,728:17,10,16,8 chr1 150937661 . A G 1917.43 PASS AC=1;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 0/1:62,70:132:99:1570,0,1288:32,30,38,32 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 1/1:0,63:63:99:1799,188,0:0,0,29,34 chr1 150937964 . AAGG A 1769.46 PASS AC=1;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 0/1:38,24:62:99:888,0,1621:19,19,12,12 chr1 150938571 . G A 450.09 PASS AC=1;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 0/1:39,24:63:99:582,0,974:21,18,12,12 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 1/1:0,64:64:99:2034,191,0:0,0,39,25 chr1 150938877 . A G 726.19 PASS AC=1;AF=0.5;AN=2;DP=55;FS=7.405;FractionInformativeReads=1;MQ=60;MQRankSum=1.344;QD=13.2;ReadPosRankSum=0.025;SOR=1.229;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:25,30:55:99:754,0,591:14,11,11,19 chr1 150939744 . C A 970.37 PASS AC=1;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 0/1:35,30:65:99:787,0,873:14,21,16,14 chr1 150940357 . G T 970.21 PASS AC=1;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 0/1:30,27:57:99:1023,0,1550:10,20,9,18 chr1 150940358 . C T 970.2 PASS AC=1;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 0/1:30,26:56:99:1023,0,1550:10,20,9,17 chr1 150941381 . C T 322.55 PASS AC=1;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 0/1:14,9:23:99:206,0,361:8,6,5,4 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 1/1:0,11:11:33:448,33,0:0,0,2,9 chr1 150947256 . C G 580.88 PASS AC=1;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 0/1:14,8:22:99:230,0,355:6,8,1,7 chr1 150958977 . T C 590.51 PASS AC=1;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 0/1:33,37:70:99:1087,0,947:19,14,19,18 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 0/1:38,29:67:99:720,0,908:24,14,22,7 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 1/1:0,7:7:21:231,21,0:0,0,2,5 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 1/1:0,85:85:99:2648,255,0:0,0,45,40 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 1/1:0,143:143:99:4187,427,0:0,0,79,64 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 1/1:0,52:52:99:1711,155,0:0,0,34,18 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 0/1:13,18:31:99:607,0,366:3,10,5,13 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 1/1:0,39:39:99:1205,117,0:0,0,14,25 chr1 150973239 . C G 641.64 PASS AC=1;AF=0.5;AN=2;DP=58;FS=4.218;FractionInformativeReads=1;MQ=60;MQRankSum=-1.322;QD=11.06;ReadPosRankSum=1.788;SOR=0.248;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:29,29:58:99:670,0,881:6,23,10,19 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 1/1:0,21:21:63:753,63,0:0,0,16,5 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 1/1:0,120:120:99:3633,359,0:0,0,64,56 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 1/1:0,96:96:99:3040,287,0:0,0,55,41 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 1/1:0,3:3:9:135,9,0:0,0,0,3 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 0/1:32,26:58:99:989,0,1277:11,21,10,16 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 0/1:3,11:14:86:344,0,86:3,0,9,2 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 0/1:7,6:13:99:231,0,268:0,7,0,6 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 0/1:20,23:43:99:697,0,518:13,7,16,7 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 0/1:35:99:10,11,5,9 chr1 150999863 . A G 2772.08 PASS AC=1;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 0/1:71,91:162:99:2226,0,1614:30,41,39,52 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 0/1:8,13:21:99:386,0,232:0,8,2,11 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 0/1:64,37:101:99:920,0,1727:26,38,16,21 chr1 151008928 . G A 196.77 PASS AC=1;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 0/1:1,4:5:31:116,0,31:1,0,3,1 chr1 151015299 . G GA 187.98 PASS AC=1;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 0/1:5,8:13:73:206,0,73:3,2,6,2 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 0/1:3,10:13:81:270,0,81:2,1,4,6 chr1 151019180 . A G 3279.75 PASS AC=1;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 0/1:47,34:81:99:939,0,1260:23,24,17,17 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 1/1:0,37:37:99:1132,111,0:0,0,18,19 chr1 151026815 . C T 3590.79 PASS AC=1;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 0/1:55,46:101:99:973,0,1432:26,29,23,23 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 1/1:0,116:116:99:3648,348,0:0,0,49,67 chr1 151031476 . T A 1281.1 PASS AC=1;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 0/1:15,26:41:99:630,0,355:8,7,14,12 chr1 151031667 . T C 2701.97 PASS AC=1;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 0/1:50,54:104:99:1193,0,1124:23,27,29,25 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 1/1:0,173:173:99:5175,518,0:0,0,88,85 chr1 151039609 . A G 1288.83 PASS AC=1;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 0/1:14,11:25:99:286,0,447:11,3,9,2 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 0/1:135,117:252:99:2827,0,3466:62,73,61,56 chr1 151070252 . CA C 744.23 PASS AC=1;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 0/1:20,24:44:99:497,0,381:15,5,19,5 chr1 151091181 . A G 5443.06 PASS AC=1;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 0/1:105,83:188:99:1830,0,2439:56,49,40,43 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 0/2:29:96:0,21,1,7 chr1 151093052 . G A 1244.24 PASS AC=1;AF=0.5;AN=2;DP=99;FS=0.764;FractionInformativeReads=1;MQ=60;MQRankSum=-0.487;QD=12.57;ReadPosRankSum=2.601;SOR=0.793;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:48,51:99:99:1272,0,1265:29,19,32,19 chr1 151093229 . CT CTT,C 331.46 PASS AC=1,0;AF=0.259,0.241;AN=2;DP=1989;set=variant3-filterInvariant4-variant5-variant6-variant7-variant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-variant18-variant19-filterInvariant22-filterInvariant23-variant24-filterInvariant26-filterInvariant29-variant31-variant32-variant33-variant34-variant36-variant38-filterInvariant39-filterInvariant40-filterInvariant42-variant44 GT:DP:GQ:SB 0/1:30:99:2,14,4,10 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 1/1:0,5:5:15:144,15,0:0,0,2,3 chr1 151093983 . T C 182.97 PASS AC=1;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 0/1:2,4:6:31:121,0,31:1,1,1,3 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 0/1:65:99:28,16,15,6 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 1/1:0,98:98:99:3141,294,0:0,0,53,45 chr1 151104598 . A G 1977.6 PASS AC=1;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 0/1:26,34:60:99:953,0,716:10,16,15,19 chr1 151104950 . G A 4188.73 PASS AC=1;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 0/1:47,56:103:99:1447,0,1186:24,23,37,19 chr1 151105824 . C G 2767.25 PASS AC=1;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 0/1:47,47:94:99:1057,0,1122:24,23,25,22 chr1 151108137 . T G 1891.68 PASS AC=1;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 0/1:49,62:111:99:1482,0,1071:27,22,35,27 chr1 151114882 . C CT 1867.97 PASS AC=1;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 0/1:40,44:84:99:1391,0,1235:22,18,24,20 chr1 151115186 . C T 1361.1 PASS AC=1;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 0/1:30,24:54:99:572,0,673:16,14,9,15 chr1 151132714 . CA CAAAAAAAAAAA,CAAAAAAAA,CAAAAAAAAAAAAAA,C 185.01 PASS AC=0,0,0,1;AF=0.2,0.1,0.1,0.2;AN=2;DP=44;FS=0;set=variant12-variant15-variant22-variant23-variant41 GT:DP:GQ:SB 0/4:8:45:2,1,4,1 chr1 151141716 . CTTT CTT,C,CT 35.17 PASS AC=0,1,0;AF=0.227,0.273,0.045;AN=2;DP=165;set=filterInvariant4-variant6-variant9-variant18-variant22-variant23-variant24-variant26-variant38-variant39-variant43 GT:DP:GQ:SB 0/2:11:99:3,3,2,3 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 1/1:0,52:52:99:1589,156,0:0,0,21,31 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 1/1:0,13:13:39:467,39,0:0,0,3,10 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 1/1:0,11:11:33:492,33,0:0,0,1,10 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 1/1:0,30:30:90:1153,90,0:0,0,5,25 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 1/1:0,112:112:99:3149,335,0:0,0,59,53 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 0/1:7:9:1,1,2,3 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 1/1:0,105:105:99:3166,314,0:0,0,47,58 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 1/1:0,74:74:99:3468,235,0:0,0,50,24 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 1/1:0,42:42:99:1351,126,0:0,0,19,23 chr1 151220878 . T C 1380.8 PASS AC=1;AF=0.5;AN=2;DP=159;FS=1.265;FractionInformativeReads=0.994;MQ=60;MQRankSum=-1.256;QD=8.68;ReadPosRankSum=-1.238;SOR=0.842;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:91,67:158:99:1409,0,2049:47,44,37,30 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 1/1:0,186:186:99:8276,560,0:0,0,99,87 chr1 151227371 . A G 464.36 PASS AC=2;AF=0.898;AN=2;DP=1241;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:776,63,0:0,0,6,15 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 1/1:0,100:100:99:3105,301,0:0,0,48,52 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 1/1:0,48:48:99:1750,143,0:0,0,8,40 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 1/1:0,100:100:99:3234,300,0:0,0,44,56 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 1/1:0,120:120:99:3843,358,0:0,0,67,53 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 1/1:0,44:44:99:1352,132,0:0,0,13,31 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 1/1:0,82:82:99:2702,246,0:0,0,55,27 chr1 151262355 . C A 1626.75 PASS AC=1;AF=0.5;AN=2;DP=113;FS=6.606;FractionInformativeReads=0.973;MQ=60;MQRankSum=-0.59;QD=14.4;ReadPosRankSum=0.027;SOR=1.402;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:52,58:110:99:1655,0,1364:32,20,43,15 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 1/1:0,54:54:99:1705,162,0:0,0,29,25 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 1/1:0,38:38:99:1224,113,0:0,0,16,22 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 1/1:0,21:21:63:673,63,0:0,0,7,14 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 1/1:0,87:87:99:2747,261,0:0,0,52,35 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 1/1:0,34:34:99:1088,102,0:0,0,15,19 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 1/1:0,9:9:27:300,27,0:0,0,3,6 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 1/1:0,107:107:99:3317,319,0:0,0,61,46 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 1/1:1,219:220:99:6496,619,0:1,0,103,116 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 1/1:0,34:34:99:1061,102,0:0,0,20,14 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 1/1:0,93:93:99:3059,279,0:0,0,39,54 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 1/1:0,36:36:99:1209,108,0:0,0,20,16 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 1/1:0,49:49:99:1569,147,0:0,0,22,27 chr1 151338176 . G A 1042.41 PASS AC=1;AF=0.5;AN=2;DP=92;FS=1.699;FractionInformativeReads=1;MQ=60;MQRankSum=0.012;QD=11.33;ReadPosRankSum=0.668;SOR=0.473;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:46,46:92:99:1071,0,1224:20,26,23,23 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 1/1:0,52:52:99:1636,154,0:0,0,19,33 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 1/1:0,54:54:99:2028,162,0:0,0,16,38 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 1/1:0,93:93:99:2780,279,0:0,0,46,47 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 1/1:0,16:16:48:644,48,0:0,0,1,15 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 1/1:0,30:30:90:1103,90,0:0,0,9,21 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 1/1:0,18:18:54:663,54,0:0,0,15,3 chr1 151380504 . AAAAG A 131.29 PASS AC=2;AF=0.55;AN=2;DP=538;set=variant4-variant5-variant6-filterInvariant7-variant9-variant10-variant11-variant12-filterInvariant14-filterInvariant15-variant17-variant18-variant23-filterInvariant27-filterInvariant28-variant29-variant33-filterInvariant34-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:16:83,16,0:0,0,5,1 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 1/1:0,41:41:99:1280,123,0:0,0,14,27 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 1/1:0,35:35:99:1227,105,0:0,0,26,9 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 1/1:0,54:54:99:1762,162,0:0,0,38,16 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 1/1:0,24:24:72:930,72,0:0,0,21,3 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 1/1:0,85:85:99:2517,255,0:0,0,32,53 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 1/1:1,29:30:51:909,51,0:1,0,8,21 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 1/1:0,51:51:99:1591,153,0:0,0,34,17 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 1/1:0,2:2:6:90,6,0:0,0,2,0 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 1/1:0,29:29:87:1224,87,0:0,0,24,5 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 1/1:0,42:42:99:1711,125,0:0,0,30,12 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 1/1:48:99:0,0,30,18 chr1 151495796 . T C 3693.27 PASS AC=1;AF=0.583;AN=2;DP=1130;FractionInformativeReads=1;MQ=60;set=variant4-variant12-variant20-variant23-variant26-variant31-variant34-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:42,36:78:99:930,0,1098:28,14,25,11 chr1 151497140 . T C 4481.03 PASS AC=1;AF=0.583;AN=2;DP=1510;MQ=60;set=variant4-variant12-variant20-variant23-variant26-variant31-variant34-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:66,30:96:99:583,0,1642:35,31,14,16 chr1 151497202 . G A 977.25 PASS AC=1;AF=0.5;AN=2;DP=330;FractionInformativeReads=1;MQ=60;set=variant12-variant23-variant37 GT:AD:DP:GQ:PL:SB 0/1:68,41:109:99:783,0,1568:32,36,21,20 chr1 151497376 . G A 802.54 PASS AC=1;AF=0.591;AN=2;DP=187;FractionInformativeReads=1;MQ=60;set=variant4-variant12-variant20-variant23-variant26-variant31-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:2,8:10:57:246,0,57:0,2,2,6 chr1 151499635 . C T 1232.05 PASS AC=1;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 0/1:23,33:56:99:787,0,575:10,13,12,21 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 1/1:0,67:67:99:1989,201,0:0,0,37,30 chr1 151501737 . T C 3392.08 PASS AC=2;AF=0.966;AN=2;DP=3816;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2763,267,0:0,0,51,38 chr1 151501841 . C G 1400.58 PASS AC=1;AF=0.5;AN=2;DP=293;FractionInformativeReads=1;MQ=60;set=variant12-variant21-variant23 GT:AD:DP:GQ:PL:SB 0/1:27,54:81:99:1387,0,584:13,14,29,25 chr1 151506526 . G A 712.47 PASS AC=1;AF=0.5;AN=2;DP=237;FractionInformativeReads=1;MQ=60;set=variant23-variant30-variant32 GT:AD:DP:GQ:PL:SB 0/1:30,30:60:99:741,0,794:18,12,18,12 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 0/1:10,7:17:99:183,0,296:8,2,4,3 chr1 151509966 . T TA 494.89 PASS AC=1;AF=0.909;AN=2;DP=1833;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:21,18:39:99:351,0,395:9,12,8,10 chr1 151510026 . A G 993.56 PASS AC=1;AF=0.932;AN=2;DP=2054;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:20,20:40:99:578,0,537:11,9,11,9 chr1 151511109 . T C 324.64 PASS AC=1;AF=0.5;AN=2;DP=155;FractionInformativeReads=1;MQ=60;set=variant12-variant21-variant23-variant37 GT:AD:DP:GQ:PL:SB 0/1:17,17:34:99:452,0,377:7,10,7,10 chr1 151512895 . A G 1530.08 PASS AC=1;AF=0.5;AN=2;DP=1297;MQ=60;set=variant-variant19-variant23-variant30-variant32-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,96:189:99:2229,0,2338:41,52,45,51 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 0/1:4,6:10:99:127,0,150:0,4,0,6 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 0/1:6,4:10:99:150,0,240:0,6,0,4 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 0/1:10:99:3,1,3,3 chr1 151538412 . G A 245.17 PASS AC=1;AF=0.571;AN=2;DP=80;MQ=60;set=variant7-variant18-variant21-variant23-variant36-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:182,0,178:4,2,5,1 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 1/1:0,12:12:39:403,39,0:0,0,2,10 chr1 151538784 . TTC T,TTCTC 252.64 PASS AC=0,1;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 0/2:47:99:11,12,13,11 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 0/1:68,57:125:99:1406,0,1769:34,34,31,26 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 1/1:0,17:17:51:655,51,0:0,0,2,15 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 0/1:5,15:20:99:506,0,161:5,0,13,2 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 1/1:0,7:7:21:253,21,0:0,0,6,1 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 0/1:48,49:97:99:1106,0,1199:23,25,26,23 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 0/1:3,8:11:88:291,0,88:1,2,0,8 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 0/1:1,3:4:15:115,0,15:1,0,3,0 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 0/1:51,55:106:99:1452,0,1296:29,22,32,23 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 0/1:8,3:11:99:102,0,238:5,3,2,1 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 1/1:0,16:16:51:496,51,0:0,0,12,4 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 0/1:17,17:34:99:550,0,559:2,15,3,14 chr1 151664882 . CTT CTTT,CTTTT,C,CT,CTTTTT 183.1 PASS AC=0,0,1,0,0;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 0/3:23:78:8,9,0,6 chr1 151668937 . TTTTCTTTCTTTCTTTC TTTTCTTTCTTTCTTTCTTTCTTTC,TTTTCTTTC,TTTTCTTTCTTTC,T,TTTTCTTTCTTTCTTTCTTTC 68.86 PASS AC=0,2,0,0,0;AF=0.067,0.4,0.267,0.033,0.033;AN=2;DP=121;FS=0;MQ=60;set=variant2-variant5-variant8-variant14-variant17-variant20-variant22-variant23-variant25-variant27-variant30-variant31-variant36-variant38-variant39 GT:DP:GQ:SB 2/2:2:7:0,0,1,1 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 1/1:0,65:65:99:2107,195,0:0,0,30,35 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 0/1:37,29:66:99:714,0,1048:18,19,13,16 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 1/1:0,69:69:99:2111,206,0:0,0,33,36 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 0/1:93,79:172:99:1879,0,2501:56,37,46,33 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 0/1:6,12:18:99:269,0,137:2,4,6,6 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 0/1:86,77:163:99:2058,0,2076:46,40,46,31 chr1 151694241 . C T 964.09 PASS AC=1;AF=0.5;AN=2;DP=366;FractionInformativeReads=1;MQ=60;set=variant-variant16-variant17-variant23-variant30-variant32-variant37 GT:AD:DP:GQ:PL:SB 0/1:23,30:53:99:798,0,548:9,14,14,16 chr1 151700189 . C CCTG 639.95 PASS AC=1;AF=0.92;AN=2;DP=1593;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:10,13:23:99:509,0,472:3,7,5,8 chr1 151732060 . A G 49.51 PASS AC=1;AF=0.614;AN=2;DP=186;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant15-variant16-variant23-variant24-variant26-variant29-variant31-variant33-variant36-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:61:75,0,61:2,0,2,0 chr1 151732700 . A G 1060.11 PASS AC=1;AF=0.571;AN=2;DP=2796;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,43:80:99:1054,0,814:17,20,19,24 chr1 151733335 . T G 535.63 PASS AC=1;AF=0.571;AN=2;DP=3351;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,47:82:99:1198,0,853:20,15,29,18 chr1 151733379 . CAAA CAAAAAAA,CAAAAA,CA,CAAAA,C,CAAAAAA,CAA,CAAAAAAAAAAAAAAAAAA 927.24 PASS AC=0,1,0,0,0,0,0,0;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 0/2:27:99:6,6,5,10 chr1 151735576 . T C 1272.45 PASS AC=1;AF=0.5;AN=2;DP=1472;MQ=60;set=variant-variant13-variant16-variant17-variant23-variant30-variant32-variant37 GT:AD:DP:GQ:PL:SB 0/1:99,118:217:99:2898,0,2010:47,52,50,68 chr1 151736268 . CTG C 940.29 PASS AC=1;AF=0.574;AN=2;DP=1566;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,26:47:99:1029,0,915:10,11,9,17 chr1 151736456 . A G 458 PASS AC=1;AF=0.5;AN=2;DP=194;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant13-variant16-variant17-variant23-variant30-variant32-variant37 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:301,0,429:8,4,7,4 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 1/1:0,152:152:99:4644,456,0:0,0,67,85 chr1 151737349 . T A 564.76 PASS AC=1;AF=0.886;AN=2;DP=2038;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:297,0,296:8,4,7,5 chr1 151738184 . ATT A,AT 1978.82 PASS AC=1,1;AF=0.125,0.852;AN=2;DP=4873;MQ=60;set=Intersection GT:DP:GQ:SB 1/2:74:99:1,1,20,52 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 1/1:0,40:40:99:1462,119,0:0,0,19,21 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 1/1:0,117:117:99:3435,350,0:0,0,57,60 chr1 151742550 . GGAGAGA G 815.28 PASS AC=1;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 0/1:22,27:49:99:1061,0,1050:12,10,21,6 chr1 151742565 . GGGAGACCATGGGGAGACGGAGAC G 911.47 PASS AC=1;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 0/1:28,27:55:99:1052,0,1195:15,13,21,6 chr1 151743870 . TA T 252.62 PASS AC=1;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 0/1:17,5:22:99:121,0,568:7,10,3,2 chr1 151744168 . T C 1274.55 PASS AC=1;AF=0.5;AN=2;DP=836;MQ=60;set=variant-variant13-variant16-variant17-variant19-variant23-variant30-variant32-variant37 GT:AD:DP:GQ:PL:SB 0/1:49,36:85:99:798,0,1189:28,21,20,16 chr1 151746079 . A T 2866.6 PASS AC=1;AF=0.5;AN=2;DP=1854;MQ=60;set=variant-variant13-variant16-variant17-variant19-variant23-variant30-variant32-variant37 GT:AD:DP:GQ:PL:SB 0/1:90,96:186:99:2513,0,2101:40,50,44,52 chr1 151746202 . T A 616.76 PASS AC=1;AF=0.5;AN=2;DP=316;MQ=60;set=variant-variant13-variant16-variant17-variant19-variant23-variant30-variant32-variant37 GT:AD:DP:GQ:PL:SB 0/1:20,18:38:99:684,0,581:5,15,2,16 chr1 151746235 . C T 351.4 PASS AC=1;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 0/1:15,15:30:99:441,0,579:2,13,5,10 chr1 151746524 . C A 549.72 PASS AC=1;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 0/1:22,26:48:99:592,0,482:11,11,13,13 chr1 151747043 . C T 1133.01 PASS AC=1;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 0/1:39,47:86:99:1184,0,993:15,24,24,23 chr1 151747733 . C T 693.15 PASS AC=1;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 0/1:24,25:49:99:610,0,605:13,11,11,14 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 1/1:0,38:38:99:1265,113,0:0,0,20,18 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 1/1:0,16:16:48:595,48,0:0,0,6,10 chr1 151751081 . G A 602.54 PASS AC=1;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 0/1:18,11:29:99:287,0,470:10,8,6,5 chr1 151751274 . C G 1704.45 PASS AC=1;AF=0.5;AN=2;DP=363;FractionInformativeReads=1;MQ=60;set=variant12-variant21-variant23 GT:AD:DP:GQ:PL:SB 0/1:55,54:109:99:1528,0,1483:36,19,36,18 chr1 151752733 . ATACTATCTATACAACCAGTCCTCAATTACTTTATATACAACCTCAGT A 304.74 PASS AC=1;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 0/1:11,8:19:99:290,0,2640:4,7,1,7 chr1 151754112 . T C 1070.35 PASS AC=1;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 0/1:36,33:69:99:853,0,874:13,23,14,19 chr1 151755284 . C G 1619.82 PASS AC=1;AF=0.5;AN=2;DP=883;FractionInformativeReads=1;MQ=60;set=variant-variant13-variant16-variant17-variant19-variant23-variant30-variant32-variant34-variant37 GT:AD:DP:GQ:PL:SB 0/1:51,50:101:99:1220,0,1280:31,20,31,19 chr1 151763246 . G A 119.26 PASS AC=1;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 0/1:2,2:4:75:78,0,75:2,0,2,0 chr1 151763767 . C T 1217.39 PASS AC=1;AF=0.5;AN=2;DP=494;MQ=60;set=variant-variant16-variant17-variant19-variant23-variant30-variant32-variant37 GT:AD:DP:GQ:PL:SB 0/1:22,47:69:99:1310,0,469:12,10,22,25 chr1 151763815 . C T 140.78 PASS AC=1;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 0/1:22,9:31:99:183,0,589:11,11,5,4 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 1/1:0,53:53:99:1527,159,0:0,0,28,25 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 1/1:0,42:42:99:1366,124,0:0,0,17,25 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 1/1:0,41:41:99:1302,123,0:0,0,18,23 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 1/1:0,15:15:45:469,45,0:0,0,10,5 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 0/1:4,2:6:72:72,0,108:1,3,0,2 chr1 151789588 . C CTGTGTG,CTGTGTGTG,CTG,CTGTGTGTGTG,CTGTG 1526.57 PASS AC=1,1,0,0,0;AF=0.318,0.602,0.023,0.034,0.011;AN=2;DP=1535;set=Intersection GT:DP:GQ:SB 1/2:25:99:0,0,21,4 chr1 151789609 . C T 1378.64 PASS AC=2;AF=0.989;AN=2;DP=2400;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1572,107,0:0,0,25,11 chr1 151789611 . C T 408.38 PASS AC=2;AF=0.909;AN=2;DP=2396;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1571,107,0:0,0,25,11 chr1 151789647 . T G 1354.99 PASS AC=1;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 0/1:62,63:125:99:1518,0,1471:37,25,38,25 chr1 151801680 . G A 214.42 PASS AC=1;AF=0.583;AN=2;DP=203;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant7-variant11-variant23-variant26-variant30-variant32-variant34-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,10:15:99:340,0,180:4,1,7,3 chr1 151803705 . C T 315.32 PASS AC=1;AF=0.5;AN=2;DP=282;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant23-variant30-variant32-variant34-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,24:44:99:636,0,573:5,15,10,14 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 1/1:0,14:14:42:510,42,0:0,0,4,10 chr1 151810304 . G C 196.82 PASS AC=1;AF=0.729;AN=2;DP=1120;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant17-variant18-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,19:38:99:552,0,505:12,7,15,4 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 1/1:0,55:55:99:1707,165,0:0,0,31,24 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 1/1:0,14:14:42:417,42,0:0,0,9,5 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 1/1:0,71:71:99:2311,213,0:0,0,35,36 chr1 151819691 . AGGAGGCAGGAGGCAGGCAGGGGAGGCAGGAGGCAGGAGGCAGGCAGG A 710.26 PASS AC=2;AF=0.966;AN=2;DP=4764;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:99:1253,127,0:0,0,8,19 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 1/1:0,151:151:99:4448,452,0:0,0,80,71 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 1/1:0,142:142:99:4102,425,0:0,0,71,71 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 1/1:0,17:17:51:600,51,0:0,0,12,5 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 1/1:0,73:73:99:2234,218,0:0,0,35,38 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 1/1:0,5:5:15:200,15,0:0,0,3,2 chr1 151846517 . C T 538.5 PASS AC=2;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 1/1:0,13:13:39:449,39,0:0,0,6,7 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 1/1:0,3:3:9:94,9,0:0,0,2,1 chr1 151862661 . G A 1781.53 PASS AC=2;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 1/1:0,58:58:99:1866,174,0:0,0,37,21 chr1 151867560 . G A 665.01 PASS AC=2;AF=0.898;AN=2;DP=2346;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1462,117,0:0,0,14,25 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 1/1:0,63:63:99:1880,189,0:0,0,33,30 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 0/1:17,19:36:99:493,0,377:11,6,12,7 chr1 151966348 . C T 1708.48 PASS AC=2;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 1/1:0,52:52:99:1732,155,0:0,0,21,31 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 0/1:47,48:95:99:1579,0,1610:20,27,22,26 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 0/1:1,3:4:34:120,0,34:0,1,0,3 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 1/1:1,91:92:99:2897,266,0:1,0,34,57 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 1/1:0,21:21:63:743,63,0:0,0,4,17 chr1 152083325 . A T 2730 PASS AC=1;AF=0.5;AN=2;DP=2796;MQ=60;set=variant2-variant11-variant15-variant16-variant17-variant21-variant23-variant28-variant29-variant30-variant32-variant36-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:77,78:155:99:1815,0,1793:37,40,38,40 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 1/1:0,86:86:99:2483,257,0:0,0,39,47 chr1 152128797 . T C 1898.46 PASS AC=1;AF=0.5;AN=2;DP=127;FS=0;FractionInformativeReads=0.992;MQ=60;MQRankSum=0.385;QD=14.95;ReadPosRankSum=0.625;SOR=0.763;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:63,63:126:99:1927,0,1916:22,41,21,42 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 1/1:0,44:44:99:1804,132,0:0,0,40,4 chr1 152184534 . C G 4572.31 PASS AC=2;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 1/1:0,95:95:99:3577,286,0:0,0,76,19 chr1 152184704 . C T 17302.2 PASS AC=2;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 1/1:0,428:428:99:12631,1282,0:0,0,211,217 chr1 152184950 . T G 11110.9 PASS AC=2;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 1/1:0,270:270:99:8573,806,0:0,0,112,158 chr1 152185095 . T A 5658.15 PASS AC=2;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 1/1:0,110:110:99:3932,330,0:0,0,52,58 chr1 152185184 . C T 7437.06 PASS AC=2;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 1/1:1,182:183:99:5649,536,0:0,1,106,76 chr1 152185762 . C G 3981.12 PASS AC=2;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 1/1:0,16:16:48:558,48,0:0,0,10,6 chr1 152186141 . C T 496.69 DRAGENHardSNP AC=2;AF=0.84;AN=2;DP=1599;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:2,67:69:99:1741,157,0:1,1,19,48 chr1 152186178 . C T 142.19 PASS AC=2;AF=0.895;AN=2;DP=353;set=filterInvariant-filterInvariant6-filterInvariant12-filterInvariant13-filterInvariant15-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant23-filterInvariant24-filterInvariant25-variant32-filterInvariant33-filterInvariant36-filterInvariant38-filterInvariant39-filterInvariant40-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:56:497,56,0:0,0,4,15 chr1 152186614 . C G 71.75 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=683;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:76,31:107:99:494,0,1748:59,17,22,9 chr1 152186699 . T A 309.08 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=14229;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:445,149:594:99:2211,0,10084:264,181,101,48 chr1 152186766 . G A 921.84 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=20029;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:475,322:797:99:5740,0,9699:213,262,158,164 chr1 152187183 . C A 666.01 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=12510;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:350,159:509:99:2971,0,8388:74,276,33,126 chr1 152187554 . C T 303.13 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=5685;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:85,52:137:99:988,0,1792:50,35,36,16 chr1 152187562 . A C 1782.51 DRAGENHardSNP AC=2;AF=1;AN=2;DP=6216;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:3,117:120:99:3074,279,0:2,1,78,39 chr1 152187588 . C T 184.98 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=8671;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:427,71:498:99:350,0,9557:255,172,47,24 chr1 152187935 . C T 1703.23 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=7765;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:136,120:256:99:4728,0,6159:85,51,93,27 chr1 152187945 . C T 1980.14 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=9686;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:154,173:327:99:5839,0,6352:97,57,125,48 chr1 152188109 . T A 1592.2 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=22758;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:545,331:876:99:5907,0,13582:366,179,131,200 chr1 152188176 . G A 1760.68 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=30834;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:1010,224:1234:99:2399,0,23020:614,396,128,96 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 0/1:1927,511:2438:99:6399,0,44954:861,1066,225,286 chr1 152188920 . C T 462.01 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=7432;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:205,75:280:99:1069,0,4452:92,113,35,40 chr1 152188998 . C T 319.16 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=4857;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:99,51:150:99:980,0,2226:26,73,15,36 chr1 152190720 . C T 166.79 PASS AC=2;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 1/1:0,3:3:9:89,9,0:0,0,3,0 chr1 152191051 . G A 4344.79 PASS AC=1;AF=0.5;AN=2;DP=2310;set=variant13-variant15-variant23-variant29-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:154,136:290:99:3531,0,4082:68,86,66,70 chr1 152191709 . C G 6813.51 PASS AC=2;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 1/1:3,308:311:99:9212,831,0:1,2,161,147 chr1 152191879 . G A 6919.62 PASS AC=2;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 1/1:0,341:341:99:10713,1022,0:0,0,164,177 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 0/1:46,261:307:99:7877,0,402:20,26,133,128 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 0/1:267,102:369:99:1549,0,7631:133,134,27,75 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 0/1:287,103:390:99:1552,0,7784:141,146,27,76 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 0/1:310,38:348:99:145,0,8675:144,166,1,37 chr1 152192293 . C T 6323.97 PASS AC=2;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 1/1:0,278:278:99:8856,833,0:0,0,127,151 chr1 152192395 . G A 2142.37 PASS AC=1;AF=0.5;AN=2;DP=2394;set=variant-variant12-variant19-variant20-variant21-variant23-variant24-variant33 GT:AD:DP:GQ:PL:SB 0/1:126,112:238:99:2786,0,3218:70,56,58,54 chr1 152192631 . C T 7465.84 PASS AC=2;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 1/1:0,371:371:99:11049,1112,0:0,0,179,192 chr1 152192687 . T C 6293.09 PASS AC=2;AF=0.989;AN=2;DP=17135;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,305:305:99:9423,914,0:0,0,134,171 chr1 152192825 . C T 1897.27 PASS AC=2;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 1/1:0,179:179:99:5633,532,0:0,0,84,95 chr1 152192978 . T C 6164.6 PASS AC=2;AF=0.989;AN=2;DP=17094;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,306:306:99:9476,916,0:0,0,173,133 chr1 152193052 . A G 7120.94 PASS AC=2;AF=0.989;AN=2;DP=18428;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,329:329:99:10412,986,0:0,0,171,158 chr1 152193121 . G T 8362.16 PASS AC=2;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 1/1:2,372:374:99:11519,1063,0:1,1,186,186 chr1 152193286 . G T 3020.87 PASS AC=2;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 1/1:1,381:382:99:17002,1082,0:0,1,193,188 chr1 152193291 . G T 9286.85 PASS AC=2;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 1/1:1,390:391:99:17043,1093,0:0,1,196,194 chr1 152193544 . A G 4795.25 PASS AC=2;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 1/1:0,144:144:99:6437,433,0:0,0,52,92 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 1/1:0,141:141:99:6412,430,0:0,0,51,90 chr1 152193851 . C T 3908.52 PASS AC=2;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 1/1:0,89:89:99:2717,267,0:0,0,36,53 chr1 152193990 . A G 1179.44 PASS AC=2;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 1/1:0,23:23:69:651,69,0:0,0,8,15 chr1 152195428 . C A 552.59 PASS AC=1;AF=0.5;AN=2;DP=180;MQ=60;set=variant-variant12-variant19-variant20-variant21-variant23-variant24-variant33 GT:AD:DP:GQ:PL:SB 0/1:4,10:14:99:315,0,125:4,0,7,3 chr1 152195728 . AT A 6864.44 PASS AC=2;AF=0.989;AN=2;DP=12115;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,212:213:99:5743,624,0:1,0,93,119 chr1 152195851 . TAGTC T 2241.7 PASS AC=2;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 1/1:0,62:62:99:2729,187,0:0,0,21,41 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 1/1:0,5:5:15:181,15,0:0,0,2,3 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 1/1:0,128:128:99:4011,383,0:0,0,84,44 chr1 152277550 . G T 3073.72 PASS AC=1;AF=0.5;AN=2;DP=609;FractionInformativeReads=1;set=variant13-variant23 GT:AD:DP:GQ:PL:SB 0/1:137,151:288:99:3884,0,3457:57,80,63,88 chr1 152278434 . T G 590.11 PASS AC=1;AF=0.5;AN=2;DP=916;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-filterInvariant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,7:19:99:233,0,437:12,0,7,0 chr1 152284759 . C T 2634.66 PASS AC=1;AF=0.5;AN=2;DP=197;FS=1.124;FractionInformativeReads=1;MQ=59.5;MQRankSum=-0.296;QD=13.37;ReadPosRankSum=2.401;SOR=0.788;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:97,100:197:99:2663,0,2730:39,58,38,62 chr1 152286126 . A G 2192.8 PASS AC=1;AF=0.5;AN=2;DP=2455;MQ=60;set=variant-variant2-variant12-variant17-variant19-variant21-variant23-variant39 GT:AD:DP:GQ:PL:SB 0/1:152,129:281:99:3206,0,3857:76,76,70,59 chr1 152384498 . G GT 162.49 PASS AC=2;AF=0.893;AN=2;DP=348;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:363,27,0:0,0,6,3 chr1 152384833 . T C 1592 PASS AC=2;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 1/1:0,39:39:99:1191,117,0:0,0,13,26 chr1 152484129 . G A 3053.34 PASS AC=2;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 1/1:0,192:192:99:6171,574,0:0,0,89,103 chr1 152487979 . C T 2256.82 PASS AC=2;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 1/1:0,80:80:99:2372,238,0:0,0,42,38 chr1 152488063 . C T 2822.4 PASS AC=2;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 1/1:0,111:111:99:3324,330,0:0,0,60,51 chr1 152488428 . T C 1482.57 PASS AC=2;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 1/1:0,36:36:99:1347,108,0:0,0,5,31 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 0/1:8,3:11:94:94,0,268:7,1,2,1 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 0/1:164,161:325:99:3924,0,4147:92,72,97,64 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 0/1:20,14:34:99:272,0,464:11,9,8,6 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 0/1:53,49:102:99:1390,0,1390:28,25,22,27 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 0/1:74,73:147:99:1744,0,1865:28,46,28,45 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 0/1:7,8:15:99:308,0,275:0,7,1,7 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 0/1:51,62:113:99:1735,0,1350:15,36,15,47 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 0/1:29,25:54:99:779,0,874:6,23,4,21 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 0/1:17,19:36:99:479,0,410:11,6,11,8 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 0/1:4,10:14:99:324,0,119:0,4,3,7 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 1/1:0,244:244:99:7225,730,0:0,0,134,110 chr1 152681680 . C CAGCTCTGGGGGCTGCTGT 526.66 PASS AC=1;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 0/1:64,36:100:99:1420,0,10209:20,44,6,30 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 0/1:6,8:14:99:318,0,503:1,5,1,7 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 0/1:25,10:35:99:263,0,766:13,12,7,3 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 0/1:11,5:16:99:137,0,325:3,8,1,4 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 0/1:50,35:85:99:877,0,1414:35,15,26,9 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 0/1:140,107:247:99:2632,0,3558:74,66,59,48 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 0/1:71,61:132:99:1465,0,1925:35,36,26,35 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 0/1:92,76:168:99:1894,0,2417:42,50,39,37 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 0/1:57,61:118:99:1479,0,1472:26,31,30,31 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 0/1:51,45:96:99:1123,0,1246:22,29,17,28 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 0/1:42,20:62:99:668,0,1661:17,25,8,12 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 0/1:41,19:60:99:671,0,1630:17,24,8,11 chr1 152730656 . A G 41.67 PASS AC=2;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 1/1:0,19:19:57:616,57,0:0,0,5,14 chr1 152732436 . G C 1323.71 PASS AC=2;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 1/1:0,99:99:99:3418,296,0:0,0,40,59 chr1 152733301 . T A 2001.06 PASS AC=2;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 1/1:0,263:263:99:7817,786,0:0,0,132,131 chr1 152734187 . G A 1445.16 PASS AC=2;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 1/1:0,107:107:99:3280,318,0:0,0,52,55 chr1 152734633 . T A 42.2 PASS AC=2;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 1/1:0,6:6:18:197,18,0:0,0,1,5 chr1 152758766 . G C 399.77 PASS AC=2;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 1/1:0,33:33:99:1063,99,0:0,0,20,13 chr1 152759678 . C T 1320.38 PASS AC=2;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 1/1:0,116:116:99:3894,347,0:0,0,85,31 chr1 152759950 . A G 1489.44 PASS AC=2;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 1/1:0,146:146:99:5008,438,0:0,0,75,71 chr1 152771293 . A G 768.97 PASS AC=2;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 1/1:0,87:87:99:2545,260,0:0,0,29,58 chr1 152777465 . A G 429.26 PASS AC=2;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 1/1:0,65:65:99:2355,195,0:0,0,38,27 chr1 152777868 . A G 1344.66 PASS AC=2;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 1/1:0,157:157:99:5955,470,0:0,0,118,39 chr1 152777964 . G A 1738.21 PASS AC=2;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 1/1:2,271:273:99:7645,766,0:1,1,121,150 chr1 152785170 . G A 2318.78 PASS AC=1;AF=0.5;AN=2;DP=1085;set=variant3-variant9-variant13-variant16-variant18-variant23-variant27-variant30 GT:AD:DP:GQ:PL:SB 0/1:59,64:123:99:1692,0,1605:29,30,34,30 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 2/2:29:99:0,0,23,6 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 0/1:2,4:6:74:121,0,74:1,1,3,1 chr1 152944594 . C T 1406.3 PASS AC=1;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 0/1:117,100:217:99:2358,0,2935:59,58,43,57 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 0/1:8,10:18:99:356,0,150:6,2,8,2 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 0/1:28,34:62:99:1036,0,935:19,9,14,20 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 0/1:54,36:90:99:878,0,1376:31,23,24,12 chr1 152974063 . G A 45.98 PASS AC=2;AF=0.816;AN=2;DP=70;FS=0;MQ=60;set=variant-variant2-variant6-variant7-variant14-variant15-variant17-variant18-variant23-variant24-variant25-variant26-variant29-variant32-variant34-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:82,6,0:0,0,2,0 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 0/1:3,6:9:67:143,0,67:2,1,3,3 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 0/1:10,15:25:99:539,0,411:5,5,9,6 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 0/1:10,15:25:99:539,0,411:5,5,9,6 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 0/1:8,12:20:99:315,0,138:4,4,5,7 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 0/1:19,26:45:99:733,0,511:11,8,17,9 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 0/1:126,119:245:99:2939,0,3028:72,54,65,54 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 0/1:42,28:70:99:947,0,1574:25,17,11,17 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 0/1:73,61:134:99:1730,0,2396:40,33,28,33 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 0/1:97,68:165:99:1638,0,2458:48,49,34,34 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 0/1:86,100:186:99:4056,0,5069:51,35,59,41 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 0/1:92,107:199:99:4080,0,5172:54,38,63,44 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 0/1:118,97:215:99:2597,0,3026:45,73,35,62 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 0/1:8,9:17:99:229,0,197:2,6,0,9 chr1 153003853 . C T 241.77 PASS AC=1;AF=0.68;AN=2;DP=159;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant10-variant13-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant33-variant34-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:67:236,0,67:0,2,0,6 chr1 153003871 . G T 136.72 PASS AC=1;AF=0.733;AN=2;DP=82;FS=0;MQ=60;set=variant-variant6-variant13-variant15-variant17-variant18-variant23-variant24-variant25-variant28-variant33-variant34-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:73:162,0,73:0,2,0,4 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 0/1:12,9:21:99:248,0,344:9,3,7,2 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 0/1:31,40:71:99:958,0,722:19,12,23,17 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 0/1:54,62:116:99:1407,0,1263:29,25,33,29 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 0/1:54,66:120:99:1492,0,1164:28,26,34,32 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 0/1:57,54:111:99:2097,0,2142:29,28,24,30 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 0/1:53,54:107:99:2103,0,2082:27,26,23,31 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 0/1:45,33:78:99:1009,0,1352:26,19,19,14 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 0/1:70,84:154:99:2058,0,1743:30,40,39,45 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 0/1:20,27:47:99:1053,0,1110:8,12,14,13 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 0/1:20,26:46:99:1053,0,1110:8,12,13,13 chr1 153013166 . T TCTCTTATC 505.1 PASS AC=1;AF=0.5;AN=2;DP=108;MQ=60;set=variant12-variant23-variant33-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,10:15:99:412,0,455:2,3,5,5 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 0/1:54:99:9,9,17,19 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 0/1:8,9:17:99:310,0,262:1,7,1,8 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 0/1:8,5:13:99:148,0,272:6,2,4,1 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 0/1:23,18:41:99:636,0,780:4,19,7,11 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 0/1:21,13:34:99:321,0,493:13,8,9,4 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 0/1:30,32:62:99:805,0,761:16,14,20,12 chr1 153065581 . T C 117.92 PASS AC=1;AF=0.593;AN=2;DP=527;MQ=60;set=variant-variant4-variant6-variant9-variant12-variant14-variant15-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,11:18:99:313,0,164:5,2,8,3 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 0/1:57,21:78:99:389,0,1594:25,32,9,12 chr1 153084795 . G C 469.48 PASS AC=1;AF=0.646;AN=2;DP=637;FractionInformativeReads=1;set=variant4-variant5-variant6-variant9-variant12-variant14-variant15-variant16-variant17-variant18-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant36-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,18:26:99:572,0,204:3,5,4,14 chr1 153113913 . A G 702.39 PASS AC=1;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 0/1:32,42:74:99:980,0,795:16,16,22,20 chr1 153122171 . G A 788.1 PASS AC=1;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 0/1:11,22:33:99:663,0,274:5,6,15,7 chr1 153122310 . G A 1294.69 PASS AC=1;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 0/1:37,52:89:99:1454,0,892:25,12,29,23 chr1 153122620 . T C 1120.78 PASS AC=1;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 0/1:67,63:130:99:1629,0,1667:27,40,24,39 chr1 153189978 . A G 270.03 PASS AC=2;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 1/1:0,14:14:42:427,42,0:0,0,8,6 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 0/1:26,21:47:99:569,0,602:14,12,8,13 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 0/1:24,31:55:99:1350,0,2501:12,12,17,14 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 0/1:20,10:30:99:261,0,636:6,14,3,7 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 0/1:16,15:31:99:322,0,444:9,7,9,6 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 0/1:12,10:22:99:303,0,357:4,8,3,7 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 0/1:28,30:58:99:865,0,749:20,8,23,7 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 0/1:38,55:93:99:1286,0,899:19,19,29,26 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 0/1:14,13:27:99:354,0,425:3,11,4,9 chr1 153277768 . C T 92.19 PASS AC=1;AF=0.7;AN=2;DP=162;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant8-variant11-variant13-variant15-variant16-variant17-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:114,0,115:2,3,2,3 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 1/1:0,60:60:99:2700,181,0:0,0,39,21 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 0/1:12,14:26:99:471,0,431:12,0,12,2 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 1/1:0,109:109:99:3237,326,0:0,0,60,49 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 0/1:44,66:110:99:1667,0,1023:19,25,26,40 chr1 153302724 . A G 3360.57 PASS AC=1;AF=0.5;AN=2;DP=277;FS=3.272;FractionInformativeReads=1;MQ=60;MQRankSum=1.517;QD=12.13;ReadPosRankSum=2.109;SOR=0.575;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:133,144:277:99:3389,0,3215:72,61,71,73 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 1/1:0,115:115:99:3839,344,0:0,0,44,71 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 0/1:36,25:61:99:663,0,1157:9,27,8,17 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 0/1:10,15:25:99:392,0,277:2,8,4,11 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 0/1:8,10:18:99:274,0,270:3,5,3,7 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 1/1:0,50:50:99:1476,150,0:0,0,31,19 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 1/1:0,7:7:21:258,21,0:0,0,5,2 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 1/1:0,77:77:99:2263,230,0:0,0,41,36 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 1/1:0,18:18:54:564,54,0:0,0,6,12 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 1/1:0,16:16:54:810,54,0:0,0,12,4 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 1/1:0,97:97:99:2687,290,0:0,0,53,44 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 1/1:0,29:29:87:1035,87,0:0,0,6,23 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 1/1:0,6:6:18:186,18,0:0,0,4,2 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 1/1:0,66:66:99:1868,197,0:0,0,38,28 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 1/1:0,82:82:99:2466,245,0:0,0,47,35 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 1/1:0,17:17:51:632,51,0:0,0,3,14 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 1/1:0,23:23:69:777,69,0:0,0,16,7 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 1/1:0,52:52:99:1609,155,0:0,0,22,30 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 1/1:0,47:47:99:2086,141,0:0,0,21,26 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 1/1:0,10:10:30:424,30,0:0,0,1,9 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 1/1:0,6:6:18:270,18,0:0,0,0,6 chr1 153321407 . C T 94.88 PASS AC=2;AF=0.868;AN=2;DP=186;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,0,3 chr1 153321413 . C G 91.72 PASS AC=2;AF=0.867;AN=2;DP=156;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,0,3 chr1 153330178 . G A 507.25 PASS AC=1;AF=0.5;AN=2;DP=251;FractionInformativeReads=1;MQ=60;set=variant6-variant9-variant12-variant18-variant23-variant26-variant27-variant33-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,10:28:99:247,0,484:12,6,5,5 chr1 153346263 . A G 1121.68 PASS AC=2;AF=0.556;AN=2;DP=460;FractionInformativeReads=1;MQ=60;set=variant6-variant12-variant23-variant27-variant33-variant37-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1555,144,0:0,0,29,19 chr1 153362507 . A G 754.26 PASS AC=2;AF=0.563;AN=2;DP=432;FractionInformativeReads=1;MQ=60;set=variant12-variant23-variant27-variant33-variant37-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1275,99,0:0,0,23,10 chr1 153363105 . T C 804.81 PASS AC=2;AF=0.571;AN=2;DP=485;MQ=60;set=variant12-variant23-variant27-variant33-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:2202,179,0:0,0,13,47 chr1 153389589 . G A 429.12 PASS AC=2;AF=0.571;AN=2;DP=219;MQ=60;set=variant12-variant23-variant27-variant33-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:821,84,0:0,0,17,11 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 1/1:0,26:26:78:792,78,0:0,0,19,7 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 0/1:84,74:158:99:1527,0,2006:48,36,39,35 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 0/1:92,84:176:99:1762,0,2082:46,46,39,45 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 0/1:27,34:61:99:1321,0,1442:14,13,16,18 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 0/1:27,33:60:99:1321,0,1442:14,13,15,18 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 0/1:27,49:76:99:1198,0,604:12,15,27,22 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 0/1:33,22:55:99:562,0,862:14,19,13,9 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 0/1:23,26:49:99:724,0,601:13,10,16,10 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 0/1:36,20:56:99:542,0,963:16,20,7,13 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 0/1:46,53:99:99:1355,0,1204:24,22,27,26 chr1 153393741 . C T 2299.31 PASS AC=1;AF=0.5;AN=2;DP=162;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.024;QD=14.19;ReadPosRankSum=0.423;SOR=0.714;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:75,87:162:99:2328,0,1782:34,41,39,48 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 0/1:55,64:119:99:1804,0,1490:24,31,26,38 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 0/1:21,21:42:99:483,0,550:11,10,12,9 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 0/1:25,18:43:99:475,0,610:13,12,9,9 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 0/1:7,8:15:99:237,0,221:1,6,2,6 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 1/1:0,87:87:99:2551,261,0:0,0,41,46 chr1 153430249 . TG T 1668.68 PASS AC=1;AF=0.63;AN=2;DP=3908;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant28-variant30-variant33-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,60:153:99:1605,0,2633:52,41,33,27 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 1/1:0,54:54:99:1903,162,0:0,0,41,13 chr1 153431406 . C G 5055.4 PASS AC=2;AF=0.977;AN=2;DP=7962;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,155:155:99:4680,464,0:0,0,66,89 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 1/1:0,51:51:99:1457,152,0:0,0,27,24 chr1 153509890 . T C 5630.16 PASS AC=1;AF=0.571;AN=2;DP=1418;MQ=60;set=variant8-variant17-variant20-variant22-variant23-variant33-variant43 GT:AD:DP:GQ:PL:SB 0/1:86,88:174:99:2070,0,2171:36,50,37,51 chr1 153519941 . G A 539.08 PASS AC=1;AF=0.667;AN=2;DP=380;MQ=60;set=variant5-variant8-variant15-variant17-variant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:17,25:42:99:595,0,462:10,7,12,13 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 1/1:0,9:9:27:229,27,0:0,0,5,4 chr1 153588340 . C T 1260.29 PASS AC=2;AF=0.603;AN=2;DP=3810;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant30-variant32-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,124:124:99:3457,369,0:0,0,69,55 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 1/1:4:12:0,0,3,1 chr1 153604029 . C T 4554.55 PASS AC=1;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 0/1:62,71:133:99:1683,0,1410:33,29,39,32 chr1 153604742 . CTT CTTT,CTTTT,C 113.99 PASS AC=0,0,1;AF=0.357,0.143,0.143;AN=2;DP=96;MQ=60;set=variant2-variant4-variant5-variant16-variant21-variant22-filterInvariant23 GT:DP:GQ:SB 0/3:9:73:2,3,0,4 chr1 153618837 . GT G,GTT 1165.19 PASS AC=1,0;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 0/1:77:99:9,54,4,10 chr1 153642372 . G T 1436.95 PASS AC=1;AF=0.538;AN=2;DP=1234;MQ=60;set=variant3-variant4-variant6-variant7-variant11-variant16-variant19-variant23-variant25-variant26-variant32-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:42,40:82:99:961,0,1202:18,24,19,21 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 1/1:0,107:107:99:3196,321,0:0,0,49,58 chr1 153651058 . C A 546.01 PASS AC=1;AF=0.5;AN=2;DP=119;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant11-variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:274,0,340:8,3,7,4 chr1 153651269 . TTCTCTCTCTC TTCTCTCTC,T,TTCTCTCTCTCTC,TTCTCTC 3503.19 PASS AC=1,0,0,0;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 0/1:84:86:33,41,5,5 chr1 153658480 . G A 1317.06 PASS AC=1;AF=0.611;AN=2;DP=1022;MQ=60;set=variant3-variant5-variant8-variant9-variant14-variant20-variant21-variant22-variant23-variant27-variant30-variant33-variant36-variant37-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,26:47:99:778,0,743:15,6,19,7 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 1/1:0,103:103:99:3065,309,0:0,0,53,50 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 1/1:0,17:17:51:684,51,0:0,0,12,5 chr1 153731750 . GAAA GAA,GA,GAAAA,G 256.6 PASS AC=2,0,0,0;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 1/1:12:36:0,0,7,5 chr1 153732640 . A G 130.47 PASS AC=2;AF=0.74;AN=2;DP=153;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant21-variant22-variant23-variant25-variant26-variant32-variant33-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:124,9,0:0,0,3,0 chr1 153732708 . CA C,AA 415.73 PASS AC=1,0;AF=0.571,0.071;AN=2;DP=153;set=variant7-variant20-variant23-variant24-variant25-variant33-filterInvariant38 GT:DP:GQ:SB 0/1:17:78:7,3,7,0 chr1 153742535 . GTGTGTGT GGTGT,G,GGTGTGT,GGT 180.72 PASS AC=1,1,0,0;AF=0.357,0.214,0.143,0.036;AN=2;DP=137;set=variant3-variant4-variant5-variant9-variant21-variant23-variant25-variant26-variant32-variant37-variant38-variant42-variant43-variant44 GT:DP:GQ:SB 2/1:12:99:0,0,11,1 chr1 153742581 . T G 233.77 PASS AC=1;AF=0.5;AN=2;DP=12;FS=0;FractionInformativeReads=0.917;MQ=58.71;MQRankSum=-0.387;QD=19.48;ReadPosRankSum=-1.749;SOR=1.609;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:262,0,193:5,1,5,0 chr1 153742603 . T G 50.19 PASS AC=1;AF=0.5;AN=2;DP=14;FS=2.522;FractionInformativeReads=1;MQ=60;MQRankSum=1.154;QD=3.58;ReadPosRankSum=1.524;SOR=0.12;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:78:78,0,204:6,1,4,3 chr1 153742610 . G T 249.57 PASS AC=1;AF=0.5;AN=2;DP=148;MQ=60;set=variant5-variant20-variant23-variant36-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,15:21:99:326,0,135:5,1,7,8 chr1 153743234 . T C 738.78 PASS AC=2;AF=0.615;AN=2;DP=2125;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant11-variant13-variant15-variant18-variant20-variant21-variant23-variant25-variant26-variant28-variant30-variant32-variant33-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2198,222,0:0,0,38,36 chr1 153743289 . C G 2464.12 PASS AC=1;AF=0.559;AN=2;DP=1230;MQ=60;set=variant3-variant5-variant7-variant10-variant11-variant17-variant18-variant20-variant21-variant23-variant33-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,42:71:99:1058,0,639:13,16,19,23 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 0/1:57,44:101:99:1096,0,1506:31,26,26,18 chr1 153777669 . G T 1178.08 PASS AC=2;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 1/1:0,36:36:99:1060,106,0:0,0,23,13 chr1 153777848 . C T 1121.74 PASS AC=2;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 1/1:0,30:30:90:1048,90,0:0,0,12,18 chr1 153779089 . GT G,GTT 3599.31 PASS AC=2,0;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 1/1:100:99:9,1,43,47 chr1 153779412 . A G 9268.77 PASS AC=2;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 1/1:0,256:256:99:7518,766,0:0,0,124,132 chr1 153780298 . C T 1928.3 PASS AC=2;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 1/1:0,59:59:99:1778,176,0:0,0,27,32 chr1 153781888 . G A 1780.99 PASS AC=2;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 1/1:0,54:54:99:1726,161,0:0,0,34,20 chr1 153784666 . CTT CTTT,CT,C,CTTTT 280.89 PASS AC=0,1,0,0;AF=0.182,0.466,0.023,0.011;AN=2;DP=1866;set=Intersection GT:DP:GQ:SB 0/2:21:48:2,3,7,9 chr1 153790790 . CTTT CTT,C,CT,CTTTT 142.98 PASS AC=0,0,1,0;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 0/3:5:17:0,1,0,4 chr1 153800931 . TACACACACAC TACAC,TAC,TACACACACACAC,TACACACACACACAC,T 206.46 PASS AC=0,2,0,0,0;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 2/2:6:19:0,0,1,5 chr1 153914261 . C G 150.97 PASS AC=1;AF=0.5;AN=2;DP=170;MQ=60;set=variant4-variant6-variant11-variant23-variant28-variant31-variant32-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:96:96,0,175:3,3,3,1 chr1 153921476 . A C 45.67 PASS AC=1;AF=0.5;AN=2;DP=289;MQ=60;set=filterInvariant4-variant5-filterInvariant23-variant32-filterInvariant37-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:36,7:43:93:93,0,2306:19,17,7,0 chr1 153921483 . A C 427.29 PASS AC=1;AF=0.5;AN=2;DP=402;MQ=60;set=variant5-filterInvariant11-variant12-filterInvariant23-variant25-variant29-filterInvariant31-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:37,6:43:72:72,0,2302:19,18,6,0 chr1 153954674 . T C 2210.62 PASS AC=1;AF=0.667;AN=2;DP=2250;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,27:56:99:543,0,759:13,16,13,14 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 1/1:1,73:74:99:2249,195,0:1,0,43,30 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 1/1:0,12:12:36:530,36,0:0,0,11,1 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 1/1:0,47:47:99:1389,140,0:0,0,19,28 chr1 154112167 . A C 531.76 PASS AC=2;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 1/1:0,15:15:43:463,43,0:0,0,11,4 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 1/1:0,20:20:60:629,60,0:0,0,14,6 chr1 154243097 . G A 1003.95 PASS AC=1;AF=0.5;AN=2;DP=642;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant8-variant12-variant15-variant23-variant30-variant36-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,30:55:99:898,0,626:11,14,14,16 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 1/1:0,54:54:99:2138,165,0:0,0,26,28 chr1 154245142 . T G 2603.07 PASS AC=1;AF=0.5;AN=2;DP=1781;MQ=60;set=variant4-variant5-variant8-variant12-variant15-variant23-variant30-variant36-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,101:178:99:2421,0,1649:37,40,42,59 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 1/1:0,13:13:39:501,39,0:0,0,2,11 chr1 154245626 . TAA TA,T 98.55 PASS AC=0,1;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 0/2:18:85:10,3,4,1 chr1 154284894 . A G 410.98 PASS AC=1;AF=0.5;AN=2;DP=557;FractionInformativeReads=1;set=variant3-variant4-variant7-variant12-variant15-variant22-variant23-variant25-variant28-variant32-variant36-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,22:40:99:545,0,439:11,7,14,8 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 0/1:12,17:29:99:373,0,277:4,8,8,9 chr1 154285390 . A T 162.19 PASS AC=1;AF=0.658;AN=2;DP=426;set=variant3-variant6-variant7-variant12-variant15-variant16-filterInvariant18-variant20-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:241,0,283:7,4,5,2 chr1 154285487 . A G 1601.87 PASS AC=1;AF=0.625;AN=2;DP=1833;FractionInformativeReads=1;set=variant3-variant4-variant6-variant7-variant12-variant15-variant16-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant36-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,32:74:99:1206,0,2240:25,17,22,10 chr1 154285494 . C T 1705.55 PASS AC=1;AF=0.625;AN=2;DP=1946;FractionInformativeReads=1;set=variant3-variant4-variant6-variant7-variant12-variant15-variant16-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant36-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,35:79:99:1282,0,2298:27,17,24,11 chr1 154285522 . G A 1366.14 PASS AC=1;AF=0.625;AN=2;DP=2471;set=variant3-variant4-variant6-variant7-variant12-variant15-variant16-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant36-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:56,45:101:99:1041,0,1333:31,25,27,18 chr1 154294560 . C T 2172.84 PASS AC=1;AF=0.5;AN=2;DP=1100;FractionInformativeReads=1;set=variant3-variant23-variant28-variant32-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:84,75:159:99:1656,0,2152:36,48,34,41 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 0/1:40,38:78:99:1035,0,1066:12,28,14,24 chr1 154296076 . T C 2770.38 PASS AC=1;AF=0.548;AN=2;DP=3290;MQ=60;set=variant3-variant6-variant11-variant13-variant15-variant16-variant18-variant20-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant36-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:69,69:138:99:1748,0,1795:45,24,43,26 chr1 154305010 . A G 341.9 PASS AC=1;AF=0.909;AN=2;DP=913;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:9,12:21:99:344,0,303:8,1,9,3 chr1 154305273 . A G 281.13 PASS AC=1;AF=0.5;AN=2;DP=24;FS=4.481;FractionInformativeReads=0.833;MQ=60;MQRankSum=1.042;QD=11.71;ReadPosRankSum=-0.579;SOR=1.981;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:8,12:20:99:309,0,144:4,4,3,9 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 0/1:72,74:146:99:1983,0,2161:34,38,33,41 chr1 154313232 . T C 329.22 PASS AC=2;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 1/1:0,20:20:60:694,60,0:0,0,14,6 chr1 154316434 . C T 1185.95 PASS AC=1;AF=0.5;AN=2;DP=1536;MQ=60;set=variant3-variant4-variant7-variant12-variant15-variant17-variant22-variant23-variant25-variant26-variant28-variant32-variant36-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,28:76:99:649,0,1268:27,21,16,12 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 0/1:64,77:141:99:1872,0,1543:30,34,41,36 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 0/1:16,29:45:99:860,0,458:9,7,16,13 chr1 154320942 . A G 904.77 PASS AC=1;AF=0.531;AN=2;DP=1298;MQ=60;set=variant3-variant4-variant7-variant9-variant12-variant15-variant17-variant22-variant23-variant25-variant26-variant28-variant32-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,29:68:99:634,0,1088:17,22,13,16 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 1/1:0,39:39:99:1458,117,0:0,0,15,24 chr1 154321084 . G T 882.05 PASS AC=1;AF=0.526;AN=2;DP=1019;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant9-variant12-variant15-variant17-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant36-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,15:38:99:411,0,618:10,13,6,9 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 0/1:2,5:7:40:132,0,40:1,1,1,4 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 1/1:0,31:31:93:872,93,0:0,0,19,12 chr1 154377898 . G A 1417.7 PASS AC=1;AF=0.574;AN=2;DP=2101;MQ=60;set=variant3-variant4-variant6-variant7-variant12-variant13-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,28:62:99:536,0,893:12,22,12,16 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 0/1:74,66:140:99:1654,0,1952:41,33,39,27 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 1/1:0,69:69:99:2048,207,0:0,0,26,43 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 0/1:6,10:16:99:398,0,218:5,1,6,4 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 0/1:15,26:41:99:660,0,444:2,13,8,18 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 1/1:0,28:28:84:875,84,0:0,0,19,9 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 0/1:16,17:33:99:308,0,318:7,9,8,9 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 0/1:26,28:54:99:563,0,606:15,11,15,13 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 0/1:40,30:70:99:666,0,1011:20,20,15,15 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 1/1:0,90:90:99:2906,270,0:0,0,43,47 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 1/1:0,38:38:99:1333,114,0:0,0,19,19 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 1/1:0,17:17:51:486,51,0:0,0,9,8 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 1/1:0,32:32:96:1049,96,0:0,0,15,17 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 0/1:124,133:257:99:3218,0,2818:48,76,50,83 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 0/1:33,38:71:99:1012,0,789:13,20,10,28 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 1/1:0,145:145:99:4447,435,0:0,0,86,59 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 0/1:114,122:236:99:2875,0,2617:58,56,69,53 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 1/1:0,229:229:99:6548,683,0:0,0,117,112 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 1/1:0,5:5:15:181,15,0:0,0,4,1 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 0/1:32,36:68:99:879,0,751:16,16,19,17 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 0/1:19,13:32:99:359,0,611:7,12,4,9 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 1/1:0,48:48:99:1520,144,0:0,0,22,26 chr1 154473660 . T C 250.55 PASS AC=1;AF=0.784;AN=2;DP=467;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-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,15:22:99:400,0,168:5,2,10,5 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 1/1:0,28:28:84:870,84,0:0,0,17,11 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 0/1:63,81:144:99:2002,0,1480:28,35,37,44 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 0/1:18,35:53:99:915,0,399:9,9,14,21 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 0/1:21,31:52:99:778,0,477:9,12,13,18 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 0/1:19,34:53:99:942,0,437:8,11,15,19 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 0/1:98,95:193:99:3624,0,4411:46,52,44,51 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 0/1:97,94:191:99:3624,0,4411:46,51,44,50 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 1/1:0,39:39:99:1742,117,0:0,0,26,13 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 0/1:27,19:46:99:488,0,733:16,11,13,6 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 0/1:28,37:65:99:1001,0,654:17,11,22,15 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 1/1:0,49:49:99:1476,147,0:0,0,31,18 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 0/1:12,16:28:99:447,0,445:10,2,12,4 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 0/1:18,14:32:99:346,0,663:12,6,11,3 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 0/1:155,144:299:99:3471,0,3698:69,86,66,78 chr1 154516571 . T C 9055.04 PASS AC=2;AF=0.955;AN=2;DP=10950;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,232:232:99:7254,695,0:0,0,92,140 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 0/1:25,36:61:99:1106,0,814:8,17,11,25 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 1/1:0,29:29:87:1068,87,0:0,0,21,8 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 0/1:16,23:39:99:720,0,406:4,12,4,19 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 1/1:1,21:22:56:828,56,0:0,1,1,20 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 0/1:100,79:179:99:1726,0,2318:44,56,36,43 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 0/1:38,63:101:99:1538,0,867:15,23,28,35 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 1/1:0,85:85:99:2691,254,0:0,0,31,54 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 1/1:0,90:90:99:2891,270,0:0,0,39,51 chr1 154554951 . A AGGGGCATG 4821.24 PASS AC=2;AF=0.943;AN=2;DP=6112;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,131:131:99:5929,404,0:0,0,60,71 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 1/1:0,30:30:90:982,90,0:0,0,19,11 chr1 154555733 . A T 1195.78 PASS AC=2;AF=0.615;AN=2;DP=1748;MQ=60;set=variant3-variant5-variant6-variant9-variant10-variant12-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1842,183,0:0,0,28,33 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 1/1:0,42:42:99:1276,126,0:0,0,23,19 chr1 154556425 . G A 650.58 PASS AC=2;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 1/1:0,42:42:99:1349,126,0:0,0,21,21 chr1 154556663 . G A 787.03 PASS AC=2;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 1/1:0,50:50:99:1518,149,0:0,0,24,26 chr1 154557685 . C T 971.02 PASS AC=2;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 1/1:0,101:101:99:3272,303,0:0,0,59,42 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 1/1:0,12:12:36:427,36,0:0,0,4,8 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 1/1:0,59:59:99:1753,176,0:0,0,24,35 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 1/1:6,82:88:99:1861,114,0:3,3,41,41 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 1/1:0,7:7:21:315,21,0:0,0,0,7 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 1/1:0,154:154:99:4751,462,0:0,0,74,80 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 1/1:0,116:116:99:3740,348,0:0,0,56,60 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 1/1:0,99:99:99:3183,297,0:0,0,50,49 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 1/1:0,144:144:99:4245,431,0:0,0,75,69 chr1 154600401 . A C 73.69 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=3833;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:89,28:117:99:571,0,2987:4,85,28,0 chr1 154600405 . T C 292.22 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=4080;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:97,28:125:99:568,0,3019:8,89,28,0 chr1 154685642 . T C 241.58 PASS AC=1;AF=0.5;AN=2;DP=18;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.53;QD=13.42;ReadPosRankSum=0.795;SOR=0.301;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:9,9:18:99:270,0,312:8,1,7,2 chr1 154687229 . A C 162.78 PASS AC=2;AF=0.583;AN=2;DP=61;FractionInformativeReads=1;MQ=60;set=variant12-variant22-variant23-variant36-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:448,33,0:0,0,9,2 chr1 154744141 . G A 589.12 PASS AC=2;AF=0.607;AN=2;DP=753;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant30-variant31-variant32-variant33-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:807,66,0:0,0,19,3 chr1 154744807 . C G,T 4201.69 PASS AC=2,0;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 1/1:155:99:0,0,57,98 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 1/1:0,117:117:99:3978,351,0:0,0,44,73 chr1 154744937 . C T 188.56 PASS AC=2;AF=0.611;AN=2;DP=1105;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant30-variant31-variant32-variant33-variant36-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1696,162,0:0,0,18,36 chr1 154832304 . T C 6867.94 PASS AC=2;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 1/1:0,151:151:99:6526,460,0:0,0,67,84 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 1/1:0,137:137:99:6070,418,0:0,0,58,79 chr1 154840516 . C A 1018.26 PASS AC=2;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 1/1:0,77:77:99:2484,230,0:0,0,40,37 chr1 154841415 . TCTCTCTCTCTCACA T 167.92 PASS AC=2;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 1/1:0,18:18:60:845,60,0:0,0,10,8 chr1 154842199 . GGCTGCTGCT GGCTGCTGCTGCTGCTGCTGCT,GGCTGCTGCTGCTGCTGCTGCTGCTGCT,GGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT,GGCTGCTGCTGCTGCTGCTGCTGCT,GGCTGCT,G,GGCTGCTGCTGCTGCT,GGCTGCTGCTGCTGCTGCT,GGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT 2072.81 PASS AC=0,0,0,2,0,0,0,0,0;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 4/4:48:99:0,0,20,28 chr1 154897561 . A C 347.17 PASS AC=1;AF=0.5;AN=2;DP=1602;set=filterInvariant2-filterInvariant4-filterInvariant5-filterInvariant7-filterInvariant8-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant15-filterInvariant16-filterInvariant21-filterInvariant22-variant23-variant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-variant29-filterInvariant30-filterInvariant31-filterInvariant33-filterInvariant34-filterInvariant36-variant37-variant38-filterInvariant39-variant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:24,9:33:99:247,0,610:4,20,9,0 chr1 154897567 . A C 526.14 PASS AC=1;AF=0.5;AN=2;DP=1855;set=filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant7-filterInvariant8-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant21-filterInvariant22-variant23-filterInvariant24-filterInvariant25-filterInvariant26-variant27-filterInvariant28-filterInvariant29-filterInvariant30-variant31-filterInvariant34-filterInvariant36-variant37-variant38-variant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:30,9:39:99:192,0,1912:8,22,9,0 chr1 154897570 . T C 520.12 PASS AC=1;AF=0.5;AN=2;DP=1810;set=filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant7-filterInvariant8-filterInvariant10-filterInvariant11-filterInvariant12-variant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant21-filterInvariant22-variant23-filterInvariant25-filterInvariant26-variant27-filterInvariant28-variant29-filterInvariant30-filterInvariant34-filterInvariant36-variant37-filterInvariant38-variant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:31,9:40:99:189,0,1944:7,24,9,0 chr1 154909268 . A G 1499.6 PASS AC=2;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 1/1:1,151:152:99:4555,410,0:0,1,63,88 chr1 154916992 . T TA 87.09 PASS AC=2;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 1/1:1,21:22:38:514,38,0:0,1,12,9 chr1 154917314 . G A 830.93 PASS AC=2;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 1/1:0,78:78:99:2437,233,0:0,0,42,36 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 1/1:0,51:51:99:1679,153,0:0,0,17,34 chr1 154919080 . C T 693.91 PASS AC=2;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 1/1:2,120:122:99:3513,313,0:1,1,54,66 chr1 154941593 . C G 130.13 PASS AC=2;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 1/1:0,9:9:27:312,27,0:0,0,7,2 chr1 154983539 . C T 708.19 PASS AC=2;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 1/1:0,25:25:75:906,75,0:0,0,6,19 chr1 154987526 . C T 2344.39 PASS AC=2;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 1/1:4,215:219:99:6211,590,0:4,0,111,104 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 1/1:2,163:165:99:5118,448,0:1,1,72,91 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 1/1:0,93:93:99:2811,278,0:0,0,45,48 chr1 154990297 . C G 665.65 PASS AC=2;AF=0.667;AN=2;DP=2171;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant22-variant23-variant24-variant25-variant29-variant30-variant31-variant33-variant34-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,75:76:99:2647,202,0:0,1,27,48 chr1 154995503 . G A 524.44 PASS AC=2;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 1/1:0,55:55:99:1499,164,0:0,0,31,24 chr1 154995909 . C T 1116.26 PASS AC=1;AF=0.5;AN=2;DP=80;FS=3.026;FractionInformativeReads=1;MQ=60;MQRankSum=0.491;QD=13.95;ReadPosRankSum=0.453;SOR=0.898;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:34,46:80:99:1144,0,764:16,18,26,20 chr1 155001929 . T C 838.82 PASS AC=2;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 1/1:0,55:55:99:1734,165,0:0,0,18,37 chr1 155003992 . C T 61.03 PASS AC=1;AF=0.5;AN=2;DP=209;MQ=60;set=variant15-variant17-variant22-variant23-variant25-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,13:28:99:469,0,764:3,12,13,0 chr1 155003994 . CA C 425.49 PASS AC=1;AF=0.5;AN=2;DP=32;FS=33.503;FractionInformativeReads=1;MQ=60;MQRankSum=0.576;QD=13.3;ReadPosRankSum=1.65;SOR=5.28;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:19,13:32:99:463,0,848:7,12,13,0 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 0/1:21,13:34:99:454,0,986:7,14,13,0 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 0/1:23,13:36:99:436,0,1238:7,16,13,0 chr1 155004009 . CACATCGGCT C 233.11 PASS AC=1;AF=0.5;AN=2;DP=323;set=variant7-variant8-variant17-variant23-variant41 GT:AD:DP:GQ:PL:SB 0/1:48,13:61:99:370,0,2048:27,21,13,0 chr1 155004021 . T C 236.73 PASS AC=1;AF=0.5;AN=2;DP=329;set=variant7-variant8-variant17-variant23-variant41 GT:AD:DP:GQ:PL:SB 0/1:49,12:61:99:377,0,1927:28,21,12,0 chr1 155006091 . A G 1040.09 PASS AC=2;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 1/1:0,158:158:99:4899,471,0:0,0,80,78 chr1 155006999 . C T 2255.89 PASS AC=2;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 1/1:0,161:161:99:4940,481,0:0,0,79,82 chr1 155007293 . C T 235.59 PASS AC=2;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 1/1:0,5:5:15:201,15,0:0,0,1,4 chr1 155007302 . C A 235.59 PASS AC=2;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 1/1:0,3:3:9:135,9,0:0,0,0,3 chr1 155019710 . A C 1270.49 PASS AC=2;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 1/1:0,78:78:99:2470,234,0:0,0,49,29 chr1 155021893 . AT A,ATT,ATTT 216.1 PASS AC=0,2,0;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 2/2:19:7:0,2,4,13 chr1 155026114 . C T 251.59 PASS AC=2;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 1/1:0,27:27:81:965,81,0:0,0,10,17 chr1 155033308 . G A 3723.62 PASS AC=2;AF=0.583;AN=2;DP=1287;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant8-variant9-variant14-variant18-variant19-variant21-variant23-variant24-variant25-variant30 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2492,236,0:0,0,26,53 chr1 155099852 . G A 249.34 PASS AC=2;AF=0.567;AN=2;DP=239;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant8-variant9-variant11-variant14-variant16-variant23-variant25-variant29-variant30-variant31-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:598,63,0:0,0,12,9 chr1 155106054 . A G 3686.31 PASS AC=2;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 1/1:0,138:138:99:4209,411,0:0,0,67,71 chr1 155106227 . A T 5014.01 PASS AC=2;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 1/1:1,136:137:99:4101,400,0:1,0,64,72 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 1/1:0,20:20:60:633,60,0:0,0,17,3 chr1 155195044 . A G 144.53 PASS AC=2;AF=1;AN=2;DP=67;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant9-variant10-variant11-variant15-variant18-variant23-variant24-variant26-variant27-variant29-variant30-variant32-variant33-variant36-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:181,15,0:0,0,1,4 chr1 155205669 . G T 4277.23 PASS AC=2;AF=0.989;AN=2;DP=9858;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,208:208:99:6436,621,0:0,0,84,124 chr1 155225025 . G C 164.62 PASS AC=1;AF=0.5;AN=2;DP=111;MQ=60;set=variant-variant6-variant14-variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:5,13:18:99:355,0,165:3,2,8,5 chr1 155231927 . C T 1499.28 PASS AC=1;AF=0.5;AN=2;DP=212;MQ=60;set=variant23-variant29 GT:AD:DP:GQ:PL:SB 0/1:45,62:107:99:1528,0,987:23,22,29,33 chr1 155254665 . T G 635.26 PASS AC=1;AF=0.5;AN=2;DP=42;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.216;QD=15.13;ReadPosRankSum=2.554;SOR=0.657;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:18,24:42:99:663,0,528:5,13,7,17 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 1/1:0,117:117:99:3541,350,0:0,0,51,66 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 1/1:0,71:71:99:2389,213,0:0,0,25,46 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 1/1:0,3:3:12:180,12,0:0,0,2,1 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 1/1:0,44:44:99:1472,132,0:0,0,32,12 chr1 155319500 . CTTT C,CT 83.87 PASS AC=1,0;AF=0.375,0.25;AN=2;DP=37;FS=0;set=variant2-variant5-variant23-variant42 GT:DP:GQ:SB 0/1:5:24:0,3,0,2 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 1/1:0,125:125:99:3922,331,0:0,0,61,64 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 1/1:0,124:124:99:5445,373,0:0,0,61,63 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 1/1:0,124:124:99:5695,382,0:0,0,61,63 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 1/1:0,121:121:99:5766,391,0:0,0,61,60 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 1/1:0,122:122:99:5439,373,0:0,0,65,57 chr1 155581279 . G A 1017.94 PASS AC=1;AF=0.5;AN=2;DP=103;FS=1.628;FractionInformativeReads=1;MQ=37.77;MQRankSum=-0.891;QD=9.88;ReadPosRankSum=-0.136;SOR=0.509;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:56,47:103:99:1046,0,1324:21,35,20,27 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 1/1:0,185:185:99:6346,556,0:0,0,92,93 chr1 155631307 . AACACAC AACAC,AACACACACACACAC,AACACACACACACACAC,AACACACACAC,AAC,AACACACACACAC,A,AACACACACACACACACACACAC,AACACACAC 598.48 PASS AC=2,0,0,0,0,0,0,0,0;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 1/1:28:84:0,0,6,22 chr1 155722506 . C G 67.15 PASS AC=2;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 1/1:0,7:7:21:276,21,0:0,0,1,6 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 1/1:0,24:24:72:767,72,0:0,0,11,13 chr1 155737425 . AACACAC AAC,AACACACAC,AACAC,A 1391.16 PASS AC=2,0,0,0;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 1/1:22:65:0,0,7,15 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 1/1:2,43:45:81:1124,81,0:0,2,16,27 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 1/1:0,41:41:99:1396,123,0:0,0,16,25 chr1 155755097 . G A 3927.49 PASS AC=2;AF=0.989;AN=2;DP=5028;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:3042,294,0:0,0,44,54 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 1/1:0,20:20:60:653,60,0:0,0,8,12 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 1/1:0,103:103:99:4588,310,0:0,0,58,45 chr1 155822971 . C T 1019.56 PASS AC=2;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 1/1:0,20:20:60:804,60,0:0,0,18,2 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 1/1:0,38:38:99:1364,114,0:0,0,29,9 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 1/1:0,107:107:99:3045,318,0:0,0,58,49 chr1 155829227 . T TTTCGGAAGAGGCGGAGTCTTCTTCCGAGGACCA 615.58 PASS AC=1;AF=0.563;AN=2;DP=870;set=variant-filterInvariant3-variant4-variant6-variant11-variant14-variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:19,16:35:99:987,0,701:10,9,8,8 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 1/1:0,184:184:99:5207,549,0:0,0,94,90 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 1/1:0,146:146:99:4300,435,0:0,0,82,64 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 1/1:0,150:150:99:4467,450,0:0,0,77,73 chr1 155850558 . T C 872.02 PASS AC=2;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 1/1:0,53:53:99:1757,159,0:0,0,15,38 chr1 155850811 . G A 509.68 PASS AC=2;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 1/1:0,8:8:24:303,24,0:0,0,6,2 chr1 155852123 . C T 3501.29 PASS AC=2;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 1/1:0,56:56:99:2143,168,0:0,0,36,20 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 1/1:9:27:0,0,7,2 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 1/1:0,72:72:99:2472,216,0:0,0,28,44 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 1/1:16,177:193:99:4302,139,0:7,9,85,92 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 1/1:0,118:118:99:3775,354,0:0,0,57,61 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 1/1:0,143:143:99:4525,428,0:0,0,61,82 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 1/1:0,46:46:99:1822,138,0:0,0,13,33 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 1/1:0,4:4:12:99,12,0:0,0,2,2 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 1/1:0,33:33:99:1091,99,0:0,0,24,9 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 1/1:0,19:19:57:844,57,0:0,0,2,17 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 1/1:0,54:54:99:1700,161,0:0,0,33,21 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 1/1:0,18:18:54:635,54,0:0,0,13,5 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 1/1:0,79:79:99:2241,237,0:0,0,42,37 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 1/1:0,371:371:99:10757,1112,0:0,0,195,176 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 1/1:0,24:24:72:996,72,0:0,0,1,23 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 1/1:0,250:250:99:7402,746,0:0,0,114,136 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 1/1:0,156:156:99:4142,463,0:0,0,70,86 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 1/1:0,40:40:99:1695,120,0:0,0,17,23 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 1/1:0,34:34:99:1579,108,0:0,0,13,21 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 1/1:0,42:42:99:1408,125,0:0,0,29,13 chr1 155947875 . A G 2954.55 PASS AC=1;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 0/1:68,51:119:99:1252,0,1585:32,36,24,27 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 1/1:0,65:65:99:1803,194,0:0,0,35,30 chr1 155979033 . C T 585.1 PASS AC=1;AF=0.5;AN=2;DP=113;FractionInformativeReads=1;MQ=60;set=variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:22,27:49:99:613,0,516:12,10,15,12 chr1 156013676 . C T 372.7 PASS AC=1;AF=0.553;AN=2;DP=1096;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant12-variant18-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant29-variant32-variant33-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:20,24:44:99:540,0,449:11,9,11,13 chr1 156020711 . T TC 428.77 PASS AC=1;AF=0.5;AN=2;DP=88;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:22,18:40:99:466,0,598:20,2,16,2 chr1 156025013 . C T 174.62 PASS AC=1;AF=0.5;AN=2;DP=49;MQ=60;set=variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:203,0,384:10,3,6,3 chr1 156025096 . C T 794.88 PASS AC=1;AF=0.528;AN=2;DP=1687;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant12-variant18-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant29-variant33-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:48,38:86:99:946,0,1129:29,19,25,13 chr1 156040310 . A G 1113.09 PASS AC=2;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 1/1:0,29:29:86:918,86,0:0,0,8,21 chr1 156042420 . C T 472.41 PASS AC=1;AF=0.5;AN=2;DP=173;FractionInformativeReads=1;MQ=60;set=variant23-variant25-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:14,19:33:99:501,0,398:8,6,10,9 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 0/1:31,31:62:99:768,0,816:18,13,16,15 chr1 156045755 . C T 1179.54 PASS AC=1;AF=0.5;AN=2;DP=134;MQ=60;set=variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:35,47:82:99:1208,0,843:20,15,24,23 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 1/1:0,30:30:90:1086,90,0:0,0,23,7 chr1 156052656 . C G 201.46 PASS AC=1;AF=0.625;AN=2;DP=104;MQ=60;set=variant5-variant10-variant12-variant20-variant22-variant23-variant25-variant30-variant34-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:59:162,0,59:2,0,2,2 chr1 156095848 . C T 76.47 PASS AC=1;AF=0.5;AN=2;DP=174;FractionInformativeReads=1;MQ=60;set=variant18-variant23-variant26-variant29-variant33-variant36-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:9,13:22:99:469,0,280:8,1,12,1 chr1 156096387 . G A 673.02 PASS AC=1;AF=0.5;AN=2;DP=361;FractionInformativeReads=1;MQ=60;set=variant18-variant23-variant26-variant29-variant33-variant36-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:24,13:37:99:292,0,695:15,9,8,5 chr1 156096417 . T G 1003.58 PASS AC=1;AF=0.5;AN=2;DP=675;MQ=60;set=variant18-variant23-variant26-variant29-variant33-variant34-variant36-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:35,25:60:99:531,0,860:19,16,14,11 chr1 156096814 . ACCCTGTCCT A 296.24 PASS AC=1;AF=0.5;AN=2;DP=165;MQ=60;set=variant18-variant23-variant26-variant29-variant33-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:13,8:21:99:298,0,703:4,9,2,6 chr1 156099630 . C G 747.87 PASS AC=1;AF=0.5;AN=2;DP=366;FractionInformativeReads=1;MQ=60;set=variant18-variant22-variant23-variant26-variant29-variant33-variant36-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:9,20:29:99:541,0,169:4,5,8,12 chr1 156099669 . T G 597.15 PASS AC=1;AF=0.5;AN=2;DP=373;FractionInformativeReads=1;MQ=60;set=variant18-variant23-variant26-variant29-variant33-variant34-variant36-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:9,13:22:99:346,0,214:4,5,4,9 chr1 156105028 . T C 797.56 PASS AC=1;AF=0.5;AN=2;DP=861;FractionInformativeReads=1;MQ=60;set=variant11-variant18-variant23-variant26-variant29-variant33-variant34-variant36-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:17,32:49:99:863,0,306:8,9,11,21 chr1 156105609 . G T 1076.87 PASS AC=1;AF=0.5;AN=2;DP=652;FractionInformativeReads=1;MQ=60;set=variant11-variant18-variant23-variant26-variant29-variant33-variant34-variant36-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:24,29:53:99:717,0,633:17,7,19,10 chr1 156105928 . G A 2042.42 PASS AC=1;AF=0.5;AN=2;DP=1870;MQ=60;set=variant11-variant18-variant23-variant26-variant29-variant33-variant34-variant36-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:77,83:160:99:1997,0,1872:32,45,37,46 chr1 156106185 . T C 364.3 PASS AC=1;AF=0.5;AN=2;DP=317;MQ=60;set=variant11-variant18-variant23-variant26-variant29-variant33-variant34-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:2,19:21:27:473,0,27:1,1,8,11 chr1 156106369 . G A 177.89 PASS AC=1;AF=0.545;AN=2;DP=101;FractionInformativeReads=1;MQ=60;set=variant11-variant18-variant23-variant26-variant29-variant33-variant34-variant36-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:99:114,0,158:4,0,3,0 chr1 156106863 . C T 2209.52 PASS AC=1;AF=0.55;AN=2;DP=2037;MQ=60;set=variant11-variant18-variant23-variant26-variant29-variant33-variant34-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:109,90:199:99:2123,0,2607:52,57,44,46 chr1 156107534 . C T 202.41 PASS AC=1;AF=0.563;AN=2;DP=570;MQ=60;set=variant-variant3-variant4-variant11-variant12-variant14-variant16-variant20-variant22-variant23-variant24-variant30-variant34-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,15:29:99:437,0,378:6,8,3,12 chr1 156108976 . G C 799.04 PASS AC=1;AF=0.55;AN=2;DP=663;FractionInformativeReads=1;MQ=60;set=variant11-variant18-variant23-variant26-variant29-variant33-variant34-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:31,41:72:99:1191,0,891:18,13,22,19 chr1 156109094 . CA C,CAA 2201.07 PASS AC=0,1;AF=0.355,0.177;AN=2;DP=6776;set=variant-filterInvariant2-variant3-variant4-variant7-filterInvariant8-filterInvariant9-filterInvariant10-variant11-filterInvariant12-filterInvariant13-variant14-variant16-variant18-filterInvariant19-variant23-filterInvariant24-filterInvariant25-variant26-filterInvariant27-variant29-filterInvariant31-filterInvariant32-variant33-variant34-variant36-filterInvariant37-variant38-variant39-variant41-filterInvariant42 GT:DP:GQ:SB 0/2:193:99:64,50,47,32 chr1 156109951 . TACACACACACACACAC TACACACACACACACACACACACACACACACACAC,TACACACACACACAC,TACACACACACACACACACACACACACACACAC,TACACAC,TACACACACACACACACAC,TACACACACACACACACACACACACACACAC,TACACACACACAC,TACACACACACACACACACAC,TACACACACAC,TACACACAC,TACACACACACACACACACACACACAC,TACACACACACACACACACACACACACAC,T,TACACACACACACACACACACAC 165.3 PASS AC=0,0,0,0,0,0,2,0,0,0,0,0,0,0;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 7/7:10:31:0,0,1,9 chr1 156123230 . C G 470.44 PASS AC=2;AF=0.553;AN=2;DP=778;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant11-variant14-variant16-variant17-variant18-variant23-variant26-variant29-variant33-variant34-variant36-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1193,123,0:0,0,23,18 chr1 156131095 . C CGGGGCGG 398.53 PASS AC=2;AF=1;AN=2;DP=62;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.742;ReadPosRankSum=0.742;set=variant2-variant4-variant5-variant10-variant13-variant15-variant17-variant22-variant23-variant27-variant28-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:15:221,15,0:0,0,2,0 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 0/1:65,36:101:99:1286,0,2655:32,33,14,22 chr1 156146218 . C T 2292.56 PASS AC=1;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 0/1:41,44:85:99:1035,0,1008:26,15,26,18 chr1 156147326 . T C 1352.98 PASS AC=1;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 0/1:28,15:43:99:513,0,814:15,13,1,14 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 0/1:70,46:116:99:940,0,1641:39,31,24,22 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 0/1:47,53:100:99:1537,0,1241:31,16,37,16 chr1 156179927 . G A 148.54 PASS AC=1;AF=0.5;AN=2;DP=30;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.154;QD=4.95;ReadPosRankSum=-2.002;SOR=0.495;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:20,10:30:99:177,0,558:13,7,6,4 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 0/1:12:44:3,1,5,3 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 0/1:14,13:27:99:332,0,368:7,7,7,6 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 0/1:11,28:39:99:1016,0,327:5,6,8,20 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 0/1:23,16:39:99:306,0,557:13,10,9,7 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 0/1:16,5:21:99:121,0,630:16,0,4,1 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 0/1:19,11:30:99:314,0,553:14,5,8,3 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 0/1:78,77:155:99:1824,0,1671:42,36,37,40 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 0/1:144,128:272:99:2951,0,3677:70,74,66,62 chr1 156206156 . G A 3500.77 PASS AC=1;AF=0.5;AN=2;DP=253;FS=1.518;FractionInformativeReads=0.996;MQ=60;MQRankSum=0.917;QD=13.84;ReadPosRankSum=3.027;SOR=0.814;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:118,134:252:99:3529,0,2801:58,60,62,72 chr1 156211825 . T C 952.16 PASS AC=2;AF=0.563;AN=2;DP=1321;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant9-variant12-variant15-variant21-variant23-variant25-variant27-variant29-variant31-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2097,201,0:0,0,31,36 chr1 156213257 . G A 582.57 PASS AC=2;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 1/1:0,48:48:99:1636,144,0:0,0,27,21 chr1 156248829 . T C 776.97 PASS AC=1;AF=0.5;AN=2;DP=120;FractionInformativeReads=1;MQ=60;set=variant12-variant23 GT:AD:DP:GQ:PL:SB 0/1:36,24:60:99:864,0,2031:16,20,8,16 chr1 156248832 . G A 836.13 PASS AC=1;AF=0.5;AN=2;DP=59;FS=2.3;FractionInformativeReads=1;MQ=60;MQRankSum=-0.256;QD=14.17;ReadPosRankSum=-2.277;SOR=1.122;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:36,23:59:99:864,0,2031:16,20,8,15 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 1/1:0,16:16:48:654,48,0:0,0,2,14 chr1 156262709 . T C 837.7 PASS AC=1;AF=0.5;AN=2;DP=380;MQ=60;set=variant21-variant23-variant29-variant31 GT:AD:DP:GQ:PL:SB 0/1:63,42:105:99:965,0,1454:37,26,27,15 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 1/1:0,68:68:99:2182,204,0:0,0,20,48 chr1 156288829 . C T 880.86 PASS AC=1;AF=0.5;AN=2;DP=85;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.349;QD=10.36;ReadPosRankSum=1.313;SOR=0.728;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:47,38:85:99:909,0,1175:19,28,15,23 chr1 156307292 . G GTA 157.44 PASS AC=1;AF=0.5;AN=2;DP=46;MQ=60;set=variant12-variant23 GT:AD:DP:GQ:PL:SB 0/1:12,7:19:99:258,0,471:8,4,6,1 chr1 156347834 . T A 1291.93 PASS AC=1;AF=0.56;AN=2;DP=2760;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant17-variant19-variant21-variant23-variant26-variant27-variant28-variant30-variant33-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:56,49:105:99:1226,0,1308:28,28,27,22 chr1 156351699 . G A 3446.93 PASS AC=1;AF=0.727;AN=2;DP=3241;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,41:87:99:892,0,1188:23,23,24,17 chr1 156351792 . G A 3053.68 PASS AC=1;AF=0.742;AN=2;DP=2825;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,41:90:99:897,0,1301:24,25,18,23 chr1 156352447 . G T 350.8 PASS AC=1;AF=0.607;AN=2;DP=558;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant17-variant19-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:132,0,174:5,1,5,1 chr1 156353970 . A G 410.83 PASS AC=1;AF=0.528;AN=2;DP=550;MQ=60;set=variant2-variant6-variant8-variant9-variant10-variant14-variant15-variant19-variant20-variant23-variant24-variant29-variant31-variant36-variant37-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,15:25:99:475,0,252:7,3,10,5 chr1 156354293 . A G 581.2 PASS AC=1;AF=0.548;AN=2;DP=2304;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant14-variant15-variant19-variant20-variant23-variant24-variant29-variant31-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,49:97:99:1151,0,1304:21,27,23,26 chr1 156354347 . TC T 402.52 PASS AC=1;AF=0.548;AN=2;DP=1599;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant14-variant15-variant19-variant20-variant23-variant24-variant29-variant31-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,32:57:99:806,0,591:9,16,14,18 chr1 156354367 . A G 538.46 PASS AC=2;AF=0.757;AN=2;DP=2477;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-variant31-variant33-variant34-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1849,165,0:0,0,21,34 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 1/1:0,10:10:30:400,30,0:0,0,9,1 chr1 156434703 . G T 1495 PASS AC=1;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 0/1:30,40:70:99:977,0,859:18,12,21,19 chr1 156446242 . C A 3100.41 PASS AC=1;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 0/1:60,62:122:99:1402,0,1514:40,20,38,24 chr1 156446450 . C T 1702.92 PASS AC=1;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 0/1:34,24:58:99:671,0,897:9,25,5,19 chr1 156446903 . T C 3769.86 PASS AC=1;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 0/1:39,65:104:99:1547,0,715:20,19,29,36 chr1 156450719 . G A 1617.2 PASS AC=1;AF=0.529;AN=2;DP=2163;MQ=60;set=variant8-variant14-variant15-variant18-variant19-variant23-variant26-variant27-variant28-variant32-variant34-variant36-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:61,49:110:99:1156,0,1539:28,33,23,26 chr1 156450740 . G A 3131.12 PASS AC=1;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 0/1:42,60:102:99:1502,0,982:18,24,28,32 chr1 156450873 . T C 663.47 PASS AC=1;AF=0.761;AN=2;DP=1206;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:10,17:27:99:443,0,246:3,7,5,12 chr1 156452870 . G A 1570.29 PASS AC=1;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 0/1:30,28:58:99:824,0,879:21,9,21,7 chr1 156453247 . T A 930.24 PASS AC=1;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 0/1:16,15:31:99:243,0,389:6,10,7,8 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 1/1:0,30:30:88:908,88,0:0,0,20,10 chr1 156460511 . C T 275.34 PASS AC=1;AF=0.529;AN=2;DP=341;FractionInformativeReads=1;MQ=60;set=variant8-variant14-variant15-variant18-variant19-variant23-variant26-variant27-variant28-variant32-variant34-variant36-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,8:11:99:185,0,104:0,3,3,5 chr1 156495521 . CAAAAAAAA CAAAAAA,C,CAAAAAAAAAAAAA,CAAAAAAAAAAA,CAAAAAAAAAA,CAAAAAAA,CAAAAAAAAAAAA,CAAAAA,CAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAA 132.92 PASS AC=0,0,1,0,1,0,0,0,0,0;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 5/3:11:99:0,1,6,4 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 1/1:0,82:82:99:2483,245,0:0,0,52,30 chr1 156498673 . T A 681.81 PASS AC=1;AF=0.538;AN=2;DP=2806;MQ=60;set=variant-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant22-variant23-variant25-variant26-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,49:116:99:1076,0,1702:39,28,30,19 chr1 156499969 . T C 2362.35 PASS AC=1;AF=0.558;AN=2;DP=6195;MQ=60;set=variant-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant22-variant23-variant25-variant26-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:102,108:210:99:2801,0,2430:42,60,42,66 chr1 156500906 . T C 296.82 PASS AC=1;AF=0.5;AN=2;DP=66;FractionInformativeReads=1;MQ=60;set=variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:16,13:29:99:325,0,365:11,5,9,4 chr1 156502991 . A G 314.32 PASS AC=1;AF=0.554;AN=2;DP=892;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant22-variant23-variant25-variant26-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,18:31:99:632,0,436:1,12,3,15 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 1/1:0,17:17:51:513,51,0:0,0,10,7 chr1 156504104 . A C 135.3 PASS AC=1;AF=0.577;AN=2;DP=392;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant22-variant23-variant25-variant26-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,8:13:99:213,0,163:5,0,5,3 chr1 156504824 . G A 654.4 PASS AC=1;AF=0.5;AN=2;DP=191;FractionInformativeReads=1;MQ=60;set=variant10-variant11-variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:13,18:31:99:515,0,363:11,2,15,3 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 1/1:0,66:66:99:2284,198,0:0,0,39,27 chr1 156518556 . G A 568.73 PASS AC=1;AF=0.5;AN=2;DP=122;FractionInformativeReads=1;MQ=60;set=variant23-variant24 GT:AD:DP:GQ:PL:SB 0/1:42,23:65:99:597,0,1168:14,28,10,13 chr1 156518730 . G A 277.33 PASS AC=1;AF=0.5;AN=2;DP=34;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:306,0,350:2,8,3,7 chr1 156520025 . C T 300.38 PASS AC=1;AF=0.5;AN=2;DP=54;FractionInformativeReads=1;MQ=60;set=variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:17,15:32:99:329,0,353:9,8,10,5 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 1/1:0,86:86:99:2375,257,0:0,0,47,39 chr1 156521480 . A G 46.5 PASS AC=1;AF=0.5;AN=2;DP=27;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:75:75,0,75:1,1,1,1 chr1 156521743 . AC A 2540.52 PASS AC=1;AF=0.5;AN=2;DP=315;MQ=60;set=variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:81,87:168:99:2578,0,2374:39,42,38,49 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 1/1:0,82:82:99:2405,246,0:0,0,46,36 chr1 156526387 . C G 548.35 PASS AC=1;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 0/1:37,54:91:99:1340,0,938:14,23,27,27 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 1/1:0,54:54:99:1914,162,0:0,0,15,39 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 1/1:0,26:26:78:799,78,0:0,0,15,11 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 1/1:0,87:87:99:2625,260,0:0,0,32,55 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 1/1:0,46:46:99:1527,138,0:0,0,33,13 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 1/1:0,110:110:99:3077,328,0:0,0,63,47 chr1 156532932 . C T 903.18 PASS AC=1;AF=0.5;AN=2;DP=244;FractionInformativeReads=1;MQ=60;set=variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:73,41:114:99:931,0,1633:38,35,21,20 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 1/1:0,94:94:99:2778,281,0:0,0,42,52 chr1 156533433 . G T 859.2 PASS AC=1;AF=0.5;AN=2;DP=119;FractionInformativeReads=1;MQ=60;set=variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:25,32:57:99:887,0,793:13,12,20,12 chr1 156534321 . CCTT C 760.27 PASS AC=1;AF=0.5;AN=2;DP=95;MQ=60;set=variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:28,21:49:99:798,0,1352:17,11,13,8 chr1 156534525 . A C 524.85 PASS AC=1;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 0/1:7,13:20:99:382,0,174:3,4,5,8 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 1/1:0,17:17:51:616,51,0:0,0,5,12 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 1/1:0,13:13:39:585,39,0:0,0,11,2 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 1/1:0,15:15:45:640,45,0:0,0,13,2 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 1/1:0,40:40:99:1460,120,0:0,0,30,10 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 1/1:0,81:81:99:2641,243,0:0,0,53,28 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 1/1:0,156:156:99:4484,467,0:0,0,72,84 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 1/1:0,47:47:99:1474,140,0:0,0,15,32 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 1/1:0,7:7:21:305,21,0:0,0,7,0 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 1/1:1,13:14:15:335,15,0:1,0,8,5 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 1/1:0,55:55:99:1800,165,0:0,0,31,24 chr1 156539320 . CTTTTTTT CTTTTTTTTT,CTTTTTTTT,CTTTTTTTTTTT,CTTTTTT,C,CTTTTTTTTTT 152.57 PASS AC=0,0,0,0,1,0;AF=0.211,0.316,0.026,0.026,0.026,0.026;AN=2;DP=556;set=variant-variant2-variant6-variant7-variant9-variant10-variant12-variant14-variant15-filterInvariant16-variant21-variant23-variant25-filterInvariant26-variant28-variant31-variant32-variant33-variant41 GT:DP:GQ:SB 0/5:15:99:2,6,2,5 chr1 156550968 . A C 135.12 PASS AC=1;AF=0.55;AN=2;DP=196;FractionInformativeReads=1;MQ=60;set=variant10-variant11-variant16-variant19-variant23-variant33-variant34-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:148,0,153:4,4,4,3 chr1 156551628 . G T 1314.97 PASS AC=1;AF=0.5;AN=2;DP=362;MQ=60;set=variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:106,60:166:99:1343,0,2988:52,54,26,34 chr1 156551848 . A G 1548.27 PASS AC=1;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 0/1:44,38:82:99:1118,0,1124:17,27,10,28 chr1 156552711 . C G 266.62 PASS AC=1;AF=0.528;AN=2;DP=282;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant22-variant23-variant25-variant31-variant32-variant34-variant36-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:299,0,341:9,0,7,1 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 1/1:0,21:21:66:877,66,0:0,0,17,4 chr1 156553102 . AG A 341.29 PASS AC=1;AF=0.524;AN=2;DP=1225;MQ=60;set=variant-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant22-variant23-variant25-variant26-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,26:54:99:807,0,880:14,14,8,18 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 0/1:56,20:76:99:290,0,2933:9,47,20,0 chr1 156553505 . T C 41.13 PASS AC=1;AF=0.5;AN=2;DP=1743;MQ=60;set=filterInvariant2-variant4-filterInvariant5-filterInvariant10-filterInvariant12-filterInvariant14-filterInvariant15-variant16-filterInvariant17-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant28-filterInvariant29-filterInvariant39-filterInvariant40-filterInvariant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:60,16:76:99:274,0,3004:11,49,16,0 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 1/1:0,18:18:54:628,54,0:0,0,5,13 chr1 156556023 . C T 49.69 PASS AC=1;AF=0.6;AN=2;DP=121;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant8-variant9-variant10-variant15-variant16-variant22-variant23-variant25-variant26-variant34-variant36-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:74:118,0,74:2,1,3,1 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 1/1:0,100:100:99:2900,299,0:0,0,58,42 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 1/1:0,23:23:69:819,69,0:0,0,8,15 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 1/1:0,22:22:66:733,66,0:0,0,11,11 chr1 156561557 . G GGGGCCGGGCC,GGGGTCGGGCC,GGGGCCGGGCCGGGCC 2495.94 PASS AC=1,1,0;AF=0.648,0.295,0.057;AN=2;DP=2606;FS=0;set=Intersection GT:DP:GQ:SB 1/2:44:99:1,0,27,16 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 1/1:1,192:193:99:5882,568,0:1,0,118,74 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 1/1:0,61:61:99:1972,183,0:0,0,17,44 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 1/1:0,24:24:72:775,72,0:0,0,16,8 chr1 156562641 . C CCA 476 PASS AC=1;AF=0.524;AN=2;DP=675;MQ=60;set=variant-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant22-variant23-variant25-variant26-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,14:25:99:471,0,361:2,9,2,12 chr1 156563375 . G A 1266.67 PASS AC=2;AF=0.932;AN=2;DP=3712;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,69:69:99:2107,206,0:0,0,33,36 chr1 156563726 . A C 3362.84 PASS AC=2;AF=0.932;AN=2;DP=6323;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:4068,390,0:0,0,57,73 chr1 156563813 . G A 2921.79 PASS AC=2;AF=0.932;AN=2;DP=4851;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2459,257,0:0,0,36,50 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 1/1:0,70:70:99:2093,209,0:0,0,27,43 chr1 156563898 . T C 1450.6 PASS AC=2;AF=0.932;AN=2;DP=2398;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1123,102,0:0,0,12,22 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 1/1:0,24:24:72:783,72,0:0,0,12,12 chr1 156564640 . G A 921.4 PASS AC=1;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 0/1:38,15:53:99:358,0,1091:18,20,8,7 chr1 156564922 . C T 3605.25 PASS AC=1;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 0/1:92,144:236:99:3831,0,2279:47,45,75,69 chr1 156565049 . A AAC 12589 PASS AC=2;AF=1;AN=2;DP=11760;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,216:216:99:9698,658,0:0,0,104,112 chr1 156565834 . G C 1008.84 PASS AC=1;AF=0.524;AN=2;DP=1822;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant22-variant23-variant25-variant26-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,36:80:99:968,0,1158:29,15,20,16 chr1 156567496 . C T 240.81 PASS AC=1;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 0/1:33,17:50:99:493,0,944:23,10,14,3 chr1 156589450 . C T 1516.59 PASS AC=1;AF=0.524;AN=2;DP=3032;MQ=60;set=variant-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant22-variant23-variant25-variant26-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,61:132:99:1578,0,1740:28,43,30,31 chr1 156594364 . T C 1393.87 PASS AC=1;AF=0.525;AN=2;DP=2654;MQ=60;set=variant-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant22-variant23-variant25-variant26-variant31-variant32-variant34-variant36-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,47:129:99:1099,0,2108:39,43,24,23 chr1 156594656 . C A 649.67 PASS AC=1;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 0/1:10,28:38:99:662,0,247:2,8,11,17 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 1/1:0,65:65:99:1833,193,0:0,0,31,34 chr1 156618768 . T G 314.43 PASS AC=2;AF=0.683;AN=2;DP=553;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:543,48,0:0,0,5,11 chr1 156626358 . C A 333.13 PASS AC=2;AF=0.667;AN=2;DP=708;MQ=60;set=variant3-filterInvariant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant29-variant30-variant31-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:544,45,0:0,0,2,13 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 1/1:0,204:204:99:6291,612,0:0,0,85,119 chr1 156627069 . A G 66.37 PASS AC=1;AF=0.5;AN=2;DP=98;FractionInformativeReads=1;MQ=60;set=variant4-variant10-variant17-variant23-variant37 GT:AD:DP:GQ:PL:SB 0/1:7,10:17:99:324,0,261:0,7,1,9 chr1 156627620 . A C 138.91 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=381;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:65,15:80:67:67,0,2903:2,63,15,0 chr1 156627625 . T C 45.07 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=183;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:61,12:73:73:73,0,2858:2,59,12,0 chr1 156628717 . C A 2165.01 PASS AC=1;AF=0.611;AN=2;DP=2273;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant29-variant30-variant31-variant36-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,49:74:99:1428,0,549:16,9,28,21 chr1 156629037 . A G 1282.37 PASS AC=1;AF=0.625;AN=2;DP=2198;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant29-variant30-variant31-variant36-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,55:97:99:1443,0,973:18,24,25,30 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 1/1:1,3:4:2:77,2,0:0,1,2,1 chr1 156639753 . G A 1584.85 PASS AC=1;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 0/1:104,103:207:99:2494,0,3022:41,63,44,59 chr1 156640156 . G A 3147.98 PASS AC=1;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 0/1:115,101:216:99:2415,0,2821:69,46,59,42 chr1 156640581 . C G 1214.82 PASS AC=1;AF=0.5;AN=2;DP=256;MQ=60;set=variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:70,56:126:99:1243,0,1868:32,38,25,31 chr1 156640678 . G A,C 355.1 PASS AC=1,0;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 0/1:72:99:17,28,4,23 chr1 156641537 . C T 1475.82 PASS AC=1;AF=0.571;AN=2;DP=2178;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant23-variant30-variant31-variant36-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,39:80:99:823,0,1131:19,22,19,20 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 1/1:0,78:78:99:2554,233,0:0,0,42,36 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 1/1:0,21:21:63:856,63,0:0,0,13,8 chr1 156692055 . AT ATT,A 74.19 PASS AC=1,0;AF=0.25,0.3;AN=2;DP=233;MQ=60;set=variant3-filterInvariant6-variant10-variant11-variant12-variant13-variant22-variant23-variant25-variant34 GT:DP:GQ:SB 0/1:18:99:3,7,2,6 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 1/1:0,13:13:39:387,39,0:0,0,7,6 chr1 156697056 . T C 3119.52 PASS AC=1;AF=0.667;AN=2;DP=1217;MQ=60;set=variant3-variant11-variant23-variant34-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:77,101:178:99:2439,0,1830:36,41,50,51 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 0/1:51,38:89:99:888,0,1281:18,33,10,28 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 1/1:0,201:201:99:5706,601,0:0,0,96,105 chr1 156706559 . A C,G 5984.76 PASS AC=0,2;AF=0.33,0.67;AN=2;DP=6753;FS=0;MQ=60;set=Intersection GT:DP:GQ:SB 2/2:128:99:0,0,76,52 chr1 156706914 . C T 152 PASS AC=1;AF=0.5;AN=2;DP=22;FS=0;FractionInformativeReads=1;MQ=60;set=variant6-variant23 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:187,0,154:3,3,3,3 chr1 156707128 . AAG A 774.01 PASS AC=1;AF=0.667;AN=2;DP=247;MQ=60;set=variant3-variant11-variant23-variant34-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,9:25:99:311,0,680:9,7,6,3 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 1/1:0,31:31:93:984,93,0:0,0,22,9 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 1/1:0,71:71:99:2228,212,0:0,0,35,36 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 0/1:42,31:73:99:768,0,1078:20,22,15,16 chr1 156715378 . C T 289.42 PASS AC=1;AF=0.5;AN=2;DP=311;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant9-variant19-variant23-variant24-variant26-variant27-variant29-variant40 GT:AD:DP:GQ:PL:SB 0/1:16,15:31:99:448,0,444:5,11,4,11 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 0/1:31,24:55:99:569,0,766:17,14,13,11 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 0/1:3,4:7:86:122,0,86:0,3,1,3 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 0/1:42,34:76:99:732,0,1005:22,20,18,16 chr1 156767253 . C T 833.39 PASS AC=1;AF=0.7;AN=2;DP=309;FractionInformativeReads=1;MQ=60;set=variant3-variant11-variant23-variant34-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,25:47:99:651,0,548:11,11,13,12 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 0/1:26,20:46:99:497,0,693:13,13,10,10 chr1 156785356 . T C 1060.39 PASS AC=1;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 0/1:20,17:37:99:506,0,557:14,6,14,3 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 0/1:86,63:149:99:1613,0,2337:37,49,27,36 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 0/1:53,43:96:99:1616,0,2808:26,27,20,23 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 0/1:51,39:90:99:1531,0,2898:24,27,17,22 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 0/1:46,41:87:99:1574,0,2450:23,23,19,22 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 1/1:0,26:26:78:868,78,0:0,0,15,11 chr1 156810221 . G C 493.49 PASS AC=1;AF=0.5;AN=2;DP=503;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant19-variant21-variant23-variant31-variant32-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,11:25:99:239,0,375:3,11,5,6 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 0/1:5,3:8:99:111,0,163:3,2,3,0 chr1 156828900 . G A 70.9 PASS AC=2;AF=0.6;AN=2;DP=48;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant13-variant23-variant31 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:174,18,0:0,0,2,4 chr1 156837847 . T C 2548.35 PASS AC=1;AF=0.5;AN=2;DP=1635;MQ=60;set=variant6-variant12-variant13-variant23-variant24-variant31 GT:AD:DP:GQ:PL:SB 0/1:134,115:249:99:2699,0,3027:70,64,67,48 chr1 156845492 . AGTGTGTGTGTGT AGTGTGTGTGTGTGTGT,A,AGTGTGTGTGTGTGTGTGT,AGTGTGTGTGT,AGTGTGTGTGTGTGT,AGTGTGTGTGTGTGTGTGTGT 809.19 PASS AC=2,0,0,0,0,0;AF=0.489,0.023,0.125,0.125,0.114,0.011;AN=2;DP=3699;set=Intersection GT:DP:GQ:SB 1/1:39:21:2,2,10,25 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 1/1:0,138:138:99:4375,413,0:0,0,80,58 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 1/1:0,27:27:81:894,81,0:0,0,16,11 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 1/1:0,44:44:99:1261,131,0:0,0,19,25 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 1/1:0,51:51:99:1444,153,0:0,0,23,28 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 1/1:0,81:81:99:3689,247,0:0,0,47,34 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 1/1:0,87:87:99:3877,262,0:0,0,49,38 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 1/1:0,91:91:99:3945,276,0:0,0,47,44 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 1/1:0,12:12:36:410,36,0:0,0,2,10 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 1/1:0,62:62:99:1953,185,0:0,0,43,19 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 1/1:0,98:98:99:2773,293,0:0,0,42,56 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 0/1:25,29:54:99:739,0,629:16,9,19,10 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 0/1:37,43:80:99:1059,0,879:21,16,23,20 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 0/1:21,25:46:99:731,0,506:14,7,19,6 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 0/1:32,28:60:99:788,0,783:17,15,12,16 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 0/1:15,5:20:99:165,0,407:5,10,1,4 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 0/1:13,22:35:99:530,0,282:9,4,14,8 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 0/1:42,32:74:99:714,0,1130:22,20,19,13 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 0/1:38,42:80:99:1008,0,974:19,19,20,22 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 0/1:62:99:11,14,17,20 chr1 156918137 . C T 1735.26 PASS AC=1;AF=0.5;AN=2;DP=597;MQ=60;set=variant5-variant9-variant14-variant23 GT:AD:DP:GQ:PL:SB 0/1:47,74:121:99:1863,0,1030:24,23,43,31 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 0/1:41,38:79:99:861,0,950:23,18,21,17 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 0/1:23,22:45:99:845,0,1111:18,5,13,9 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 0/1:53,57:110:99:1433,0,1316:21,32,24,33 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 0/1:11,10:21:99:330,0,332:3,8,2,8 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 0/1:26,16:42:99:457,0,764:6,20,3,13 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 0/1:100,94:194:99:2179,0,2568:54,46,44,50 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 0/1:25,69:94:99:2006,0,581:11,14,32,37 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 0/1:84,59:143:99:1253,0,2071:45,39,30,29 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 0/1:52,74:126:99:1793,0,1077:24,28,30,44 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 0/1:24,31:55:99:911,0,702:13,11,17,14 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 0/1:11,22:33:99:615,0,275:5,6,13,9 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 0/1:30,37:67:99:1031,0,744:17,13,23,14 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 0/1:76,54:130:99:1301,0,1851:39,37,22,32 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 0/1:25,43:68:99:1033,0,572:17,8,27,16 chr1 157092437 . C A 1077.01 PASS AC=1;AF=0.5;AN=2;DP=192;FractionInformativeReads=1;MQ=60;set=variant9-variant23 GT:AD:DP:GQ:PL:SB 0/1:62,38:100:99:811,0,1526:28,34,16,22 chr1 157094030 . CAAA CAA,C,CA 886.14 PASS AC=1,1,0;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 2/1:91:99:11,8,51,21 chr1 157094550 . T C 177.98 PASS AC=1;AF=0.5;AN=2;DP=518;set=variant-variant2-variant4-variant6-variant10-variant12-variant15-filterInvariant16-variant17-variant18-variant22-filterInvariant23-filterInvariant25-variant26-filterInvariant31-variant34-variant36-variant37-variant39-variant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:18,4:22:64:64,0,477:1,17,4,0 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 1/1:0,35:35:99:1086,104,0:0,0,19,16 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 1/1:1,35:36:61:985,61,0:0,1,14,21 chr1 157484453 . G A 567.79 PASS AC=2;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 1/1:0,69:69:99:2152,206,0:0,0,32,37 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 1/1:0,57:57:99:1858,171,0:0,0,28,29 chr1 157485561 . G A 666.67 PASS AC=2;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 1/1:1,72:73:99:2566,208,0:0,1,44,28 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 1/1:0,12:12:36:491,36,0:0,0,1,11 chr1 157491173 . T A 1493.9 PASS AC=2;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 1/1:0,44:44:99:1362,132,0:0,0,17,27 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 1/1:0,298:298:99:8764,891,0:0,0,160,138 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 1/1:0,44:44:99:1411,131,0:0,0,30,14 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 1/1:0,219:219:99:6639,656,0:0,0,119,100 chr1 157502812 . C A 2184.78 PASS AC=1;AF=0.5;AN=2;DP=186;FS=1.139;FractionInformativeReads=0.995;MQ=60;MQRankSum=1.202;QD=11.75;ReadPosRankSum=2.773;SOR=0.797;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:86,99:185:99:2213,0,2043:43,43,47,52 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 1/1:1,192:193:99:5779,533,0:0,1,91,101 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 1/1:0,28:28:83:963,83,0:0,0,20,8 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 1/1:0,99:99:99:2887,296,0:0,0,49,50 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 1/1:0,102:102:99:3085,306,0:0,0,59,43 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 0/1:107,88:195:99:2015,0,2483:51,56,41,47 chr1 157543762 . C T 6660.09 PASS AC=2;AF=0.83;AN=2;DP=9542;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,181:181:99:6681,544,0:0,0,83,98 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 0/1:33,29:62:99:1022,0,1278:17,16,14,15 chr1 157544850 . C T 519.28 PASS AC=1;AF=0.646;AN=2;DP=1358;MQ=60;set=variant-variant4-variant5-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,38:63:99:1017,0,672:8,17,13,25 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 0/1:25,31:56:99:797,0,628:12,13,17,14 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 0/1:28,21:49:99:578,0,733:16,12,11,10 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 0/1:16,11:27:99:273,0,520:2,14,2,9 chr1 157550066 . T C 1645.14 PASS AC=1;AF=0.646;AN=2;DP=4028;MQ=60;set=variant-variant4-variant5-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,72:155:99:1618,0,1939:44,39,37,35 chr1 157557701 . G A 795.25 PASS AC=1;AF=0.648;AN=2;DP=1223;MQ=60;set=variant-variant2-variant4-variant5-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,26:40:99:662,0,311:9,5,16,10 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 0/1:37,21:58:99:522,0,959:13,24,7,14 chr1 157559122 . C T 1837.53 PASS AC=1;AF=0.542;AN=2;DP=1449;MQ=60;set=variant4-variant5-variant19-variant23-variant25-variant27-variant30-variant31-variant32-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,52:130:99:1139,0,1826:39,39,22,30 chr1 157566019 . G A 326.38 PASS AC=1;AF=0.611;AN=2;DP=446;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-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:117,0,156:4,0,3,2 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 0/1:48,30:78:99:611,0,1122:21,27,14,16 chr1 157567751 . A G 293.08 PASS AC=2;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 1/1:0,70:70:99:2076,210,0:0,0,38,32 chr1 157647789 . C A 6471.1 PASS AC=1;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 0/1:198,207:405:99:5437,0,4882:107,91,117,90 chr1 157648098 . G A 2491.98 PASS AC=1;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 0/1:76,78:154:99:2161,0,2118:33,43,31,47 chr1 157651017 . T C 346.97 PASS AC=1;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 0/1:12,7:19:99:174,0,395:2,10,2,5 chr1 157652929 . TA T 581.22 PASS AC=1;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 0/1:45,23:68:99:487,0,1095:29,16,17,6 chr1 157718283 . A T 1682.86 PASS AC=1;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 0/1:24,30:54:99:733,0,512:14,10,20,10 chr1 157771880 . C T 2164.43 PASS AC=2;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 1/1:0,126:126:99:3891,376,0:0,0,62,64 chr1 157802877 . T C 1050.89 PASS AC=2;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 1/1:0,73:73:99:2119,219,0:0,0,38,35 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 1/1:0,90:90:99:2820,270,0:0,0,43,47 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 1/1:0,166:166:99:5149,497,0:0,0,66,100 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 1/1:0,84:84:99:2907,252,0:0,0,60,24 chr1 158045655 . A G 317.23 PASS AC=1;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 0/1:5,5:10:99:151,0,153:4,1,3,2 chr1 158045749 . A G 536.5 PASS AC=1;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 0/1:10,15:25:99:379,0,254:6,4,9,6 chr1 158045764 . G A 956.66 PASS AC=1;AF=0.633;AN=2;DP=411;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant8-variant10-variant13-variant16-variant19-variant23-variant25-variant26-variant30-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:14,10:24:99:248,0,355:9,5,6,4 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 0/1:11,6:17:99:169,0,350:8,3,6,0 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 1/1:13:39:0,0,13,0 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 1/1:0,75:75:99:2317,225,0:0,0,48,27 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 1/1:0,68:68:99:1961,203,0:0,0,40,28 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 1/1:0,161:161:99:4836,480,0:0,0,95,66 chr1 158058266 . CTTTT CT,CTTT,CTT,CTTTTT,C 337.49 PASS AC=1,0,0,0,0;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 0/1:57:99:14,20,1,22 chr1 158065762 . C T 129.16 PASS AC=1;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 0/1:13,8:21:99:175,0,371:6,7,3,5 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 1/1:0,45:45:99:1468,135,0:0,0,21,24 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 1/1:0,158:158:99:4766,473,0:0,0,75,83 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 1/1:0,211:211:99:6242,632,0:0,0,111,100 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 1/1:0,217:217:99:7011,651,0:0,0,111,106 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 1/1:0,30:30:90:1029,90,0:0,0,15,15 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 1/1:0,50:50:99:1540,150,0:0,0,27,23 chr1 158150826 . GA G 2436.31 PASS AC=1;AF=0.5;AN=2;DP=467;MQ=60;set=variant9-variant23-variant32 GT:AD:DP:GQ:PL:SB 0/1:88,71:159:99:2280,0,2975:40,48,31,40 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 1/1:0,134:134:99:4384,400,0:0,0,57,77 chr1 158224575 . CTGTGTGTGTGTGTGTGTG C,CTGTGTGTGTG,CTGTGTGTGTGTG,CTGTGTGTG,CTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTG,CTGTG,CTGTGTG 1394.96 PASS AC=0,1,1,0,0,0,0,0;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 2/3:33:99:1,0,10,22 chr1 158297864 . C A 710.19 PASS AC=1;AF=0.5;AN=2;DP=493;MQ=60;set=variant2-variant18-variant23-variant26-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,28:67:99:693,0,1052:16,23,10,18 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 1/1:0,6:6:18:186,18,0:0,0,4,2 chr1 158518050 . A G 322.74 PASS AC=1;AF=0.55;AN=2;DP=200;FractionInformativeReads=1;MQ=60;set=variant2-variant9-variant12-variant19-variant21-variant22-variant23-variant26-variant32-variant36 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:171,0,153:1,4,0,5 chr1 158532614 . G A 1821.5 PASS AC=1;AF=0.5;AN=2;DP=1233;MQ=60;set=variant9-variant19-variant21-variant22-variant23-variant26-variant32-variant36 GT:AD:DP:GQ:PL:SB 0/1:93,75:168:99:1868,0,2347:45,48,36,39 chr1 158565115 . G T 224.2 PASS AC=1;AF=0.682;AN=2;DP=110;MQ=60;set=variant8-variant13-variant14-variant18-variant22-variant23-variant24-variant28-variant34-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:99:198,0,113:3,0,5,0 chr1 158577167 . A T 832.07 PASS AC=1;AF=0.583;AN=2;DP=1254;FractionInformativeReads=1;MQ=60;set=variant8-variant11-variant13-variant14-variant18-variant22-variant23-variant24-variant28-variant34-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:32,41:73:99:967,0,684:18,14,16,25 chr1 158580921 . GCACA GCACACACACACACA,GCA,GCACACACACA,G,GCACACA,GCACACACACACACACA,GCGCACACA,GCACACACA,GCACACACACACA 1968.25 PASS AC=0,0,0,0,1,0,0,0,0;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 0/5:87:99:12,27,16,32 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 1/1:0,35:35:99:1041,105,0:0,0,20,15 chr1 158589105 . T C 1486.45 PASS AC=1;AF=0.5;AN=2;DP=284;FractionInformativeReads=1;MQ=60;set=variant23-variant39 GT:AD:DP:GQ:PL:SB 0/1:59,62:121:99:1515,0,1427:30,29,33,29 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 1/1:0,39:39:99:1257,117,0:0,0,29,10 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 1/1:0,82:82:99:2524,246,0:0,0,39,43 chr1 158637728 . T C 719.28 PASS AC=1;AF=0.5;AN=2;DP=137;FractionInformativeReads=1;MQ=60;set=variant23-variant39 GT:AD:DP:GQ:PL:SB 0/1:40,30:70:99:748,0,1008:20,20,16,14 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 0/1:27:94:8,12,2,5 chr1 158639029 . A G 80.46 PASS AC=1;AF=0.5;AN=2;DP=127;MQ=60;set=variant5-variant10-variant16-variant17-variant21-variant23-variant25-variant27-variant33-variant39 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:99:114,0,162:3,1,3,0 chr1 158639601 . A G 1596.92 PASS AC=2;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 1/1:0,71:71:99:2193,213,0:0,0,29,42 chr1 158644105 . T A 986.87 PASS AC=2;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 1/1:0,49:49:99:1524,146,0:0,0,30,19 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 1/1:0,78:78:99:2169,233,0:0,0,43,35 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 1/1:0,32:32:96:922,96,0:0,0,14,18 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 1/1:0,8:8:24:352,24,0:0,0,7,1 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 1/1:0,124:124:99:3594,371,0:0,0,61,63 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 1/1:0,67:67:99:1999,200,0:0,0,27,40 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 1/1:0,40:40:99:1451,119,0:0,0,32,8 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 1/1:83:99:1,1,53,28 chr1 158656632 . G GA,GAA 1067.42 PASS AC=0,2;AF=0.455,0.489;AN=2;DP=1004;MQ=60;set=Intersection GT:DP:GQ:SB 2/2:14:42:0,0,0,14 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 1/1:0,13:13:39:448,39,0:0,0,0,13 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 1/1:0,6:6:18:256,18,0:0,0,0,6 chr1 158724537 . T C 4904.03 PASS AC=1;AF=0.619;AN=2;DP=7812;MQ=60;set=variant7-variant8-variant9-variant12-variant13-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:182,175:357:99:4269,0,4405:103,79,100,75 chr1 158735281 . G C 166.48 PASS AC=1;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 0/1:1,8:9:19:289,0,19:1,0,7,1 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 1/1:0,150:150:99:4402,447,0:0,0,75,75 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 1/1:0,167:167:99:5000,501,0:0,0,89,78 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 1/1:0,169:169:99:5112,507,0:0,0,84,85 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 1/1:0,91:91:99:2836,273,0:0,0,41,50 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 1/1:0,92:92:99:2945,275,0:0,0,48,44 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 0/1:35,34:69:99:911,0,750:12,23,12,22 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 0/1:14,13:27:99:379,0,390:4,10,3,10 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 0/1:58,38:96:99:857,0,1421:33,25,25,13 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 0/1:74,55:129:99:1264,0,1879:31,43,21,34 chr1 158906555 . A C 320.04 PASS AC=1;AF=0.571;AN=2;DP=421;FractionInformativeReads=1;set=variant2-variant3-variant6-variant7-variant8-variant12-variant13-variant16-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:333,0,397:10,1,9,0 chr1 158909164 . C A 2376.71 PASS AC=1;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 0/1:22,21:43:99:696,0,704:15,7,14,7 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 1/1:0,49:49:99:1585,147,0:0,0,34,15 chr1 158943295 . TCACACA TCACACACACA,TCACACACA,TCA,TCACA,T 527.17 PASS AC=1,1,0,0,0;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 2/1:15:99:0,0,14,1 chr1 158943328 . T C 405.5 PASS AC=1;AF=0.5;AN=2;DP=278;FractionInformativeReads=1;set=variant6-variant10-variant16-variant20-variant23-variant24-variant27 GT:AD:DP:GQ:PL:SB 0/1:22,11:33:99:282,0,677:17,5,9,2 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 0/1:46,50:96:99:1240,0,1131:29,17,31,19 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 1/1:0,14:14:51:725,51,0:0,0,5,9 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 1/1:13:46:0,0,6,7 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 1/1:0,15:15:45:435,45,0:0,0,9,6 chr1 158979950 . A G 240.92 PASS AC=1;AF=0.5;AN=2;DP=402;MQ=60;set=variant9-variant14-variant15-variant23-variant26-variant27-variant28-variant34-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,11:24:99:253,0,298:5,8,4,7 chr1 158985673 . G A 763.98 PASS AC=1;AF=0.5;AN=2;DP=133;MQ=60;set=variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:35,36:71:99:792,0,835:17,18,19,17 chr1 158988463 . G A 227.15 PASS AC=1;AF=0.5;AN=2;DP=40;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:9,9:18:99:255,0,208:2,7,2,7 chr1 158990247 . A G 1303.38 PASS AC=1;AF=0.536;AN=2;DP=821;FractionInformativeReads=1;MQ=60;set=variant10-variant14-variant17-variant20-variant23-variant25-variant33-variant34-variant36-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,34:71:99:830,0,963:13,24,15,19 chr1 159002222 . A G 825.42 PASS AC=1;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 0/1:16,8:24:99:228,0,518:13,3,7,1 chr1 159002301 . T C 2128.8 PASS AC=1;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 0/1:80,46:126:99:922,0,1923:51,29,25,21 chr1 159002377 . C A 2913.52 PASS AC=1;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 0/1:102,76:178:99:1646,0,2261:51,51,40,36 chr1 159002389 . T A 2762.21 PASS AC=1;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 0/1:97,75:172:99:1617,0,2274:47,50,39,36 chr1 159021364 . G A 369.45 PASS AC=1;AF=0.5;AN=2;DP=238;FractionInformativeReads=1;MQ=60;set=variant17-variant20-variant23-variant24-variant25-variant33-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:18,10:28:99:322,0,591:15,3,9,1 chr1 159021445 . A G 1084.04 PASS AC=1;AF=0.545;AN=2;DP=1158;MQ=60;set=variant10-variant17-variant20-variant23-variant24-variant25-variant33-variant36-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,53:119:99:1217,0,1694:38,28,32,21 chr1 159024424 . A T 408.4 PASS AC=1;AF=0.545;AN=2;DP=187;FractionInformativeReads=1;MQ=60;set=variant10-variant17-variant20-variant23-variant24-variant25-variant33-variant36-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:163,0,189:5,0,5,2 chr1 159024668 . A T 3092.45 PASS AC=1;AF=0.545;AN=2;DP=2354;MQ=60;set=variant10-variant17-variant20-variant23-variant24-variant25-variant33-variant36-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,101:169:99:2778,0,1792:43,25,62,39 chr1 159032255 . G T 1502.35 PASS AC=1;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 0/1:28,23:51:99:555,0,786:19,9,15,8 chr1 159046610 . T G 980.58 PASS AC=1;AF=0.5;AN=2;DP=538;MQ=60;set=variant17-variant20-variant23-variant24-variant25-variant33-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:44,22:66:99:453,0,1036:21,23,9,13 chr1 159169641 . T C 1398.35 PASS AC=2;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 1/1:0,100:100:99:3404,300,0:0,0,32,68 chr1 159170316 . A G 199.75 PASS AC=2;AF=0.75;AN=2;DP=87;FractionInformativeReads=1;set=variant4-variant14-variant17-variant23-variant29-variant33 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:742,51,0:0,0,14,3 chr1 159170986 . T G 483.06 PASS AC=2;AF=0.677;AN=2;DP=600;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant31-variant33-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:664,51,0:0,0,12,5 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 1/1:0,188:188:99:5615,563,0:0,0,87,101 chr1 159174885 . T C 2382.21 PASS AC=1;AF=0.556;AN=2;DP=2638;MQ=60;set=variant3-variant9-variant11-variant14-variant15-variant16-variant19-variant20-variant23-variant24-variant26-variant28-variant33-variant36-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:71,64:135:99:1732,0,1755:26,45,21,43 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 0/1:42,39:81:99:1126,0,1345:10,32,11,28 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 1/1:0,34:34:99:1150,102,0:0,0,9,25 chr1 159175193 . A G 1371.11 PASS AC=1;AF=0.611;AN=2;DP=1143;set=variant3-variant14-variant15-variant20-variant23-variant24-variant33-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:55,53:108:99:1192,0,1281:35,20,30,23 chr1 159175354 . G A 5261.06 PASS AC=2;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 1/1:0,262:262:99:7866,784,0:0,0,136,126 chr1 159175527 . G A 872.75 PASS AC=1;AF=0.538;AN=2;DP=2788;MQ=60;set=variant-variant3-variant5-variant7-variant8-variant16-variant17-variant22-variant23-variant27-variant30-variant31-variant41 GT:AD:DP:GQ:PL:SB 0/1:101,95:196:99:2221,0,2495:41,60,39,56 chr1 159259680 . T G 37.69 PASS AC=2;AF=0.696;AN=2;DP=411;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant31-variant33-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:795,54,0:0,0,0,18 chr1 159272060 . T C 799.33 PASS AC=1;AF=0.587;AN=2;DP=1643;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant27-variant30-variant31-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:44,18:62:99:390,0,1110:25,19,13,5 chr1 159320979 . G A 1556.04 PASS AC=2;AF=0.69;AN=2;DP=3403;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant33-variant36-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2332,250,0:0,0,44,41 chr1 159402172 . T C 1824.13 PASS AC=1;AF=0.5;AN=2;DP=159;FS=2.793;FractionInformativeReads=1;MQ=60;MQRankSum=-0.694;QD=11.47;ReadPosRankSum=0.189;SOR=0.713;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:87,72:159:99:1852,0,2179:41,46,38,34 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 1/1:0,101:101:99:3580,304,0:0,0,39,62 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 1/1:0,54:54:99:1710,162,0:0,0,23,31 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 1/1:0,68:68:99:2094,204,0:0,0,43,25 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 1/1:0,349:349:99:10152,1042,0:0,0,166,183 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 1/1:0,208:208:99:6326,621,0:0,0,94,114 chr1 159409857 . A G 4955.12 PASS AC=2;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 1/1:0,142:142:99:4616,426,0:0,0,57,85 chr1 159505297 . C T 4735.51 PASS AC=2;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 1/1:0,166:166:99:5153,497,0:0,0,95,71 chr1 159558258 . A G 1938.82 PASS AC=1;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 0/1:79,85:164:99:2132,0,1924:42,37,41,44 chr1 159683091 . G A 5142.92 PASS AC=1;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 0/1:43,51:94:99:1258,0,1087:21,22,25,26 chr1 159684047 . CCACACACACACA CCACACACACACACA,CCACA,C,CCA,CCACACACA,CCACACACACACACACA,CCACACACACA 220.97 PASS AC=0,1,0,0,0,0,0;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 0/2:12:99:1,3,2,6 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 0/1:32,9:41:94:94,0,598:16,16,5,4 chr1 159684186 . T A 1698.42 PASS AC=1;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 0/1:33,24:57:99:542,0,931:15,18,11,13 chr1 159772291 . G A 1568.75 PASS AC=1;AF=0.5;AN=2;DP=382;FractionInformativeReads=1;MQ=60;set=variant22-variant23-variant38 GT:AD:DP:GQ:PL:SB 0/1:56,60:116:99:1461,0,1371:28,28,28,32 chr1 159778699 . G A 923.54 PASS AC=2;AF=0.638;AN=2;DP=3006;set=variant2-variant4-variant5-variant6-variant7-variant11-variant12-variant13-variant15-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:2900,298,0:0,0,66,34 chr1 159785284 . C G 3280.67 PASS AC=2;AF=0.78;AN=2;DP=10308;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-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,217:217:99:6501,649,0:0,0,127,90 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 1/1:0,107:107:99:3645,328,0:0,0,70,37 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 0/1:19,40:59:99:865,0,338:9,10,21,19 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 1/1:0,106:106:99:3183,318,0:0,0,59,47 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 0/1:90,49:139:99:1160,0,2126:43,47,25,24 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 0/1:66,73:139:99:1722,0,1578:28,38,30,43 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 0/1:14:99:0,7,0,7 chr1 159827365 . CA CAAAA,CAAA,CAA,CAAAAA,C 141.87 PASS AC=0,1,0,0,0;AF=0.214,0.286,0.071,0.071,0.024;AN=2;DP=207;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant15-variant16-variant19-variant22-variant23-variant24-variant27-variant28-variant32-variant34-variant36-variant38-variant42-variant43 GT:DP:GQ:SB 0/2:14:52:2,2,5,5 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 0/1:22,19:41:99:468,0,502:14,8,12,7 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 1/1:0,53:53:99:1957,159,0:0,0,34,19 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 0/1:31,28:59:99:712,0,733:20,11,19,9 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 1/1:0,64:64:99:1944,191,0:0,0,23,41 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 1/1:0,27:27:81:882,81,0:0,0,10,17 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 1/1:0,78:78:99:2671,232,0:0,0,26,52 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 1/1:0,35:35:99:990,104,0:0,0,21,14 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 1/1:0,45:45:99:1385,134,0:0,0,28,17 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 1/1:0,13:13:39:560,39,0:0,0,8,5 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 1/1:0,82:82:99:2441,246,0:0,0,49,33 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 1/1:0,47:47:99:1538,141,0:0,0,13,34 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 0/1:65,58:123:99:1381,0,1625:34,31,33,25 chr1 159862686 . C G 71.99 PASS AC=1;AF=0.5;AN=2;DP=26;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant33 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:99:100,0,204:5,3,3,1 chr1 159890459 . T C 1848.02 PASS AC=2;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 1/1:0,75:75:99:2556,225,0:0,0,23,52 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 1/1:0,27:27:80:876,80,0:0,0,22,5 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 1/1:0,16:16:47:512,47,0:0,0,4,12 chr1 159896885 . C CAG 44.12 PASS AC=1;AF=0.5;AN=2;DP=11;FS=0;FractionInformativeReads=0.727;MQ=60;MQRankSum=1.067;QD=4.01;ReadPosRankSum=1.589;SOR=0.693;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:6,2:8:45:45,0,162:3,3,1,1 chr1 159896887 . C G 98.9 PASS AC=1;AF=0.643;AN=2;DP=88;set=variant3-variant8-variant9-variant10-variant16-variant23-variant38 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:150,0,219:3,3,2,2 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 1/1:0,72:72:99:2274,215,0:0,0,48,24 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 1/1:0,49:49:99:1558,147,0:0,0,19,30 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 2/2:88:99:0,0,38,50 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 1/1:0,101:101:99:3506,303,0:0,0,45,56 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 1/1:0,58:58:99:1960,174,0:0,0,26,32 chr1 159902526 . T C 2242.06 PASS AC=1;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 0/1:13,36:49:99:1124,0,276:4,9,9,27 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 1/1:0,54:54:99:1896,162,0:0,0,32,22 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 1/1:0,8:8:24:316,24,0:0,0,1,7 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 1/1:0,18:18:57:852,57,0:0,0,16,2 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 1/1:0,19:19:57:852,57,0:0,0,17,2 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 1/1:0,41:41:99:1229,122,0:0,0,18,23 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 1/1:0,32:32:96:1033,96,0:0,0,8,24 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 1/1:0,60:60:99:2021,180,0:0,0,24,36 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 1/1:0,101:101:99:3236,303,0:0,0,61,40 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 1/1:0,308:308:99:8678,925,0:0,0,160,148 chr1 159999185 . CTTT CTTTTT,CTTTT,CT,C 157.74 PASS AC=0,1,0,0;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 0/2:17:51:2,4,1,10 chr1 159999567 . CTTT CTT,CTTTTTTTT,C,CTTTT,CTTTTTT,CTTTTTTT,CT,CTTTTT 155.41 PASS AC=0,0,0,0,0,0,0,2;AF=0.16,0.02,0.02,0.16,0.04,0.04,0.04,0.06;AN=2;DP=1524;set=variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-filterInvariant16-variant19-variant23-variant26-variant27-variant28-filterInvariant29-variant31-variant32-variant34-variant36-variant38-variant39-variant40-variant43-variant44 GT:DP:GQ:SB 8/8:17:8:0,2,7,8 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 0/1:39,48:87:99:1292,0,920:20,19,20,28 chr1 160001350 . G A 1891.19 PASS AC=1;AF=0.5;AN=2;DP=157;FS=2.016;FractionInformativeReads=1;MQ=60;MQRankSum=-0.802;QD=12.05;ReadPosRankSum=2.389;SOR=0.911;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:68,89:157:99:1919,0,1648:34,34,49,40 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 1/1:0,14:14:42:525,42,0:0,0,8,6 chr1 160009163 . GACACACACACACAC GACACAC,GACAC,GACACACACACAC,GACACACACAC,GACACACACACACACAC,GACACACACACACACACACAC,GACACACAC,G,GAC 93.39 PASS AC=2,0,0,0,0,0,0,0,0;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 1/1:3:10:0,0,2,1 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 0/1:13,19:32:99:481,0,241:7,6,10,9 chr1 160011512 . G A 2787.79 PASS AC=1;AF=0.5;AN=2;DP=680;FractionInformativeReads=1;MQ=60;set=variant6-variant12-variant23 GT:AD:DP:GQ:PL:SB 0/1:115,117:232:99:2922,0,2885:53,62,58,59 chr1 160040074 . G T 180.17 PASS AC=1;AF=0.583;AN=2;DP=61;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant12-variant23-variant26-variant39 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:37:70,0,37:1,1,0,2 chr1 160054894 . G T 113.02 PASS AC=1;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 0/1:5,5:10:99:114,0,197:1,4,2,3 chr1 160057964 . C T 471.99 PASS AC=1;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 0/1:27,35:62:99:811,0,666:15,12,18,17 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 0/1:25,28:53:99:689,0,662:14,11,14,14 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 0/1:22,19:41:99:430,0,601:13,9,9,10 chr1 160059748 . C A 1320.52 PASS AC=1;AF=0.5;AN=2;DP=252;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant12-variant23-variant26-variant39 GT:AD:DP:GQ:PL:SB 0/1:18,20:38:99:792,0,1271:10,8,10,10 chr1 160059760 . G C 364.55 PASS AC=1;AF=0.5;AN=2;DP=317;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant12-variant23-variant26-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:23,18:41:99:684,0,1340:13,10,10,8 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 0/1:19,11:30:99:240,0,560:9,10,4,7 chr1 160061384 . C T 279.63 PASS AC=1;AF=0.5;AN=2;DP=147;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant12-variant23-variant26-variant39 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:271,0,175:3,3,5,3 chr1 160061414 . G A 300.03 PASS AC=1;AF=0.5;AN=2;DP=152;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant12-variant23-variant26-variant39 GT:AD:DP:GQ:PL:SB 0/1:7,11:18:99:348,0,264:5,2,8,3 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 0/1:25,27:52:99:716,0,606:16,9,14,13 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 0/1:35,32:67:99:815,0,901:24,11,17,15 chr1 160062340 . G A 2303.63 PASS AC=1;AF=0.5;AN=2;DP=808;MQ=60;set=variant3-variant6-variant12-variant23-variant26-variant39 GT:AD:DP:GQ:PL:SB 0/1:55,54:109:99:1333,0,1455:28,27,30,24 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 0/1:70,56:126:99:1290,0,1628:33,37,25,31 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 0/1:66,69:135:99:1763,0,1777:34,32,41,28 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 0/1:20,18:38:99:479,0,491:12,8,13,5 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 1/1:0,55:55:99:1816,164,0:0,0,41,14 chr1 160083544 . G A 718.29 PASS AC=1;AF=0.5;AN=2;DP=205;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant12-variant23-variant26-variant39 GT:AD:DP:GQ:PL:SB 0/1:14,18:32:99:448,0,375:5,9,6,12 chr1 160085604 . C G 691.05 PASS AC=1;AF=0.5;AN=2;DP=72;FS=0.918;FractionInformativeReads=1;MQ=60;MQRankSum=-2.034;QD=9.6;ReadPosRankSum=-2.181;SOR=0.903;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:40,32:72:99:719,0,967:23,17,20,12 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 0/1:3,3:6:99:113,0,119:0,3,1,2 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 1/1:0,36:36:99:1090,108,0:0,0,22,14 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 1/1:0,37:37:99:1642,111,0:0,0,23,14 chr1 160091136 . T C 967.79 PASS AC=1;AF=0.5;AN=2;DP=301;MQ=60;set=variant3-variant6-variant12-variant23-variant26-variant39 GT:AD:DP:GQ:PL:SB 0/1:24,21:45:99:542,0,634:8,16,6,15 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 1/1:0,142:142:99:4230,425,0:0,0,63,79 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 1/1:0,106:106:99:3359,318,0:0,0,45,61 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 1/1:0,8:8:24:311,24,0:0,0,1,7 chr1 160095127 . T A 661.5 PASS AC=2;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 1/1:0,31:31:93:1000,93,0:0,0,9,22 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 1/1:0,77:77:99:2419,230,0:0,0,40,37 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 1/1:0,12:12:36:448,36,0:0,0,8,4 chr1 160105367 . C T 1496.82 PASS AC=1;AF=0.5;AN=2;DP=677;set=variant3-variant6-variant12-variant23-variant26-variant39 GT:AD:DP:GQ:PL:SB 0/1:45,43:88:99:1218,0,1117:23,22,15,28 chr1 160109408 . A AC 4940.47 PASS AC=1;AF=0.556;AN=2;DP=1450;MQ=60;set=variant-variant3-variant6-variant12-variant23-variant26-variant27-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:67,75:142:99:2243,0,1941:31,36,40,35 chr1 160109636 . C G 4335.58 PASS AC=1;AF=0.556;AN=2;DP=1796;MQ=60;set=variant-variant3-variant6-variant12-variant23-variant26-variant27-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:101,75:176:99:2976,0,5081:49,52,37,38 chr1 160109656 . G C 4542.39 PASS AC=1;AF=0.556;AN=2;DP=1911;MQ=60;set=variant-variant3-variant6-variant12-variant23-variant26-variant27-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:99,85:184:99:3008,0,4910:47,52,42,43 chr1 160109788 . C T 1314.23 PASS AC=1;AF=0.556;AN=2;DP=715;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant12-variant23-variant26-variant27-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:30,43:73:99:954,0,780:9,21,17,26 chr1 160109835 . G A 527.35 PASS AC=1;AF=0.556;AN=2;DP=312;MQ=60;set=variant-variant3-variant6-variant12-variant23-variant26-variant27-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:411,0,452:4,12,5,12 chr1 160111798 . G A 1420.14 PASS AC=1;AF=0.556;AN=2;DP=685;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant12-variant23-variant26-variant27-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:39,38:77:99:930,0,938:19,20,19,19 chr1 160112659 . G T 1096.77 PASS AC=1;AF=0.563;AN=2;DP=267;MQ=60;set=variant-variant3-variant6-variant12-variant23-variant26-variant27-variant39 GT:AD:DP:GQ:PL:SB 0/1:19,15:34:99:570,0,1071:12,7,8,7 chr1 160112660 . C T 1096.77 PASS AC=1;AF=0.563;AN=2;DP=269;MQ=60;set=variant-variant3-variant6-variant12-variant23-variant26-variant27-variant39 GT:AD:DP:GQ:PL:SB 0/1:20,15:35:99:570,0,1071:13,7,8,7 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 0/1:49,35:84:99:800,0,1245:23,26,19,16 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 0/1:34,28:62:99:712,0,789:16,18,12,16 chr1 160121899 . A G 1909.29 PASS AC=1;AF=0.563;AN=2;DP=767;MQ=60;set=variant-variant3-variant6-variant12-variant23-variant26-variant27-variant39 GT:AD:DP:GQ:PL:SB 0/1:58,39:97:99:867,0,1266:29,29,22,17 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 0/1:28,20:48:99:521,0,829:18,10,13,7 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 0/1:37,38:75:99:868,0,861:21,16,25,13 chr1 160125802 . C T 1121.2 PASS AC=1;AF=0.5;AN=2;DP=912;MQ=60;set=variant-variant3-variant23-variant26-variant27-variant39 GT:AD:DP:GQ:PL:SB 0/1:55,66:121:99:1758,0,1248:33,22,39,27 chr1 160126020 . G A 455.97 PASS AC=1;AF=0.5;AN=2;DP=236;FractionInformativeReads=1;MQ=60;set=variant-variant23-variant26-variant27 GT:AD:DP:GQ:PL:SB 0/1:27,21:48:99:540,0,743:10,17,6,15 chr1 160128671 . G A 500.5 PASS AC=1;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 0/1:15,9:24:99:282,0,505:11,4,8,1 chr1 160128994 . C T 1046.66 PASS AC=1;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 0/1:22,13:35:99:460,0,823:3,19,1,12 chr1 160134056 . G A 1570.49 PASS AC=1;AF=0.5;AN=2;DP=1016;MQ=60;set=variant-variant23-variant26-variant27-variant30 GT:AD:DP:GQ:PL:SB 0/1:100,108:208:99:2609,0,2277:54,46,54,54 chr1 160134205 . C T 810.02 PASS AC=1;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 0/1:24,32:56:99:913,0,719:3,21,8,24 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 0/1:58,49:107:99:1133,0,1490:38,20,31,18 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 0/1:31,32:63:99:958,0,839:9,22,6,26 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 1/1:0,80:80:99:2286,238,0:0,0,46,34 chr1 160141268 . T C 859.73 PASS AC=1;AF=0.545;AN=2;DP=1082;MQ=60;set=variant2-variant9-variant11-variant12-variant16-variant17-variant23-variant31-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,46:89:99:1138,0,1135:22,21,24,22 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 0/1:42,43:85:99:1149,0,1167:20,22,22,21 chr1 160141636 . C T 1342.01 PASS AC=2;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 1/1:0,68:68:99:1990,204,0:0,0,27,41 chr1 160145688 . C G 449.7 PASS AC=1;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 0/1:38,28:66:99:691,0,1014:22,16,18,10 chr1 160145707 . C T 485.2 PASS AC=1;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 0/1:44,26:70:99:574,0,1067:23,21,16,10 chr1 160147065 . C T 178.44 PASS AC=1;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 0/1:13,8:21:99:253,0,354:9,4,7,1 chr1 160147148 . A G 440.68 PASS AC=1;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 0/1:38,23:61:99:593,0,860:21,17,13,10 chr1 160147502 . T G 690.82 PASS AC=1;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 0/1:53,41:94:99:972,0,1311:26,27,15,26 chr1 160147517 . A G 969.12 PASS AC=1;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 0/1:56,37:93:99:1364,0,2799:26,30,13,24 chr1 160147521 . C T 972.07 PASS AC=1;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 0/1:56,37:93:99:1364,0,2793:26,30,13,24 chr1 160151345 . CAA CA,C 42.41 PASS AC=1,0;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 0/1:7:3:1,0,6,0 chr1 160151450 . T C 2302.92 PASS AC=1;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 0/1:19,33:52:99:958,0,383:12,7,23,10 chr1 160152382 . C T 1015.23 PASS AC=1;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 0/1:48,28:76:99:548,0,1137:23,25,15,13 chr1 160163446 . C T 267.8 PASS AC=1;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 0/1:21,13:34:99:359,0,626:15,6,11,2 chr1 160163509 . C T 955.24 PASS AC=1;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 0/1:37,33:70:99:862,0,995:24,13,22,11 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 1/1:0,10:10:30:362,30,0:0,0,8,2 chr1 160165095 . A C 380.41 PASS AC=1;AF=0.625;AN=2;DP=1133;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant19-filterInvariant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,18:31:99:545,0,295:8,5,14,4 chr1 160165451 . C T 581.77 PASS AC=1;AF=0.661;AN=2;DP=866;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,13:17:96:308,0,96:2,2,6,7 chr1 160168323 . CG C 704.9 PASS AC=1;AF=0.5;AN=2;DP=47;FS=7.475;FractionInformativeReads=1;MQ=60;MQRankSum=-1.866;QD=15;ReadPosRankSum=-0.203;SOR=1.981;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:25,22:47:99:742,0,866:17,8,19,3 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 1/1:0,116:116:99:3474,346,0:0,0,72,44 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 1/1:0,31:31:93:1082,93,0:0,0,24,7 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 1/1:0,89:89:99:2763,266,0:0,0,52,37 chr1 160187173 . A G 1388.28 PASS AC=1;AF=0.886;AN=2;DP=2037;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:20,17:37:99:440,0,590:12,8,10,7 chr1 160254955 . G A 738.43 PASS AC=1;AF=0.5;AN=2;DP=363;MQ=60;set=variant5-variant6-variant12-variant15-variant21-variant23 GT:AD:DP:GQ:PL:SB 0/1:34,36:70:99:962,0,956:11,23,10,26 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 1/1:0,177:177:99:5263,529,0:0,0,88,89 chr1 160281924 . C A 312.34 PASS AC=1;AF=0.5;AN=2;DP=107;FractionInformativeReads=1;MQ=60;set=variant5-variant12-variant15-variant21-variant23 GT:AD:DP:GQ:PL:SB 0/1:3,12:15:84:441,0,84:0,3,1,11 chr1 160318984 . T C 810.14 PASS AC=1;AF=0.5;AN=2;DP=201;FractionInformativeReads=1;MQ=60;set=variant22-variant23-variant25-variant37 GT:AD:DP:GQ:PL:SB 0/1:19,15:34:99:465,0,483:6,13,4,11 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 1/1:0,7:7:21:271,21,0:0,0,6,1 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 0/1:28,26:54:99:646,0,845:17,11,15,11 chr1 160394155 . CT C 1846.39 PASS AC=1;AF=0.5;AN=2;DP=476;MQ=60;set=variant10-variant15-variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:64,51:115:99:1712,0,2235:27,37,16,35 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 0/1:34:99:14,9,8,3 chr1 160395419 . T C 981.08 PASS AC=1;AF=0.5;AN=2;DP=57;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.131;QD=17.21;ReadPosRankSum=-0.602;SOR=0.593;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:17,40:57:99:1009,0,412:9,8,20,20 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 1/1:0,96:96:99:2635,287,0:0,0,44,52 chr1 160397344 . C CATTATT,CATTATTATT,CATTATTATTATT,CATT 254.46 PASS AC=0,0,0,1;AF=0.4,0.133,0.033,0.133;AN=2;DP=798;set=variant-variant2-variant3-variant12-variant13-variant15-variant16-variant21-variant23-variant24-variant29-variant38-variant40-variant42-variant44 GT:DP:GQ:SB 0/4:16:99:4,5,4,3 chr1 160455109 . A T 112.45 PASS AC=2;AF=0.964;AN=2;DP=334;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-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:238,24,0:0,0,5,3 chr1 160456712 . G C 394.55 PASS AC=1;AF=0.583;AN=2;DP=315;FractionInformativeReads=1;MQ=60;set=variant3-variant9-variant11-variant12-variant15-variant21-variant23-variant34-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,8:26:99:245,0,605:10,8,4,4 chr1 160458782 . A G 1743.56 PASS AC=1;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 0/1:48,52:100:99:1265,0,1147:28,20,34,18 chr1 160459909 . C A 1127.8 PASS AC=1;AF=0.583;AN=2;DP=808;MQ=60;set=variant3-variant9-variant11-variant12-variant15-variant21-variant23-variant34-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,30:67:99:631,0,841:20,17,17,13 chr1 160460099 . T A 116.76 PASS AC=1;AF=0.591;AN=2;DP=130;FractionInformativeReads=1;MQ=60;set=variant3-variant9-variant11-variant12-variant15-variant21-variant23-variant34-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,9:12:56:267,0,56:0,3,3,6 chr1 160466356 . A G 172.58 PASS AC=1;AF=0.577;AN=2;DP=201;FractionInformativeReads=1;MQ=60;set=variant3-variant9-variant11-variant12-variant15-variant21-variant23-variant34-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,9:12:72:280,0,72:0,3,2,7 chr1 160493178 . AT A,ATT 100.75 PASS AC=2,0;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 1/1:6:18:0,0,1,5 chr1 160511648 . C T 306.43 PASS AC=2;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 1/1:0,31:31:93:899,93,0:0,0,19,12 chr1 160512224 . G A 9813.49 PASS AC=2;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 1/1:2,271:273:99:8465,770,0:1,1,127,144 chr1 160512616 . G A 14591.2 PASS AC=2;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 1/1:0,345:345:99:10365,1031,0:0,0,167,178 chr1 160512813 . T C 8329.3 PASS AC=2;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 1/1:0,241:241:99:7512,720,0:0,0,96,145 chr1 160513183 . A G 9074.39 PASS AC=2;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 1/1:0,186:186:99:5420,557,0:0,0,100,86 chr1 160513392 . T TTTATTATTA,TTTATTATTATTA,TTTTTTATTATTA 202.83 PASS AC=2,0,0;AF=0.796,0.093,0.019;AN=2;DP=771;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:3:8:0,0,1,2 chr1 160513456 . G A 1958.51 PASS AC=2;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 1/1:0,44:44:99:1480,132,0:0,0,34,10 chr1 160513626 . G A 10862.5 PASS AC=2;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 1/1:0,288:288:99:8311,862,0:0,0,151,137 chr1 160514859 . G A 406.71 PASS AC=2;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 1/1:0,28:28:84:928,84,0:0,0,12,16 chr1 160514955 . T C 660.48 PASS AC=2;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 1/1:0,25:25:75:725,75,0:0,0,10,15 chr1 160515266 . G A 2230.33 PASS AC=2;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 1/1:0,77:77:99:2153,229,0:0,0,36,41 chr1 160516049 . A G 66.22 PASS AC=2;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 1/1:0,13:13:39:463,39,0:0,0,8,5 chr1 160516308 . A G 1147.09 PASS AC=2;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 1/1:0,32:32:96:1090,96,0:0,0,19,13 chr1 160577890 . T G 229.75 PASS AC=2;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 1/1:0,11:11:33:367,33,0:0,0,8,3 chr1 160578541 . C CA 1697.91 PASS AC=2;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 1/1:0,65:65:99:2642,199,0:0,0,32,33 chr1 160580015 . A G 2130.04 PASS AC=2;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 1/1:2,139:141:99:3978,372,0:1,1,60,79 chr1 160582213 . C A 514.62 PASS AC=2;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 1/1:0,37:37:99:1208,111,0:0,0,21,16 chr1 160582248 . C G 541.06 PASS AC=2;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 1/1:0,48:48:99:1556,144,0:0,0,26,22 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 1/1:0,69:69:99:2085,207,0:0,0,43,26 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 1/1:0,39:39:99:1305,117,0:0,0,11,28 chr1 160604172 . T G 62.99 PASS AC=2;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 1/1:0,3:3:9:94,9,0:0,0,2,1 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 1/1:0,20:20:60:669,60,0:0,0,7,13 chr1 160648549 . C T 251.9 PASS AC=2;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 1/1:0,7:7:21:221,21,0:0,0,5,2 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 1/1:0,7:7:21:227,21,0:0,0,7,0 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 1/1:0,49:49:99:1594,147,0:0,0,32,17 chr1 160653299 . G A 1514.93 PASS AC=1;AF=0.579;AN=2;DP=1864;set=variant2-variant5-variant6-variant7-variant8-variant10-variant13-variant15-variant16-variant21-variant23-variant24-variant28-variant29-variant36-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:48,34:82:99:729,0,1412:32,16,22,12 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 0/1:93:99:36,22,22,13 chr1 160653567 . T G 2182.69 PASS AC=1;AF=0.5;AN=2;DP=349;FractionInformativeReads=1;MQ=60;set=variant13-variant23 GT:AD:DP:GQ:PL:SB 0/1:106,86:192:99:2160,0,2632:47,59,44,42 chr1 160681863 . G T 81.49 PASS AC=2;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 1/1:0,6:6:18:189,18,0:0,0,2,4 chr1 160717693 . G GT 185.1 PASS AC=1;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 0/1:6,3:9:96:96,0,160:5,1,3,0 chr1 160717741 . A G 37.69 PASS AC=1;AF=0.595;AN=2;DP=340;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant8-variant16-variant17-variant18-variant20-variant22-variant23-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,13:21:99:365,0,254:7,1,10,3 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 1/1:0,55:55:99:1766,165,0:0,0,28,27 chr1 160722063 . C T 255.6 PASS AC=1;AF=0.5;AN=2;DP=43;FractionInformativeReads=1;MQ=60;set=variant23-variant37 GT:AD:DP:GQ:PL:SB 0/1:16,11:27:99:284,0,461:4,12,3,8 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 1/1:0,26:26:78:986,78,0:0,0,7,19 chr1 160723256 . A G 4997.43 PASS AC=1;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 0/1:60,60:120:99:1567,0,1475:26,34,20,40 chr1 160723448 . T G 662.73 PASS AC=1;AF=0.587;AN=2;DP=955;MQ=60;set=variant5-variant6-variant7-variant8-variant13-variant14-variant16-variant17-variant18-variant20-variant22-variant23-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,16:36:99:448,0,508:11,9,4,12 chr1 160723517 . A G 918.41 PASS AC=1;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 0/1:9,16:25:99:479,0,208:4,5,9,7 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 1/1:0,23:23:69:804,69,0:0,0,17,6 chr1 160766179 . C CT 806.66 PASS AC=2;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 1/1:0,25:25:75:727,75,0:0,0,6,19 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 1/1:1,92:93:99:2809,269,0:1,0,34,58 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 0/1:61,48:109:99:1080,0,1509:36,25,27,21 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 0/1:10,11:21:99:340,0,317:1,9,2,9 chr1 160846284 . T G 310.29 PASS AC=2;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 1/1:0,10:10:30:304,30,0:0,0,7,3 chr1 160849030 . T A 70.45 PASS AC=2;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 1/1:0,18:18:54:637,54,0:0,0,15,3 chr1 160849060 . G A 193.9 PASS AC=2;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 1/1:0,40:40:99:1246,119,0:0,0,29,11 chr1 160849082 . A G 606.39 PASS AC=2;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 1/1:0,52:52:99:1666,156,0:0,0,36,16 chr1 160849367 . G T 306.11 PASS AC=2;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 1/1:0,13:13:39:574,39,0:0,0,1,12 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 0/1:2,2:4:75:75,0,78:0,2,0,2 chr1 160850280 . G A 617.56 PASS AC=2;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 1/1:0,49:49:99:1448,146,0:0,0,30,19 chr1 160850878 . C T 1374.25 PASS AC=1;AF=0.5;AN=2;DP=98;FS=0.815;FractionInformativeReads=1;MQ=60;MQRankSum=-0.754;QD=14.02;ReadPosRankSum=2.923;SOR=0.814;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:47,51:98:99:1402,0,1193:32,15,36,15 chr1 160850936 . T C 436.59 PASS AC=2;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 1/1:0,168:168:99:5061,503,0:0,0,99,69 chr1 160851534 . A G 87.17 PASS AC=2;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 1/1:0,4:4:12:180,12,0:0,0,4,0 chr1 160851564 . C G 37.72 PASS AC=2;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 1/1:0,12:12:36:471,36,0:0,0,11,1 chr1 160851594 . GAAAAAAA G,GAAAAAA 82.47 PASS AC=2,0;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 1/1:22:69:0,0,18,4 chr1 160851619 . A G 294.37 PASS AC=2;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 1/1:0,37:37:99:1482,114,0:0,0,28,9 chr1 160851826 . A T 493.18 PASS AC=2;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 1/1:0,74:74:99:2532,220,0:0,0,30,44 chr1 160851894 . G A 889.94 PASS AC=2;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 1/1:0,82:82:99:2669,244,0:0,0,45,37 chr1 160852022 . C T 807.5 PASS AC=2;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 1/1:0,139:139:99:4014,416,0:0,0,62,77 chr1 160852046 . T C 760.58 PASS AC=2;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 1/1:0,112:112:99:3305,335,0:0,0,48,64 chr1 160854526 . G A 136.21 PASS AC=2;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 1/1:0,21:21:63:696,63,0:0,0,14,7 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 0/1:59,42:101:99:894,0,1328:33,26,17,25 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 1/1:0,99:99:99:3577,303,0:0,0,47,52 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 0/1:39,27:66:99:695,0,1202:21,18,17,10 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 0/1:13,25:38:99:865,0,431:1,12,3,22 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 0/1:39:99:12,3,14,10 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 0/1:16,23:39:99:632,0,405:8,8,14,9 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 0/1:63,41:104:99:976,0,1757:33,30,19,22 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 0/1:51,40:91:99:1008,0,1166:28,23,23,17 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 0/1:82,50:132:99:1812,0,6298:38,44,25,25 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 0/1:80,48:128:99:1812,0,6298:37,43,23,25 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 0/1:80,47:127:99:1775,0,6260:37,43,23,24 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 0/1:58,92:150:99:2386,0,1341:29,29,47,45 chr1 161008572 . C A 1515.26 PASS AC=1;AF=0.5;AN=2;DP=1835;MQ=60;set=variant-variant2-variant9-variant10-variant11-variant20-variant23-variant27-variant29-variant31-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:98,52:150:99:1207,0,2679:48,50,23,29 chr1 161008803 . G T 310.64 PASS AC=1;AF=0.5;AN=2;DP=1010;MQ=60;set=variant-variant2-variant9-variant10-variant11-variant20-variant23-variant27-variant29-variant31-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:44,40:84:99:890,0,1044:16,28,14,26 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 0/1:15,16:31:99:451,0,457:3,12,5,11 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 0/1:35:99:12,10,12,1 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 0/1:26,19:45:99:501,0,688:13,13,8,11 chr1 161012760 . T C 851.26 PASS AC=1;AF=0.5;AN=2;DP=889;MQ=60;set=variant-variant2-variant9-variant10-variant11-variant20-variant23-variant27-variant29-variant31-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:32,41:73:99:1119,0,815:11,21,15,26 chr1 161013312 . T C 581.2 PASS AC=1;AF=0.5;AN=2;DP=508;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant9-variant10-variant11-variant20-variant23-variant27-variant29-variant31-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,22:47:99:589,0,603:10,15,6,16 chr1 161019039 . A G 1618.39 PASS AC=1;AF=0.5;AN=2;DP=143;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.418;QD=11.32;ReadPosRankSum=0.168;SOR=0.669;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:74,69:143:99:1647,0,1698:36,38,34,35 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 0/1:53,32:85:99:837,0,1260:25,28,15,17 chr1 161023279 . TC T 318.08 PASS AC=1;AF=0.5;AN=2;DP=201;set=variant-variant2-variant9-variant10-variant11-variant20-variant23-variant27-variant29-variant31-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:192,0,822:1,5,0,5 chr1 161023281 . TCTCTCTCTCTCTCTC T,TTCTCTCTCTCTCTC 314.97 PASS AC=1,0;AF=0.462,0.038;AN=2;DP=217;set=variant-variant2-variant9-variant10-variant11-variant20-variant23-variant27-variant29-variant31-variant38-variant41-variant42 GT:DP:GQ:SB 0/1:12:99:2,5,0,5 chr1 161026079 . A T 92.47 PASS AC=1;AF=0.5;AN=2;DP=173;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant8-variant9-variant10-variant20-variant23-variant27-variant29-variant31-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:93:208,0,93:3,2,6,0 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 0/1:15,10:25:99:355,0,1019:12,3,8,2 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 0/1:15,8:23:99:247,0,436:3,12,2,6 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 0/1:9,10:19:99:309,0,295:1,8,5,5 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 0/1:3,5:8:99:201,0,136:3,0,5,0 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 0/1:24,18:42:99:438,0,637:16,8,13,5 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 1/1:0,113:113:99:3528,341,0:0,0,59,54 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 0/1:55,72:127:99:1845,0,1301:32,23,39,33 chr1 161102428 . AGCCGCCGCC A,AGCCGCC,AGCCGCCGCCGCC 175.67 PASS AC=0,1,0;AF=0.25,0.125,0.125;AN=2;DP=79;MQ=60;set=variant19-variant23-variant26-variant33 GT:DP:GQ:SB 0/2:15:99:4,7,2,2 chr1 161147292 . G T 1371.23 PASS AC=1;AF=0.5;AN=2;DP=107;FS=3.793;FractionInformativeReads=1;MQ=60;MQRankSum=-0.807;QD=12.82;ReadPosRankSum=1.087;SOR=0.404;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:54,53:107:99:1399,0,1533:16,38,20,33 chr1 161165724 . GACAC GACACAC,G,GACACACAC,GAC 158.12 PASS AC=1,0,0,0;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 0/1:14:15:2,1,4,7 chr1 161184059 . CTGTGTGTGTG CTGTGTGTGTGTG,CTGTGTGTGTGTGTGTG,CTGTGTGTG,CTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTG,C,CTGTGTGTGTGTGTGTGTGTG 260.2 PASS AC=0,0,1,0,0,0,0;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 0/3:39:99:5,22,3,9 chr1 161192845 . CCACACACACACACA CCA,CCACACACA,CCACACACACACA,C,CCACACACACA,CCACA,CCACACACACACACACA,CCACACACACACACACACA,CCACACACACACACACACACACA,CCACACA 256.52 PASS AC=0,1,0,0,0,0,0,0,0,0;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 0/2:39:99:2,10,12,15 chr1 161197244 . C A 285.01 PASS AC=1;AF=0.563;AN=2;DP=334;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant10-variant11-variant12-variant18-variant22-variant23-variant28-variant29-variant34-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,12:17:99:358,0,150:3,2,7,5 chr1 161199579 . G A 1033.68 PASS AC=1;AF=0.5;AN=2;DP=97;FS=1.674;FractionInformativeReads=0.99;MQ=60;MQRankSum=-2.122;QD=10.66;ReadPosRankSum=-1.564;SOR=0.507;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:51,45:96:99:1062,0,1359:20,31,20,25 chr1 161200487 . C A 353.21 PASS AC=1;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 0/1:13,23:36:99:713,0,382:9,4,14,9 chr1 161203227 . G A 89.95 PASS AC=1;AF=0.625;AN=2;DP=107;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant10-variant11-variant18-variant23-variant28-variant29-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:153,0,160:1,4,0,4 chr1 161204906 . G A 251.83 PASS AC=1;AF=0.604;AN=2;DP=603;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant18-variant21-variant22-variant23-variant27-variant28-variant29-variant33-variant34-variant36-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,17:20:35:462,0,35:2,1,8,9 chr1 161253657 . C T 350.51 PASS AC=2;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 1/1:0,34:34:99:1051,102,0:0,0,12,22 chr1 161253684 . AT A 174.31 PASS AC=2;AF=0.533;AN=2;DP=305;MQ=60;set=variant2-variant6-variant10-variant12-variant18-variant19-variant21-variant22-variant23-variant29-variant30-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:555,51,0:0,0,5,12 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 1/1:0,34:34:99:1236,102,0:0,0,19,15 chr1 161276804 . CAAAAAAAAAA C,CAAAAAA,CAAAAAAAA,CAAAAAAA 408.21 PASS AC=0,0,1,0;AF=0.083,0.167,0.083,0.208;AN=2;DP=138;set=variant-variant3-variant11-variant15-variant23-variant24-variant25-variant31-variant32-variant36-variant38-variant40 GT:DP:GQ:SB 0/3:4:17:1,0,3,0 chr1 161479745 . A G 3428.86 PASS AC=1;AF=0.625;AN=2;DP=10311;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:144,136:280:99:3066,0,3502:70,74,70,66 chr1 161487863 . C T 1352.63 PASS AC=2;AF=0.545;AN=2;DP=1614;set=variant-variant7-variant14-variant16-variant21-variant22-variant23-variant34-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,163:163:99:4590,488,0:0,0,86,77 chr1 161488017 . T C 868.13 PASS AC=2;AF=0.545;AN=2;DP=874;set=variant-variant7-variant14-variant16-variant21-variant22-variant23-variant34-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2569,261,0:0,0,33,54 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 1/1:0,77:77:99:3398,232,0:0,0,31,46 chr1 161494322 . A C 838.29 PASS AC=2;AF=0.605;AN=2;DP=1498;set=variant-variant2-variant3-variant6-variant7-variant11-variant13-variant14-variant16-variant21-variant22-variant23-variant28-variant34-variant36-variant37-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:3184,214,0:0,0,30,41 chr1 161495040 . C T 3383.21 PASS AC=2;AF=0.545;AN=2;DP=3427;set=variant-variant7-variant14-variant16-variant21-variant22-variant23-variant34-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,242:242:99:7660,720,0:0,0,131,111 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 1/1:0,457:457:99:13291,1362,0:0,0,204,253 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 1/1:2,143:145:99:4582,400,0:1,1,65,78 chr1 161496134 . C G 407.9 PASS AC=1;AF=0.5;AN=2;DP=843;FractionInformativeReads=1;set=variant-variant7-variant14-variant16-variant21-variant22-variant23-variant34-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:42,29:71:99:812,0,1236:20,22,14,15 chr1 161496178 . G A 491.91 PASS AC=1;AF=0.5;AN=2;DP=983;set=variant-variant7-variant14-variant16-variant21-variant22-variant23-variant34-variant36-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:58,27:85:99:823,0,1684:34,24,16,11 chr1 161496530 . C G 74.13 PASS AC=1;AF=0.54;AN=2;DP=619;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant14-variant15-variant17-variant19-variant20-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant33-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,14:29:99:502,0,451:3,12,1,13 chr1 161514542 . A C 954.66 PASS AC=1;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 0/1:40,33:73:99:872,0,925:24,16,21,12 chr1 161518172 . C T 854.56 PASS AC=1;AF=0.5;AN=2;DP=2580;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant14-variant15-variant17-variant19-variant20-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant33-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,43:87:99:1066,0,1150:28,16,29,14 chr1 161518908 . C T 286.78 PASS AC=1;AF=0.667;AN=2;DP=333;FractionInformativeReads=1;set=variant-variant7-variant16-variant21-variant22-variant23-variant34-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:20,13:33:99:349,0,583:4,16,2,11 chr1 161559327 . A G 126.28 PASS AC=1;AF=0.867;AN=2;DP=2239;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,30:63:99:737,0,767:19,14,21,9 chr1 161561236 . C T 459.58 PASS AC=1;AF=0.727;AN=2;DP=1038;set=variant-variant5-variant6-variant7-variant8-variant9-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant27-variant31-variant32-variant33-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,15:29:99:425,0,422:3,11,1,14 chr1 161561287 . A G 163.06 PASS AC=1;AF=0.987;AN=2;DP=410;FS=0;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-filterInvariant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:34:106,0,34:0,1,1,2 chr1 161565324 . C T 1306.35 PASS AC=1;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 0/1:63,52:115:99:1164,0,1397:36,27,30,22 chr1 161565622 . A G 107 PASS AC=1;AF=0.688;AN=2;DP=55;FractionInformativeReads=1;set=variant7-variant12-variant17-variant21-variant22-variant23-variant34-variant41 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:131,0,101:0,3,0,4 chr1 161577204 . G T 4843.08 PASS AC=2;AF=0.594;AN=2;DP=3297;set=variant-variant2-variant5-variant8-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant34-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:8,154:162:99:5153,287,0:4,4,37,117 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 1/1:0,57:57:99:2281,171,0:0,0,7,50 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 1/1:0,41:41:99:1567,123,0:0,0,17,24 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 1/1:0,76:76:99:2307,227,0:0,0,38,38 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 1/1:0,44:44:99:1972,132,0:0,0,3,41 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 1/1:0,45:45:99:1918,135,0:0,0,3,42 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 1/1:0,21:21:66:987,66,0:0,0,16,5 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 1/1:0,26:26:78:1126,78,0:0,0,19,7 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 1/1:0,69:69:99:3034,208,0:0,0,19,50 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 1/1:0,66:66:99:3034,208,0:0,0,17,49 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 1/1:0,35:35:99:1188,105,0:0,0,6,29 chr1 161596283 . G A 1419.83 PASS AC=2;AF=0.966;AN=2;DP=2667;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1932,147,0:0,0,5,44 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 1/1:0,124:124:99:3571,371,0:0,0,70,54 chr1 161600287 . AT A 784.17 PASS AC=2;AF=0.603;AN=2;DP=1191;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-variant36-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:861,75,0:0,0,8,17 chr1 161600345 . C T 69.04 PASS AC=2;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 1/1:0,7:7:21:210,21,0:0,0,1,6 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 1/1:0,21:21:63:808,63,0:0,0,19,2 chr1 161601118 . G C 884.48 PASS AC=1;AF=0.62;AN=2;DP=1441;FractionInformativeReads=1;set=variant4-variant5-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant30-variant31-variant32-variant34-variant36-variant37-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,25:53:99:800,0,834:6,22,4,21 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 1/1:0,43:43:99:1533,129,0:0,0,8,35 chr1 161641384 . G A 701.08 PASS AC=1;AF=0.5;AN=2;DP=1198;FractionInformativeReads=1;set=variant-variant5-variant8-variant14-variant15-variant17-variant18-variant20-variant23-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,50:98:99:1290,0,1320:22,26,27,23 chr1 161642985 . G A 951.06 PASS AC=1;AF=0.636;AN=2;DP=1554;set=variant-variant2-variant10-variant21-variant22-variant23-variant29-variant32-variant34-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:52,51:103:99:1132,0,1232:23,29,24,27 chr1 161643327 . C G 83.47 PASS AC=1;AF=0.5;AN=2;DP=183;FractionInformativeReads=1;set=filterInvariant8-filterInvariant15-variant20-filterInvariant23 GT:AD:DP:GQ:PL:SB 0/1:32,8:40:99:107,0,744:16,16,5,3 chr1 161643663 . C T 188.78 PASS AC=1;AF=0.833;AN=2;DP=176;FractionInformativeReads=1;set=variant-variant8-variant14-variant15-filterInvariant16-variant18-variant20-variant23-variant33-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,12:28:99:306,0,411:6,10,5,7 chr1 161645259 . T G 227.59 PASS AC=1;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 0/1:11,12:23:99:297,0,324:3,8,4,8 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 1/1:2,305:307:99:8953,869,0:1,1,174,131 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 1/1:2,357:359:99:10849,1027,0:1,1,180,177 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 1/1:0,8:8:24:313,24,0:0,0,1,7 chr1 161680258 . G A 4606.22 PASS AC=2;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 1/1:0,147:147:99:4408,440,0:0,0,79,68 chr1 161680868 . T C 254.9 PASS AC=2;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 1/1:0,14:14:42:443,42,0:0,0,9,5 chr1 161683136 . G A 9395.66 PASS AC=2;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 1/1:0,202:202:99:6246,603,0:0,0,118,84 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 1/1:0,15:15:45:449,45,0:0,0,8,7 chr1 161691433 . C T 610.68 PASS AC=2;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 1/1:0,24:24:72:663,72,0:0,0,11,13 chr1 161695381 . G C 61.77 PASS AC=1;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 0/1:2,2:4:37:75,0,37:1,1,2,0 chr1 161695639 . G T 3137.09 PASS AC=2;AF=0.852;AN=2;DP=5681;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3331,326,0:0,0,64,45 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 1/1:0,174:174:99:5275,521,0:0,0,95,79 chr1 161696782 . G C 1298.61 PASS AC=2;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 1/1:0,62:62:99:1911,186,0:0,0,23,39 chr1 161696998 . C G 488.36 PASS AC=2;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 1/1:0,8:8:24:312,24,0:0,0,5,3 chr1 161698011 . CGGGGG CG,CGGG,C,CGG,CGGGG 7611.69 PASS AC=2,0,0,0,0;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 1/1:125:99:0,0,40,85 chr1 161698019 . G C 7619.45 PASS AC=2;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 1/1:0,125:125:99:5269,376,0:0,0,40,85 chr1 161721351 . A G 959.06 PASS AC=2;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 1/1:0,23:23:69:724,69,0:0,0,16,7 chr1 161721707 . C T 4371.28 PASS AC=2;AF=0.659;AN=2;DP=3155;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant10-variant12-variant13-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant27-variant29-variant34-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:3491,351,0:0,0,65,52 chr1 161722779 . C CAAA,CAA 848.2 PASS AC=2,0;AF=0.795,0.08;AN=2;DP=1237;set=Intersection GT:DP:GQ:SB 1/1:32:99:0,0,26,6 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 1/1:0,67:67:99:2060,201,0:0,0,33,34 chr1 161751741 . A G 4040.09 PASS AC=1;AF=0.568;AN=2;DP=2627;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant10-variant15-variant17-variant20-variant21-variant22-variant23-variant27-variant29-variant32-variant33-variant34-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,63:107:99:1433,0,1157:26,18,32,31 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 1/1:0,3:3:9:94,9,0:0,0,2,1 chr1 161823011 . T A 509.88 PASS AC=1;AF=0.707;AN=2;DP=1051;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,18:26:99:447,0,239:7,1,12,6 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 0/1:39,29:68:99:828,0,1188:15,24,11,18 chr1 161928327 . A G 2859.41 PASS AC=2;AF=0.798;AN=2;DP=4040;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2041,210,0:0,0,33,37 chr1 161928568 . G A 785.78 PASS AC=2;AF=0.798;AN=2;DP=982;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:574,60,0:0,0,9,11 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 1/1:0,13:13:39:398,39,0:0,0,4,9 chr1 161929459 . CAAAAAAA CAA,CA,C,CAAA,CAAAAA,CAAAA 1635.02 PASS AC=1,1,0,0,0,0;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 2/1:59:99:0,3,49,7 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 1/1:0,231:231:99:7216,691,0:0,0,120,111 chr1 161929878 . TAA TA,TAAA,T 6397.56 PASS AC=2,0,0;AF=0.761,0.068,0.011;AN=2;DP=11482;set=Intersection GT:DP:GQ:SB 1/1:182:95:8,11,87,76 chr1 161930476 . C T 1413.35 PASS AC=1;AF=0.78;AN=2;DP=2048;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-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,24:39:99:717,0,374:8,7,11,13 chr1 161930908 . G A 2855.39 PASS AC=1;AF=0.786;AN=2;DP=3677;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,47:89:99:1127,0,953:21,21,23,24 chr1 161931167 . A G 2005.96 PASS AC=1;AF=0.786;AN=2;DP=2607;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,40:64:99:1019,0,668:15,9,27,13 chr1 161931361 . ATT AT,A,ATTT 447.62 PASS AC=1,0,0;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 0/1:106:99:43,42,6,15 chr1 161931538 . G T 2952.11 PASS AC=1;AF=0.786;AN=2;DP=3534;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,30:74:99:738,0,1106:16,28,12,18 chr1 161931562 . G A 454.94 PASS AC=1;AF=0.565;AN=2;DP=2198;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,25:57:99:567,0,788:13,19,12,13 chr1 161931628 . G C 2740.83 PASS AC=1;AF=0.786;AN=2;DP=2241;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,13:29:99:446,0,552:8,8,4,9 chr1 161931802 . A G 12726.2 PASS AC=1;AF=0.786;AN=2;DP=13657;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:170,159:329:99:3576,0,4301:101,69,84,75 chr1 161931915 . AT A 10987.3 PASS AC=1;AF=0.786;AN=2;DP=13811;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:144,148:292:99:3278,0,3136:62,82,71,77 chr1 161932193 . C T 789.47 PASS AC=1;AF=0.565;AN=2;DP=2612;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,45:78:99:1260,0,908:19,14,21,24 chr1 161932324 . A G 6734.58 PASS AC=1;AF=0.786;AN=2;DP=7709;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,83:169:99:1987,0,2009:46,40,39,44 chr1 161933048 . G A 14720.1 PASS AC=1;AF=0.786;AN=2;DP=14218;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:190,162:352:99:3948,0,4605:93,97,68,94 chr1 161933066 . G C 14283.5 PASS AC=1;AF=0.83;AN=2;DP=14017;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:181,139:320:99:3464,0,4382:83,98,62,77 chr1 161933896 . G A 1031.09 PASS AC=1;AF=0.5;AN=2;DP=312;FractionInformativeReads=1;MQ=60;set=variant9-variant13-variant23-variant30 GT:AD:DP:GQ:PL:SB 0/1:53,39:92:99:912,0,1327:21,32,15,24 chr1 161953015 . A G 6026.67 PASS AC=2;AF=0.75;AN=2;DP=5419;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:3,121:124:99:3531,284,0:2,1,79,42 chr1 161954448 . C T 371.58 PASS AC=2;AF=0.757;AN=2;DP=556;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:390,33,0:0,0,8,3 chr1 161967681 . A G 2066.81 PASS AC=2;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 1/1:1,110:111:99:3141,289,0:1,0,59,51 chr1 161976234 . A G 2940.75 PASS AC=2;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 1/1:0,123:123:99:3629,367,0:0,0,70,53 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 1/1:3,110:113:99:2957,273,0:2,1,54,56 chr1 162257033 . C G 1146.83 PASS AC=2;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 1/1:0,30:30:90:921,90,0:0,0,18,12 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 0/1:8,13:21:99:389,0,217:6,2,9,4 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 0/1:23,24:47:99:695,0,646:15,8,16,8 chr1 162313518 . A G 1043.35 PASS AC=1;AF=0.591;AN=2;DP=2262;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant10-variant12-variant13-variant15-variant17-variant18-variant21-variant23-variant25-variant27-variant29-variant33-variant37-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,38:87:99:923,0,1294:33,16,24,14 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 1/1:0,159:159:99:4604,477,0:0,0,89,70 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 0/1:46,38:84:99:872,0,1192:17,29,12,26 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 0/1:1,3:4:30:123,0,30:0,1,2,1 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 0/1:34,30:64:99:716,0,780:16,18,14,16 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 1/1:0,56:56:99:1654,168,0:0,0,23,33 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 0/1:55,51:106:99:1250,0,1456:32,23,28,23 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 1/1:0,14:14:42:465,42,0:0,0,6,8 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 1/2:27:99:0,0,15,12 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 1/1:0,38:38:99:1182,114,0:0,0,16,22 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 1/1:0,32:32:96:1003,96,0:0,0,13,19 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 1/1:0,37:37:99:1274,111,0:0,0,21,16 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 0/1:12,21:33:99:623,0,310:8,4,13,8 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 0/1:37,32:69:99:777,0,864:22,15,19,13 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 0/1:34,29:63:99:831,0,1034:20,14,20,9 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 1/1:0,228:228:99:6901,682,0:0,0,123,105 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 0/1:46,87:133:99:2353,0,1183:14,32,29,58 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 0/1:11,14:25:99:342,0,332:5,6,6,8 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 0/1:14,11:25:99:285,0,373:6,8,5,6 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 1/1:0,89:89:99:2807,267,0:0,0,43,46 chr1 162343774 . A G 1242.02 PASS AC=2;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 1/1:1,122:123:99:3717,330,0:1,0,70,52 chr1 162344102 . C T 898.02 PASS AC=2;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 1/1:0,132:132:99:3817,393,0:0,0,64,68 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 1/1:0,67:67:99:2150,201,0:0,0,24,43 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 1/1:0,80:80:99:2601,239,0:0,0,55,25 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 1/1:0,14:14:42:523,42,0:0,0,0,14 chr1 162346433 . CA C 1249.58 PASS AC=2;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 1/1:0,116:116:99:3545,349,0:0,0,68,48 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 1/1:0,59:59:99:1979,176,0:0,0,38,21 chr1 162352111 . G A 152.64 PASS AC=2;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 1/1:0,31:31:93:981,93,0:0,0,10,21 chr1 162353726 . T C 1182.86 PASS AC=2;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 1/1:0,96:96:99:2923,288,0:0,0,50,46 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 1/1:0,68:68:99:1974,204,0:0,0,38,30 chr1 162355883 . G A 622.89 PASS AC=2;AF=0.621;AN=2;DP=2339;MQ=60;set=variant2-variant3-variant5-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant25-variant26-variant28-variant29-variant30-variant32-variant34-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2086,204,0:0,0,35,33 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 1/1:0,14:14:42:529,42,0:0,0,7,7 chr1 162356392 . G C 574.93 PASS AC=2;AF=0.677;AN=2;DP=1207;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant28-variant29-variant30-variant32-variant34-variant36-filterInvariant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:785,69,0:0,0,13,10 chr1 162356487 . G T 618.09 PASS AC=2;AF=0.677;AN=2;DP=1260;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant28-variant29-variant30-variant32-variant34-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1414,128,0:0,0,25,18 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 1/1:0,308:308:99:8965,920,0:0,0,161,147 chr1 162367071 . C T 706.33 PASS AC=2;AF=0.621;AN=2;DP=3050;MQ=60;set=variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant25-variant26-variant28-variant29-variant30-variant32-variant34-variant36-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,115:115:99:3632,344,0:0,0,55,60 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 0/2:13:99:8,1,3,1 chr1 162496065 . CTT CT,C 2174.09 PASS AC=1,0;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 0/1:163:99:38,26,51,48 chr1 162557578 . C T 96.2 PASS AC=1;AF=0.5;AN=2;DP=107;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant8-variant11-variant13-variant17-variant18-variant20-variant23-variant25-variant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,9:15:99:301,0,230:0,6,1,8 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 0/1:29,21:50:99:471,0,679:13,16,10,11 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 1/1:0,13:13:39:420,39,0:0,0,7,6 chr1 162675040 . T C 230.35 PASS AC=1;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 0/1:2,2:4:37:70,0,37:1,1,0,2 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 1/1:0,88:88:99:2632,264,0:0,0,53,35 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 1/1:0,14:14:42:560,42,0:0,0,2,12 chr1 162736851 . G GAAAA,GAA,GAAA 872.08 PASS AC=1,1,0;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 2/1:12:99:0,0,12,0 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 1/1:0,15:15:45:667,45,0:0,0,15,0 chr1 162737116 . C G 2168.55 PASS AC=1;AF=0.579;AN=2;DP=1350;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant7-variant10-variant13-variant14-variant17-variant20-variant22-variant23-variant24-variant32-variant33-variant34-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,33:65:99:807,0,803:14,18,16,17 chr1 162737338 . G C 238.54 PASS AC=2;AF=1;AN=2;DP=139;FS=0;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,0,3 chr1 162740327 . T C 2330.27 PASS AC=2;AF=0.989;AN=2;DP=6334;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,152:152:99:4878,455,0:0,0,65,87 chr1 162741794 . C T 142.08 PASS AC=1;AF=0.5;AN=2;DP=88;FractionInformativeReads=1;MQ=60;set=variant17-variant22-variant23-variant33-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:231,0,267:7,1,6,2 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 1/1:0,52:52:99:1525,155,0:0,0,21,31 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 1/1:0,48:48:99:1432,144,0:0,0,18,30 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 1/1:0,29:29:87:949,87,0:0,0,8,21 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 1/1:0,28:28:87:1138,87,0:0,0,8,20 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 1/2:16:99:0,0,6,10 chr1 162754049 . G A 904.69 PASS AC=1;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 0/1:15,12:27:99:293,0,469:11,4,9,3 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 1/1:0,21:21:63:857,63,0:0,0,2,19 chr1 162760551 . C T 5695.74 PASS AC=1;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 0/1:76,114:190:99:2565,0,1707:48,28,66,48 chr1 162760554 . T C 5843.37 PASS AC=2;AF=0.989;AN=2;DP=9636;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,199:199:99:7579,598,0:0,0,117,82 chr1 162765475 . G C 1631.55 PASS AC=2;AF=0.989;AN=2;DP=1707;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:564,60,0:0,0,11,9 chr1 162765636 . AAGTCTTAGATGAAG A 767.4 PASS AC=1;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 0/1:6,7:13:99:278,0,797:1,5,2,5 chr1 162766476 . C T 5111.7 PASS AC=1;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 0/1:63,64:127:99:1501,0,1499:30,33,33,31 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 1/1:0,12:12:36:448,36,0:0,0,3,9 chr1 162774236 . A G 85.66 PASS AC=1;AF=0.615;AN=2;DP=333;FractionInformativeReads=1;set=variant2-variant3-variant5-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:194,0,176:2,5,1,6 chr1 162775267 . C T 787.6 PASS AC=1;AF=0.611;AN=2;DP=2252;set=variant-variant2-variant3-variant5-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,29:55:99:733,0,600:14,12,18,11 chr1 162787243 . T A 34.4 PASS AC=1;AF=0.72;AN=2;DP=416;set=filterInvariant-filterInvariant3-variant5-variant6-filterInvariant8-variant9-variant10-filterInvariant11-variant12-filterInvariant15-filterInvariant16-variant18-filterInvariant19-variant23-filterInvariant24-variant25-filterInvariant26-variant27-variant32-filterInvariant33-variant34-variant39-variant40-variant41-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:9,5:14:99:122,0,248:6,3,5,0 chr1 162821080 . ATTTT ATT,ATTT,A,AT 63.07 PASS AC=0,0,1,0;AF=0.286,0.071,0.071,0.071;AN=2;DP=142;MQ=60;set=variant5-variant7-variant18-variant23-filterInvariant25-variant26-filterInvariant28 GT:DP:GQ:SB 0/3:10:80:6,1,2,1 chr1 162821291 . A G 617.16 PASS AC=1;AF=0.706;AN=2;DP=2171;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,24:68:99:583,0,1042:21,23,7,17 chr1 162822616 . A C 616.74 PASS AC=1;AF=0.5;AN=2;DP=788;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant7-variant13-variant23-variant25-variant26-variant29-variant32-variant33-variant34-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,31:64:99:791,0,918:15,18,11,20 chr1 162822771 . A C 1277.87 PASS AC=2;AF=0.919;AN=2;DP=1842;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1456,120,0:0,0,24,16 chr1 162823107 . T A 349.27 PASS AC=1;AF=0.5;AN=2;DP=304;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant7-variant13-variant23-variant25-variant26-variant29-variant32-variant33-variant34-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,6:22:99:201,0,537:2,14,0,6 chr1 162825258 . T C 1317.07 PASS AC=1;AF=0.531;AN=2;DP=1142;MQ=60;set=variant4-variant6-variant7-variant9-variant13-variant23-variant25-variant26-variant29-variant30-variant32-variant33-variant34-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,44:75:99:1120,0,871:19,12,25,19 chr1 163038613 . C A 770.75 PASS AC=1;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 0/1:21,25:46:99:598,0,584:16,5,14,11 chr1 163038684 . C A 1494.78 PASS AC=1;AF=0.6;AN=2;DP=558;MQ=60;set=variant11-variant12-variant23-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:43,46:89:99:1151,0,1010:21,22,30,16 chr1 163038853 . G A 1101.79 PASS AC=1;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 0/1:34,23:57:99:555,0,874:12,22,10,13 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 1/1:0,11:11:33:492,33,0:0,0,5,6 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 1/1:0,21:21:63:729,63,0:0,0,16,5 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 1/1:13:39:0,0,8,5 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 1/1:0,149:149:99:4672,445,0:0,0,89,60 chr1 163045748 . GA G 7255.15 PASS AC=2;AF=0.955;AN=2;DP=12099;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,213:213:99:6078,640,0:0,0,93,120 chr1 163112037 . G A 312.01 PASS AC=1;AF=0.563;AN=2;DP=520;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant11-variant14-variant15-variant17-variant19-variant20-variant23-variant24-variant27-variant30-variant31-variant33-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:12,18:30:99:498,0,267:9,3,12,6 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 0/1:105,86:191:99:1947,0,2728:52,53,40,46 chr1 163113375 . G C 2116.38 PASS AC=2;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 1/1:0,156:156:99:4603,467,0:0,0,72,84 chr1 163113566 . A T 2843.74 PASS AC=2;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 1/1:0,114:114:99:3369,341,0:0,0,58,56 chr1 163114605 . G A 962.62 PASS AC=2;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 1/1:0,74:74:99:2450,222,0:0,0,29,45 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 0/1:288:99:94,95,46,53 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 0/1:34,29:63:99:726,0,946:14,20,9,20 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=2;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 1/1:0,53:53:99:1618,159,0:0,0,19,34 chr1 163142555 . G A 419.76 PASS AC=1;AF=0.66;AN=2;DP=331;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant17-variant18-variant19-variant20-variant22-variant23-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:61:160,0,61:0,2,1,4 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 0/1:7,8:15:99:230,0,233:6,1,6,2 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 0/1:13,19:32:99:503,0,330:8,5,12,7 chr1 163295678 . A C 2203.68 PASS AC=1;AF=0.713;AN=2;DP=1697;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-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,23:37:99:899,0,423:12,2,23,0 chr1 163297896 . G A 191.9 PASS AC=1;AF=0.5;AN=2;DP=196;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant9-variant23-variant27-variant34-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:7,13:20:99:314,0,168:4,3,10,3 chr1 163298768 . T TA,TAA 496.23 PASS AC=1,0;AF=0.516,0.016;AN=2;DP=1703;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant13-variant14-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-filterInvariant36-variant38-variant39-variant40-variant41-variant43 GT:DP:GQ:SB 0/1:28:99:4,11,2,11 chr1 163307944 . T C 288.25 PASS AC=1;AF=0.641;AN=2;DP=780;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant13-variant14-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,16:29:99:454,0,360:3,10,5,11 chr1 163308027 . TAA TA,TAAA,TAAAA,T 185.95 PASS AC=0,1,0,0;AF=0.25,0.125,0.375,0.042;AN=2;DP=88;MQ=60;set=variant2-variant3-variant12-variant15-variant16-variant23-variant26-variant27-variant31-variant32-variant33-variant36 GT:DP:GQ:SB 0/2:5:6:1,1,1,2 chr1 163309219 . A T 2397.06 PASS AC=1;AF=0.641;AN=2;DP=3066;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant13-variant14-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:64,33:97:99:617,0,1603:32,32,15,18 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 1/1:0,38:38:99:1149,113,0:0,0,14,24 chr1 163315350 . G C 224.75 PASS AC=1;AF=0.672;AN=2;DP=251;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant13-variant14-variant15-variant16-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:72:72,0,129:3,1,2,0 chr1 163318934 . A C 85.7 PASS AC=1;AF=0.5;AN=2;DP=131;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant9-variant23-variant27-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:10,9:19:99:301,0,316:2,8,2,7 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 1/1:0,3:3:9:135,9,0:0,0,1,2 chr1 164529120 . G A 2969.63 PASS AC=2;AF=0.682;AN=2;DP=704;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant11-variant16-variant17-variant23-variant24-variant25-variant30-variant34-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1678,146,0:0,0,37,12 chr1 164529284 . GTTTT G 3850.2 PASS AC=1;AF=0.571;AN=2;DP=1139;MQ=60;set=variant3-variant9-variant11-variant17-variant23-variant24-variant34 GT:AD:DP:GQ:PL:SB 0/1:88,45:133:99:1499,0,5171:45,43,21,24 chr1 164529471 . G C 2634.49 PASS AC=1;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 0/1:47,56:103:99:1407,0,1056:20,27,21,35 chr1 164532325 . T C 535.43 PASS AC=1;AF=0.531;AN=2;DP=509;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant10-variant11-variant13-variant17-variant18-variant23-variant31-variant33-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,22:43:99:606,0,638:17,4,16,6 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 1/1:0,40:40:99:1187,120,0:0,0,17,23 chr1 164559536 . A G 1363.49 PASS AC=2;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 1/1:0,27:27:81:916,81,0:0,0,20,7 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 0/1:8,3:11:61:61,0,236:2,6,1,2 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 1/1:0,19:19:57:707,57,0:0,0,4,15 chr1 164816726 . C T 952.06 PASS AC=2;AF=0.591;AN=2;DP=755;FractionInformativeReads=1;MQ=60;set=variant9-variant13-variant17-variant20-variant23-variant25-variant26-variant31-variant33-variant34-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1900,174,0:0,0,27,31 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 1/1:0,20:20:60:817,60,0:0,0,18,2 chr1 165172005 . A C 313.62 PASS AC=1;AF=0.5;AN=2;DP=166;FractionInformativeReads=1;MQ=60;set=variant13-variant16-variant19-variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:18,13:31:99:330,0,493:9,9,6,7 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 1/1:0,116:116:99:3634,348,0:0,0,45,71 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 0/1:21,21:42:99:551,0,571:7,14,6,15 chr1 165180089 . T A 2615.26 PASS AC=2;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 1/1:0,80:80:99:2549,240,0:0,0,32,48 chr1 165218679 . C T 2140.46 PASS AC=1;AF=0.583;AN=2;DP=1401;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant23-variant24-variant29-variant34-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,21:65:99:434,0,1263:29,15,13,8 chr1 165325493 . A C 289.57 PASS AC=1;AF=0.553;AN=2;DP=593;MQ=60;set=variant-variant3-variant7-variant10-variant12-variant17-variant20-variant21-variant22-variant23-variant25-variant30-variant31-variant32-variant33-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,14:28:99:303,0,323:7,7,6,8 chr1 165325827 . A C 850.58 PASS AC=1;AF=0.553;AN=2;DP=1981;MQ=60;set=variant-variant3-variant7-variant10-variant12-variant17-variant20-variant21-variant22-variant23-variant25-variant30-variant31-variant32-variant33-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,57:111:99:1315,0,1138:27,27,30,27 chr1 165370212 . G A 3206.99 PASS AC=1;AF=0.619;AN=2;DP=2581;set=variant-variant2-variant3-variant4-variant10-variant12-variant17-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,39:86:99:865,0,1132:17,30,15,24 chr1 165370400 . G C 1777.84 PASS AC=1;AF=0.595;AN=2;DP=1031;MQ=60;set=variant-variant2-variant3-variant4-variant10-variant12-variant17-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,25:45:99:732,0,664:17,3,17,8 chr1 165370475 . G C 1541.76 PASS AC=1;AF=0.591;AN=2;DP=1876;MQ=60;set=variant-variant2-variant3-variant4-variant10-variant12-variant17-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,41:80:99:1042,0,985:19,20,28,13 chr1 165370757 . G A 251.22 PASS AC=2;AF=0.676;AN=2;DP=381;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant12-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:397,33,0:0,0,2,9 chr1 165375835 . A G 41.43 PASS AC=1;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 0/1:13,15:28:99:469,0,346:9,4,10,5 chr1 165375895 . A C 410.32 PASS AC=1;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 0/1:19,22:41:99:599,0,483:11,8,12,10 chr1 165376043 . T C 1442.4 PASS AC=1;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 0/1:52,41:93:99:955,0,1215:29,23,19,22 chr1 165376229 . C G 1006.96 PASS AC=1;AF=0.6;AN=2;DP=350;MQ=60;set=variant3-variant8-variant9-variant19-variant20-variant23-variant24-variant29-variant30-variant34 GT:AD:DP:GQ:PL:SB 0/1:9,18:27:99:698,0,544:2,7,6,12 chr1 165376233 . G C 1006.96 PASS AC=1;AF=0.6;AN=2;DP=335;MQ=60;set=variant3-variant8-variant9-variant19-variant20-variant23-variant24-variant29-variant30-variant34 GT:AD:DP:GQ:PL:SB 0/1:9,17:26:99:698,0,544:2,7,5,12 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 1/1:0,20:20:60:660,60,0:0,0,15,5 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 1/1:0,150:150:99:4143,446,0:0,0,78,72 chr1 165378729 . TACAC TAC,T 228.31 PASS AC=1,1;AF=0.58,0.42;AN=2;DP=1438;FS=0;set=Intersection GT:DP:GQ:SB 2/1:28:99:0,0,19,9 chr1 165378992 . C T 1155.28 PASS AC=1;AF=0.583;AN=2;DP=753;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant17-variant21-variant22-variant23-variant24-variant25-variant27-variant31-variant32-variant33-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,17:38:99:442,0,536:8,13,5,12 chr1 165386567 . C T 71.22 PASS AC=1;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 0/1:10,5:15:99:168,0,315:2,8,0,5 chr1 165389129 . G A 1027.79 PASS AC=1;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 0/1:65,51:116:99:1144,0,1526:36,29,30,21 chr1 165389285 . C G 3375.62 PASS AC=1;AF=0.625;AN=2;DP=3731;set=variant-variant2-variant3-variant4-variant6-variant7-variant10-variant12-variant13-variant14-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,41:98:99:882,0,1433:30,27,16,25 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 0/1:14,10:24:99:294,0,352:7,7,6,4 chr1 165513439 . A C 162.06 PASS AC=2;AF=0.955;AN=2;DP=887;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:864,60,0:0,0,10,10 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 1/1:23:75:0,0,14,9 chr1 165513463 . C G 151.64 PASS AC=2;AF=0.807;AN=2;DP=947;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:75:1060,75,0:0,0,14,9 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 0/1:4,8:12:99:283,0,143:3,1,7,1 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 1/1:0,136:136:99:4261,408,0:0,0,66,70 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 1/1:0,35:35:99:1141,105,0:0,0,12,23 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 0/1:16,14:30:99:381,0,497:3,13,4,10 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 0/1:53,66:119:99:1574,0,1280:24,29,30,36 chr1 165621129 . CAAAAA CAAAAAAAAAAA,CAAAAAAAAAAAA,CAAAAAAAAAAAAA,C,CAAAA,CAAAAAAAAAA,CAAAAAAAAAAAAAA 319.55 PASS AC=0,0,0,0,0,2,0;AF=0.267,0.317,0.133,0.017,0.033,0.1,0.033;AN=2;DP=240;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant31-variant34-variant36-variant38-variant39-variant40-variant41-variant44 GT:DP:GQ:SB 6/6:1:8:0,0,1,0 chr1 165621322 . TATTATC T 1339.4 PASS AC=1;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 0/1:35,21:56:99:756,0,2737:12,23,6,15 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 1/1:2,47:49:97:1477,97,0:1,1,16,31 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 1/1:0,16:16:48:612,48,0:0,0,13,3 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 1/1:0,34:34:99:1208,102,0:0,0,25,9 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 1/1:0,43:43:99:1273,128,0:0,0,16,27 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 0/1:14:10:1,1,5,7 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 1/1:0,6:6:18:229,18,0:0,0,1,5 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 1/1:0,65:65:99:2038,194,0:0,0,22,43 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 1/1:0,13:13:39:522,39,0:0,0,2,11 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 1/1:0,32:32:95:1047,95,0:0,0,25,7 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 1/1:0,17:17:51:745,51,0:0,0,2,15 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 1/1:0,14:14:42:630,42,0:0,0,2,12 chr1 165649715 . T C 1380.69 PASS AC=1;AF=0.5;AN=2;DP=426;FractionInformativeReads=1;MQ=60;set=variant15-variant16-variant23-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:40,39:79:99:980,0,974:24,16,24,15 chr1 165721223 . T C 663.56 PASS AC=2;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 1/1:0,23:23:69:810,69,0:0,0,18,5 chr1 165721489 . ATT AT,A 67.51 PASS AC=0,1;AF=0.269,0.231;AN=2;DP=488;set=filterInvariant-variant9-filterInvariant15-variant18-filterInvariant21-variant23-variant24-variant25-variant27-variant29-filterInvariant37-variant39-variant42 GT:DP:GQ:SB 0/2:11:28:0,2,2,7 chr1 165727274 . CTCT C 1899.33 PASS AC=1;AF=0.594;AN=2;DP=1474;MQ=60;set=variant6-variant8-variant9-variant11-variant15-variant18-variant19-variant21-variant23-variant24-variant28-variant31-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:33,38:71:99:1471,0,1462:16,17,16,22 chr1 165737704 . C G 3492.72 PASS AC=2;AF=0.977;AN=2;DP=5910;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3374,326,0:0,0,64,45 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 1/1:0,45:45:99:1368,134,0:0,0,15,30 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 1/1:0,15:15:45:461,45,0:0,0,6,9 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 1/1:0,149:149:99:4636,445,0:0,0,79,70 chr1 166029970 . T C 1899.53 PASS AC=1;AF=0.725;AN=2;DP=3599;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-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,41:68:99:931,0,610:10,17,19,22 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 1/1:0,10:10:30:443,30,0:0,0,2,8 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 1/1:0,127:127:99:3915,380,0:0,0,57,70 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 1/1:0,5:5:15:144,15,0:0,0,3,2 chr1 166591043 . T C 1199.5 PASS AC=1;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 0/1:8,9:17:99:333,0,238:8,0,9,0 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 1/1:0,68:68:99:1972,203,0:0,0,29,39 chr1 166816108 . T A 415.3 PASS AC=1;AF=0.594;AN=2;DP=1235;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant9-variant13-variant15-variant20-variant21-variant23-variant24-variant26-variant28-variant33-variant34-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,32:72:99:738,0,1145:15,25,12,20 chr1 166818566 . A G 1906.96 PASS AC=1;AF=0.577;AN=2;DP=2003;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant9-variant21-variant23-variant24-variant26-variant28-variant33-variant34-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,62:123:99:1600,0,1443:32,29,32,30 chr1 166820186 . G A 1177.11 PASS AC=1;AF=0.583;AN=2;DP=1357;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant9-variant21-variant23-variant24-variant26-variant28-variant33-variant34-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,31:89:99:918,0,1605:35,23,20,11 chr1 166820284 . A T 1884.4 PASS AC=1;AF=0.583;AN=2;DP=2219;MQ=60;set=variant2-variant3-variant9-variant21-variant23-variant24-variant26-variant28-variant33-variant34-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:108,65:173:99:1482,0,2798:60,48,41,24 chr1 166822183 . G A 3242.36 PASS AC=1;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 0/1:61,61:122:99:1402,0,1501:33,28,29,32 chr1 166824386 . G GT 1569.25 PASS AC=1;AF=0.5;AN=2;DP=446;MQ=60;set=variant23-variant43 GT:AD:DP:GQ:PL:SB 0/1:108,80:188:99:1607,0,2471:57,51,44,36 chr1 166824667 . C G 766.37 PASS AC=1;AF=0.5;AN=2;DP=116;FractionInformativeReads=1;MQ=60;set=variant8-variant23 GT:AD:DP:GQ:PL:SB 0/1:40,22:62:99:614,0,1303:13,27,12,10 chr1 166825127 . A AC 10713.1 PASS AC=1;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 0/1:102,94:196:99:3179,0,3299:53,49,46,48 chr1 166826198 . A G 8707.75 PASS AC=1;AF=0.5;AN=2;DP=1971;MQ=60;set=variant3-variant23-variant34-variant43 GT:AD:DP:GQ:PL:SB 0/1:226,210:436:99:5172,0,5776:120,106,110,100 chr1 166827602 . A T 360.97 PASS AC=1;AF=0.583;AN=2;DP=424;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant9-variant21-variant23-variant24-variant26-variant28-variant33-variant34-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,24:41:99:528,0,360:7,10,12,12 chr1 166838866 . A AATTTT 342.9 PASS AC=1;AF=0.604;AN=2;DP=663;MQ=60;set=variant2-variant3-variant4-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant33-variant34-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,11:20:99:435,0,572:0,9,4,7 chr1 166839174 . G A 525.04 PASS AC=1;AF=0.542;AN=2;DP=485;MQ=60;set=variant2-variant3-variant9-variant23-variant24-variant26-variant28-variant33-variant34-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,21:28:99:586,0,165:1,6,6,15 chr1 166845750 . T C 203.2 PASS AC=1;AF=0.5;AN=2;DP=86;FractionInformativeReads=1;MQ=60;set=variant3-variant23-variant34-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:189,0,221:1,6,2,5 chr1 166944273 . TCA TCACA,T 67.11 PASS AC=1,0;AF=0.25,0.25;AN=2;DP=15;FS=0;MQ=60;set=variant23-variant30 GT:DP:GQ:SB 0/1:9:99:3,2,3,1 chr1 166958601 . T C 2644.54 PASS AC=1;AF=0.6;AN=2;DP=2508;MQ=60;set=variant2-variant3-variant9-variant13-variant15-variant20-variant23-variant24-variant26-variant28-variant33-variant34-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:85,85:170:99:2144,0,2075:40,45,42,43 chr1 166958710 . T G 1547.04 PASS AC=1;AF=0.567;AN=2;DP=1590;MQ=60;set=variant2-variant3-variant9-variant13-variant15-variant20-variant23-variant24-variant26-variant28-variant33-variant34-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:63,49:112:99:1241,0,1476:27,36,15,34 chr1 166958937 . G T 855.99 PASS AC=1;AF=0.577;AN=2;DP=514;FractionInformativeReads=1;MQ=60;set=variant3-variant9-variant13-variant15-variant20-variant23-variant26-variant28-variant33-variant34-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,24:41:99:700,0,422:10,7,17,7 chr1 166960745 . T G 158.39 PASS AC=1;AF=0.5;AN=2;DP=16;FS=0;FractionInformativeReads=1;MQ=60;set=variant8-variant23 GT:AD:DP:GQ:PL:SB 0/1:5,2:7:69:69,0,153:2,3,0,2 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 0/1:14,11:25:99:373,0,393:10,4,10,1 chr1 166963234 . T C 2953.53 PASS AC=1;AF=0.705;AN=2;DP=1365;MQ=60;set=variant3-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant20-variant21-variant23-variant26-variant31-variant32-variant33-variant34-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,20:45:99:437,0,672:15,10,11,9 chr1 166974420 . T C 1131.02 PASS AC=1;AF=0.625;AN=2;DP=778;MQ=60;set=variant3-variant9-variant23-variant26-variant33-variant34-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,36:73:99:897,0,941:14,23,17,19 chr1 167022262 . T G 1359.32 PASS AC=2;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 1/1:0,24:24:72:737,72,0:0,0,14,10 chr1 167022381 . A G 1312.84 PASS AC=2;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 1/1:0,38:38:99:1171,114,0:0,0,19,19 chr1 167022701 . A G 446.78 PASS AC=2;AF=0.558;AN=2;DP=953;MQ=60;set=variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant15-variant16-variant17-variant18-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,41:42:80:1248,80,0:0,1,20,21 chr1 167022920 . C G 1394.02 PASS AC=2;AF=0.596;AN=2;DP=1856;MQ=60;set=variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant15-variant16-variant17-variant18-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1417,138,0:0,0,22,24 chr1 167023082 . G GC 1133.46 PASS AC=2;AF=0.558;AN=2;DP=1928;MQ=60;set=variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant15-variant16-variant17-variant18-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1959,174,0:0,0,29,29 chr1 167023426 . C T 1246.12 PASS AC=2;AF=0.558;AN=2;DP=2392;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant15-variant16-variant17-variant18-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,62:62:99:1904,185,0:0,0,24,38 chr1 167059336 . C T 411.53 PASS AC=1;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 0/1:6,8:14:99:239,0,229:5,1,7,1 chr1 167059462 . G C 2276.88 PASS AC=1;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 0/1:56,60:116:99:1535,0,1267:34,22,37,23 chr1 167059575 . G T 4486.06 PASS AC=1;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 0/1:83,84:167:99:1999,0,1958:41,42,39,45 chr1 167059760 . A G 1383.36 PASS AC=1;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 0/1:14,22:36:99:628,0,365:6,8,7,15 chr1 167059830 . A G 961.77 PASS AC=1;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 0/1:14,11:25:99:420,0,553:8,6,3,8 chr1 167059833 . A G 961.77 PASS AC=1;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 0/1:13,11:24:99:420,0,553:7,6,3,8 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 0/1:10,6:16:99:181,0,316:8,2,2,4 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 0/1:38,22:60:99:546,0,1003:26,12,16,6 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 0/1:14,11:25:99:370,0,485:12,2,7,4 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 0/1:65,48:113:99:1213,0,1648:34,31,22,26 chr1 167096337 . A G 2808.57 PASS AC=1;AF=0.5;AN=2;DP=514;FractionInformativeReads=1;MQ=60;set=variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:105,117:222:99:2837,0,2590:56,49,62,55 chr1 167097070 . G A 1083.24 PASS AC=1;AF=0.5;AN=2;DP=317;FractionInformativeReads=1;MQ=60;set=variant23-variant34-variant43 GT:AD:DP:GQ:PL:SB 0/1:63,48:111:99:1111,0,1621:27,36,24,24 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 0/1:53,52:105:99:1521,0,1414:27,26,28,24 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 0/1:67,70:137:99:1688,0,1577:29,38,34,36 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 0/1:37,23:60:99:508,0,1075:23,14,11,12 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 0/1:42,35:77:99:1322,0,2271:26,16,23,12 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 0/1:43,35:78:99:1322,0,2271:27,16,24,11 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 0/1:81,98:179:99:1972,0,1585:38,43,44,54 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 1/1:0,321:321:99:9469,962,0:0,0,149,172 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 0/1:4,14:18:83:345,0,83:3,1,8,6 chr1 167307677 . A G 46.75 PASS AC=2;AF=0.9;AN=2;DP=18;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.231;ReadPosRankSum=0.358;set=variant12-variant23-variant25-variant33-variant36 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:127,9,0:0,0,0,3 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 0/1:5,7:12:99:164,0,106:1,4,0,7 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 0/1:17,11:28:99:269,0,522:12,5,8,3 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 0/1:63,44:107:99:1075,0,1598:26,37,14,30 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 0/1:52:99:10,22,4,16 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 0/1:189:99:54,39,55,41 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 0/2:80:99:13,8,27,32 chr1 167389405 . CTT C,CT 1467.81 PASS AC=0,1;AF=0.261,0.568;AN=2;DP=4343;set=Intersection GT:DP:GQ:SB 0/2:42:76:1,8,8,25 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 0/1:21,22:43:99:656,0,473:7,14,3,19 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 1/1:0,14:14:42:568,42,0:0,0,1,13 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 0/1:11,5:16:99:170,0,391:11,0,5,0 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 0/1:37,26:63:99:568,0,1031:16,21,13,13 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 0/1:21,37:58:99:994,0,505:10,11,15,22 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 1/1:0,58:58:99:2295,174,0:0,0,25,33 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 0/1:66,34:100:99:935,0,1954:43,23,24,10 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 1/1:0,117:117:99:3613,350,0:0,0,70,47 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 1/1:0,150:150:99:4876,449,0:0,0,68,82 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 1/1:0,250:250:99:7526,748,0:0,0,138,112 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 1/1:0,160:160:99:5587,478,0:0,0,64,96 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 0/1:130,97:227:99:2372,0,3238:64,66,49,48 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 0/1:28,14:42:99:347,0,829:10,18,3,11 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 0/1:46,70:116:99:1444,0,1039:25,21,37,33 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 0/1:22,35:57:99:1318,0,872:8,14,14,21 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 1/1:0,44:44:99:1367,132,0:0,0,21,23 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 1/1:241:99:1,0,103,137 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 1/1:0,190:190:99:8482,572,0:0,0,83,107 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 1/1:0,112:112:99:5128,343,0:0,0,69,43 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 1/1:0,170:170:99:4963,509,0:0,0,80,90 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 1/1:0,74:74:99:2425,222,0:0,0,26,48 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 1/1:0,18:18:54:693,54,0:0,0,2,16 chr1 167404078 . G A 525.81 PASS AC=2;AF=0.886;AN=2;DP=2347;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1737,176,0:0,0,35,24 chr1 167404179 . G A 340.71 PASS AC=2;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 1/1:1,38:39:75:1058,75,0:1,0,17,21 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 1/1:0,18:18:54:730,54,0:0,0,1,17 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 1/1:0,310:310:99:9537,928,0:0,0,146,164 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 1/1:0,235:235:99:6970,703,0:0,0,113,122 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 1/1:0,56:56:99:1710,167,0:0,0,34,22 chr1 167522453 . C T 515.73 PASS AC=1;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 0/1:6,5:11:99:101,0,157:4,2,3,2 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 0/1:18,10:28:99:191,0,394:9,9,4,6 chr1 167599533 . C T 2101.5 PASS AC=1;AF=0.625;AN=2;DP=514;MQ=60;set=variant2-variant4-variant9-variant17-variant20-variant21-variant23-variant32 GT:AD:DP:GQ:PL:SB 0/1:27,22:49:99:517,0,829:19,8,16,6 chr1 167758901 . A G 875.37 PASS AC=1;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 0/1:27,23:50:99:616,0,604:14,13,10,13 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 0/1:20,16:36:99:409,0,555:12,8,9,7 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 0/1:71,90:161:99:2282,0,1849:23,48,32,58 chr1 167760522 . G C 905.9 PASS AC=1;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 0/1:22,26:48:99:687,0,603:14,8,12,14 chr1 167760731 . T C 3254.42 PASS AC=1;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 0/1:52,36:88:99:785,0,1359:23,29,18,18 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 0/1:49,30:79:99:739,0,1229:19,30,15,15 chr1 167778705 . A C 538.25 PASS AC=1;AF=0.542;AN=2;DP=256;FractionInformativeReads=1;MQ=60;set=variant11-variant13-variant14-variant20-variant23-variant25-variant26-variant29-variant30-variant34-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:267,0,272:7,2,7,0 chr1 167778843 . G A 2506.82 PASS AC=1;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 0/1:88,77:165:99:1821,0,2072:50,38,46,31 chr1 167779865 . A C 497.13 PASS AC=1;AF=0.556;AN=2;DP=444;MQ=60;set=variant14-variant20-variant23-variant25-variant26-variant30-variant34-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,20:35:99:517,0,393:9,6,11,9 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 0/1:29,37:66:99:823,0,682:17,12,20,17 chr1 167803432 . C T 278.27 PASS AC=1;AF=0.643;AN=2;DP=180;FractionInformativeReads=1;MQ=60;set=variant14-variant20-variant23-variant25-variant26-variant30-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:482,0,426:5,11,5,12 chr1 167805439 . G A 449.54 PASS AC=1;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 0/1:31,22:53:99:486,0,758:16,15,12,10 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 1/1:0,49:49:99:1419,146,0:0,0,19,30 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 1/1:0,28:28:84:921,84,0:0,0,7,21 chr1 167806714 . G A 483.43 PASS AC=1;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 0/1:7,14:21:99:388,0,208:1,6,4,10 chr1 167815167 . T C 2898.38 PASS AC=1;AF=0.647;AN=2;DP=1813;FractionInformativeReads=1;set=variant2-variant4-variant5-variant8-variant15-variant16-variant22-variant23-variant24-variant25-variant28-variant31-variant32-variant34-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:57,51:108:99:1235,0,1428:34,23,26,25 chr1 167815610 . C A 810 PASS AC=1;AF=0.675;AN=2;DP=539;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant8-variant10-variant15-variant16-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant34-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:11,13:24:99:391,0,273:3,8,3,10 chr1 167817639 . A G 3206.75 PASS AC=2;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 1/1:0,68:68:99:2011,204,0:0,0,31,37 chr1 167823512 . T C 1678.05 PASS AC=1;AF=0.667;AN=2;DP=1295;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant10-variant11-variant13-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,21:47:99:541,0,705:17,9,15,6 chr1 167825485 . T C 3035.54 PASS AC=1;AF=0.654;AN=2;DP=2791;MQ=60;set=variant-variant2-variant4-variant8-variant10-variant11-variant13-variant15-variant16-variant18-variant21-variant22-variant23-variant24-variant25-variant28-variant31-variant32-variant33-variant34-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:65,48:113:99:1066,0,1656:33,32,26,22 chr1 167825718 . C T 358.76 PASS AC=1;AF=0.647;AN=2;DP=276;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant8-variant11-variant15-variant16-variant18-variant22-variant23-variant24-variant28-variant29-variant31-variant32-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:272,0,263:0,7,2,7 chr1 167839578 . G A 415.95 PASS AC=1;AF=0.571;AN=2;DP=679;MQ=60;set=variant-variant2-variant5-variant16-variant23-variant25-variant29-variant31-variant32-variant33-variant34-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,35:64:99:826,0,738:9,20,13,22 chr1 167844553 . C A 254.84 PASS AC=1;AF=0.55;AN=2;DP=1130;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,23:34:99:649,0,271:3,8,8,15 chr1 167844582 . C G 120.16 PASS AC=1;AF=0.55;AN=2;DP=701;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,18:24:99:488,0,108:2,4,6,12 chr1 167844668 . C CT 37.58 PASS AC=2;AF=0.917;AN=2;DP=231;FS=0;MQ=60;set=variant-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-variant32-variant33-variant34-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:187,15,0:0,0,0,5 chr1 167849318 . A G 587.66 PASS AC=1;AF=0.538;AN=2;DP=1243;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant16-variant17-variant18-variant19-variant21-variant23-variant25-variant29-variant31-variant32-variant33-variant34-variant36-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,13:32:99:364,0,568:14,5,10,3 chr1 167849414 . A G 1225.66 PASS AC=1;AF=0.697;AN=2;DP=3960;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,51:119:99:1269,0,1644:40,28,30,21 chr1 167886502 . A T 1148.22 PASS AC=1;AF=0.529;AN=2;DP=964;MQ=60;set=variant-variant2-variant5-variant6-variant11-variant16-variant17-variant23-variant25-variant29-variant31-variant32-variant33-variant34-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,20:48:99:611,0,913:6,22,7,13 chr1 167889094 . T A 95.22 PASS AC=2;AF=0.567;AN=2;DP=128;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant11-variant16-variant17-variant23-variant25-variant29-variant31-variant32-variant34-variant39-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,3,1 chr1 167893759 . G A 541.08 PASS AC=1;AF=0.583;AN=2;DP=1251;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant18-variant19-variant21-variant23-variant25-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,14:37:99:354,0,565:14,9,7,7 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 1/1:0,75:75:99:2197,225,0:0,0,41,34 chr1 167971979 . G T 49.73 PASS AC=2;AF=0.845;AN=2;DP=161;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant36-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:310,21,0:0,0,1,6 chr1 167971980 . C G 49.73 PASS AC=2;AF=0.845;AN=2;DP=155;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant36-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:310,21,0:0,0,1,6 chr1 167973976 . C T 2553.32 PASS AC=1;AF=0.529;AN=2;DP=4547;set=variant-variant2-variant5-variant6-variant11-variant16-variant17-variant23-variant25-variant29-variant31-variant32-variant33-variant34-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:159,110:269:99:2518,0,3921:80,79,54,56 chr1 167985326 . TG T 794.86 PASS AC=1;AF=0.6;AN=2;DP=1543;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant18-variant19-variant21-variant23-variant25-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,20:41:99:580,0,610:9,12,7,13 chr1 167988653 . A G 1178.39 PASS AC=1;AF=0.543;AN=2;DP=2253;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant10-variant11-variant16-variant17-variant22-variant23-variant25-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:60,39:99:99:952,0,1487:36,24,26,13 chr1 167992344 . T A 549.51 PASS AC=1;AF=0.617;AN=2;DP=1517;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant18-variant19-variant21-variant23-variant25-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,17:39:99:502,0,622:6,16,3,14 chr1 168025538 . T C 61.77 PASS AC=1;AF=0.591;AN=2;DP=1506;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:11,33:44:99:864,0,204:6,5,13,20 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 0/1:10,14:24:99:338,0,234:4,6,4,10 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 0/1:9,6:15:99:174,0,204:3,6,1,5 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 1/1:0,5:5:15:181,15,0:0,0,1,4 chr1 168056724 . A G 1522.46 PASS AC=1;AF=0.613;AN=2;DP=2351;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,27:46:99:732,0,532:15,4,18,9 chr1 168059866 . A G 945.07 PASS AC=1;AF=0.597;AN=2;DP=3349;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,50:93:99:1345,0,1070:22,21,25,25 chr1 168066659 . A G 180.9 PASS AC=1;AF=0.581;AN=2;DP=696;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:187,0,244:3,6,3,5 chr1 168073601 . C A 168.07 PASS AC=1;AF=0.565;AN=2;DP=1055;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,10:31:99:245,0,501:11,10,7,3 chr1 168074145 . G A 592.61 PASS AC=1;AF=0.567;AN=2;DP=2373;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant29-variant31-variant32-variant33-variant34-variant36-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,41:63:99:1082,0,586:9,13,18,23 chr1 168106716 . T C 579.6 PASS AC=1;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 0/1:45,33:78:99:733,0,1076:19,26,15,18 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 0/1:25,20:45:99:460,0,737:16,9,12,8 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 0/1:6,7:13:99:276,0,395:2,4,1,6 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 0/1:56,71:127:99:1679,0,1250:31,25,35,36 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 0/1:30,50:80:99:1172,0,788:12,18,24,26 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 0/1:110,133:243:99:5172,0,5035:59,51,71,62 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 0/1:109,136:245:99:5251,0,4947:59,50,70,66 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 0/1:155,161:316:99:3770,0,3706:79,76,76,85 chr1 168262522 . AGTGTGT AGTGTGTGT,AGTGTGTGTGT,AGTGT,AGTGTTTGTGTGT,AGT,AGTGTGTGTGTGT,A 284.09 PASS AC=0,1,0,0,0,0,0;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 0/2:25:99:5,11,1,8 chr1 168267092 . A G 238.32 PASS AC=1;AF=0.5;AN=2;DP=40;FractionInformativeReads=1;MQ=60;set=variant2-variant10-variant23 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:31:124,0,31:0,1,1,3 chr1 168269338 . A C 308.83 PASS AC=1;AF=0.5;AN=2;DP=83;FractionInformativeReads=1;MQ=60;set=variant2-variant10-variant11-variant13-variant23-variant37 GT:AD:DP:GQ:PL:SB 0/1:6,2:8:66:66,0,243:6,0,2,0 chr1 168274201 . G A 787.99 PASS AC=1;AF=0.744;AN=2;DP=4242;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,37:77:99:876,0,927:22,18,19,18 chr1 168278264 . G A 440.3 PASS AC=2;AF=0.786;AN=2;DP=1575;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1150,93,0:0,0,7,24 chr1 168282261 . T A 2210.78 PASS AC=2;AF=0.64;AN=2;DP=3517;MQ=60;set=variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant28-variant30-variant31-variant32-variant34-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,114:114:99:3753,342,0:0,0,48,66 chr1 168283158 . AAAAG A 810.04 PASS AC=2;AF=0.646;AN=2;DP=841;MQ=60;set=variant3-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant20-variant21-variant23-variant25-variant28-variant30-variant31-variant32-variant34-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1711,120,0:0,0,28,12 chr1 168510122 . T A 119.28 PASS AC=2;AF=0.671;AN=2;DP=1268;set=variant-variant2-variant4-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-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:882,72,0:0,0,23,1 chr1 168511155 . T C 634.81 PASS AC=2;AF=0.679;AN=2;DP=4209;set=variant-variant2-variant4-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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:2647,284,0:0,0,52,43 chr1 168511284 . T C 311.85 PASS AC=2;AF=0.559;AN=2;DP=1815;set=variant-variant2-variant7-variant11-variant12-variant19-variant23-variant24-variant27-variant28-variant29-variant31-variant32-variant36-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1591,147,0:0,0,14,35 chr1 168511321 . C T 311.96 PASS AC=2;AF=0.625;AN=2;DP=480;set=variant7-variant8-filterInvariant12-variant17-variant23-variant24-filterInvariant29-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:209,18,0:0,0,1,5 chr1 168511325 . G C 286.61 PASS AC=2;AF=0.625;AN=2;DP=454;FractionInformativeReads=1;set=variant7-variant8-filterInvariant12-variant17-variant23-filterInvariant24-filterInvariant29-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:12:139,12,0:0,0,0,2 chr1 168513129 . C T 1457.97 PASS AC=2;AF=0.567;AN=2;DP=2648;set=variant-variant2-variant7-variant11-variant12-variant19-variant23-variant24-variant27-variant28-variant29-variant32-variant36-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,180:180:99:5174,539,0:0,0,94,86 chr1 168513243 . G A 519.59 PASS AC=2;AF=0.559;AN=2;DP=1072;set=variant-variant2-variant7-variant11-variant12-variant19-variant23-variant24-variant27-variant28-variant29-variant31-variant32-variant36-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2166,195,0:0,0,23,42 chr1 168545758 . C T 160.19 PASS AC=1;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 0/1:8,3:11:99:102,0,315:8,0,3,0 chr1 168545864 . A G 1349.89 PASS AC=1;AF=0.542;AN=2;DP=1349;set=variant2-variant4-variant8-variant9-variant13-variant14-variant15-variant21-variant23-variant33-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:30,42:72:99:1146,0,758:20,10,29,13 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 1/1:0,109:109:99:3185,326,0:0,0,53,56 chr1 168549234 . T C 165.88 PASS AC=1;AF=0.5;AN=2;DP=510;FractionInformativeReads=1;set=variant2-variant7-variant11-filterInvariant12-variant19-variant23-variant24-variant27-variant28-variant29-variant32-variant36-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,9:34:99:242,0,843:21,4,8,1 chr1 168549254 . A G 450.08 PASS AC=1;AF=0.5;AN=2;DP=862;set=variant-variant2-variant7-variant11-variant12-filterInvariant19-variant23-variant24-variant27-variant28-variant29-variant32-variant36-variant39-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:37,21:58:99:456,0,1072:28,9,14,7 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 0/1:39,139:178:99:3599,0,650:14,25,65,74 chr1 168549440 . T G 150.18 PASS AC=1;AF=0.5;AN=2;DP=374;FractionInformativeReads=1;set=filterInvariant7-variant23 GT:AD:DP:GQ:PL:SB 0/1:132,27:159:99:396,0,3401:61,71,7,20 chr1 168549453 . T C 266.42 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=134;FS=32.353;FractionInformativeReads=1;MQ=58.25;MQRankSum=-6.385;QD=1.99;ReadPosRankSum=-3.27;SOR=4.932;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:118,16:134:99:295,0,4579:48,70,0,16 chr1 168549459 . A G 190.05 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=117;FS=24.094;FractionInformativeReads=1;MQ=58.1;MQRankSum=-5.659;QD=1.62;ReadPosRankSum=-3.638;SOR=4.447;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:104,13:117:99:218,0,4388:41,63,0,13 chr1 168698173 . C T 874.26 PASS AC=1;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 0/1:39,49:88:99:1250,0,961:27,12,31,18 chr1 169076212 . G C 756.34 PASS AC=1;AF=0.619;AN=2;DP=1597;MQ=60;set=variant-variant4-variant6-variant10-variant12-variant16-variant17-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,33:61:99:863,0,579:11,17,13,20 chr1 169079805 . CTTT CTT,C,CT 56.75 PASS AC=0,0,1;AF=0.2,0.05,0.25;AN=2;DP=486;set=variant-variant2-variant3-variant4-variant7-variant14-variant16-variant21-variant23-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant38-variant40-filterInvariant44 GT:DP:GQ:SB 0/3:15:99:5,2,5,3 chr1 169080837 . C T 186.63 PASS AC=2;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 1/1:0,27:27:81:985,81,0:0,0,5,22 chr1 169094100 . T A 717 PASS AC=2;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 1/1:0,61:61:99:1860,181,0:0,0,37,24 chr1 169099061 . G A 259.1 PASS AC=2;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 1/1:0,25:25:75:814,75,0:0,0,18,7 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 0/1:88:99:21,29,16,22 chr1 169102223 . G C 333.34 PASS AC=2;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 1/1:0,29:29:87:1069,87,0:0,0,7,22 chr1 169138027 . A G 872.04 PASS AC=2;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 1/1:1,58:59:99:1736,167,0:1,0,27,31 chr1 169138307 . C A 597.69 PASS AC=2;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 1/1:0,29:29:87:852,87,0:0,0,15,14 chr1 169138318 . T A 519.43 PASS AC=2;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 1/1:0,30:30:90:910,90,0:0,0,17,13 chr1 169138868 . C T 303.58 PASS AC=2;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 1/1:0,21:21:63:776,63,0:0,0,4,17 chr1 169159866 . G T 483.35 PASS AC=2;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 1/1:0,55:55:99:1685,165,0:0,0,34,21 chr1 169160037 . T TAAGAAAACAACCAGAAAAATGGTGAAGTGCTATTTAGACACTTCAG,TAAGAAAACAACCAGAAAAATGGTGAAGTGCTATTTAGACACTTCAGTGTTGGCAATCAAGG,TAAGAAAACAACCAGAAAAATGGTGAAGTGCTA,TAAGAAAACAACCAGAAAAATGGTGAAGTGCTATTTAGACACTTCAGTG 407.01 PASS AC=0,2,0,0;AF=0.083,0.5,0.083,0.167;AN=2;DP=131;set=variant5-variant23-variant34-variant38-variant42-variant44 GT:DP:GQ:SB 2/2:20:56:0,0,6,14 chr1 169200111 . C T 431.64 PASS AC=2;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 1/1:0,35:35:99:1066,105,0:0,0,13,22 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 1/1:0,19:19:57:670,57,0:0,0,4,15 chr1 169256501 . C T 810.09 PASS AC=2;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 1/1:0,41:41:99:1323,122,0:0,0,30,11 chr1 169268077 . T C 160.43 PASS AC=2;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 1/1:0,15:15:45:510,45,0:0,0,3,12 chr1 169272299 . A T 531.79 PASS AC=2;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 1/1:0,53:53:99:1410,158,0:0,0,27,26 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 1/1:0,12:12:36:529,36,0:0,0,4,8 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 1/1:0,12:12:36:529,36,0:0,0,4,8 chr1 169279196 . T TA 636.86 PASS AC=2;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 1/1:0,38:38:99:1204,123,0:0,0,24,14 chr1 169293721 . G A 622.72 PASS AC=2;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 1/1:0,66:66:99:2092,198,0:0,0,25,41 chr1 169337376 . C T 741.2 PASS AC=2;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 1/1:0,74:74:99:2217,221,0:0,0,37,37 chr1 169337638 . C T 200.7 PASS AC=2;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 1/1:1,33:34:64:937,64,0:0,1,12,21 chr1 169337677 . A ATTG 166.66 PASS AC=2;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 1/1:0,15:15:45:645,45,0:0,0,2,13 chr1 169338520 . A AT,ATT,ATTT 80.75 PASS AC=2,0,0;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 1/1:7:21:0,0,6,1 chr1 169345704 . G A 574.21 PASS AC=2;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 1/1:0,38:38:99:1271,114,0:0,0,29,9 chr1 169346528 . AT A 899.93 PASS AC=2;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 1/1:0,75:75:99:2782,226,0:0,0,26,49 chr1 169349608 . C CTA 160.6 PASS AC=2;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 1/1:0,12:12:39:575,39,0:0,0,12,0 chr1 169351596 . A G 302.6 PASS AC=2;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 1/1:1,21:22:25:689,25,0:1,0,7,14 chr1 169356833 . G T 376.01 PASS AC=2;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 1/1:0,37:37:99:1305,111,0:0,0,17,20 chr1 169364014 . C G 261.88 PASS AC=2;AF=0.778;AN=2;DP=372;FractionInformativeReads=1;MQ=60;set=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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:308,24,0:0,0,7,1 chr1 169365116 . GT GTTT,GTT,G 922.5 PASS AC=2,0,0;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 1/1:35:17:3,1,28,3 chr1 169390957 . A T 761.35 PASS AC=2;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 1/1:0,48:48:99:1691,144,0:0,0,25,23 chr1 169391154 . A G 1013.41 PASS AC=2;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 1/1:0,83:83:99:2555,249,0:0,0,42,41 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 1/1:0,53:53:99:1634,158,0:0,0,26,27 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 1/1:0,114:114:99:3702,342,0:0,0,45,69 chr1 169493953 . A C 901.59 PASS AC=2;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 1/1:0,52:52:99:1739,156,0:0,0,38,14 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 1/1:0,16:16:48:619,48,0:0,0,13,3 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 0/1:106,90:196:99:2094,0,2811:51,55,50,40 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 0/1:146,133:279:99:3122,0,3966:74,72,69,64 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 1/1:0,123:123:99:3715,368,0:0,0,72,51 chr1 169519304 . A G 118.4 PASS AC=1;AF=0.5;AN=2;DP=34;FS=0;FractionInformativeReads=1;MQ=60;set=variant14-variant23 GT:AD:DP:GQ:PL:SB 0/1:11,10:21:99:262,0,301:4,7,3,7 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 1/1:0,14:14:42:526,42,0:0,0,12,2 chr1 169528580 . C T 1262.83 PASS AC=2;AF=0.625;AN=2;DP=1500;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant29-variant31-variant36-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,87:88:99:2725,253,0:0,1,32,55 chr1 169528722 . C T 179.11 PASS AC=2;AF=0.625;AN=2;DP=139;MQ=60;set=variant6-variant7-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant29-variant31-variant36-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:317,27,0:0,0,2,7 chr1 169529826 . C A 2224.28 PASS AC=2;AF=0.625;AN=2;DP=2772;MQ=60;set=variant6-variant7-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant29-variant31-variant36-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,164:164:99:5161,492,0:0,0,77,87 chr1 169529973 . C T 663.3 PASS AC=2;AF=0.625;AN=2;DP=921;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant29-variant31-variant36-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1879,165,0:0,0,13,42 chr1 169541513 . C G 1436.03 PASS AC=1;AF=0.625;AN=2;DP=404;FractionInformativeReads=1;MQ=60;set=variant10-variant13-variant19-variant23-variant29-variant31-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,24:53:99:668,0,773:19,10,15,9 chr1 169551549 . T TAA,TA 193.17 PASS AC=0,2;AF=0.357,0.333;AN=2;DP=206;MQ=60;set=variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant18-variant19-variant22-variant23-variant24-variant25-variant29-variant37-variant38-filterInvariant39-variant41-variant42 GT:DP:GQ:SB 2/2:14:45:0,0,11,3 chr1 169562904 . C T 1636.5 PASS AC=2;AF=0.643;AN=2;DP=2203;MQ=60;set=variant6-variant7-variant10-variant12-variant13-variant16-variant18-variant19-variant23-variant29-variant31-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,124:124:99:3825,371,0:0,0,74,50 chr1 169564130 . T G 1075.2 PASS AC=2;AF=0.604;AN=2;DP=768;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant8-variant9-variant10-variant13-variant14-variant16-variant18-variant19-variant22-variant23-variant24-variant25-variant29-variant30-variant31-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:686,60,0:0,0,7,13 chr1 169565346 . C A 1005.34 PASS AC=2;AF=0.615;AN=2;DP=1616;MQ=60;set=variant6-variant10-variant13-variant18-variant19-variant23-variant29-variant31-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3295,332,0:0,0,50,61 chr1 169565393 . C A 961.3 PASS AC=2;AF=0.615;AN=2;DP=1387;MQ=60;set=variant6-variant10-variant13-variant18-variant19-variant23-variant29-variant31-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2542,268,0:0,0,41,49 chr1 169566308 . G A 1641.33 PASS AC=2;AF=0.615;AN=2;DP=1611;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant13-variant18-variant19-variant23-variant29-variant31-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:4652,316,0:0,0,44,59 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 1/1:0,101:101:99:4585,310,0:0,0,45,56 chr1 169566326 . G A 1561.98 PASS AC=2;AF=0.615;AN=2;DP=1471;MQ=60;set=variant6-variant10-variant13-variant18-variant19-variant23-variant29-variant31-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:2787,285,0:0,0,42,53 chr1 169572545 . CTGTGTGTG CTGTGTGTGTG,C,CTGTGTGTGTGTG,CTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTG,CTGTG,CTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTG,CTCTGTGTGTGTGTGTGTGTG 34.15 PASS AC=1,0,0,0,0,0,1,0,0,0;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 1/7:13:99:0,0,1,12 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 0/1:15,18:33:99:589,0,523:14,1,14,4 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 0/1:48,39:87:99:989,0,1143:24,24,18,21 chr1 169673838 . G A 1345.65 PASS AC=1;AF=0.594;AN=2;DP=740;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant13-variant14-variant16-variant18-variant23-variant24-variant27-variant31-variant32-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:21,26:47:99:638,0,532:7,14,9,17 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 0/1:35,43:78:99:993,0,707:17,18,24,19 chr1 169677709 . A G 6258.95 PASS AC=1;AF=0.646;AN=2;DP=4664;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant18-variant20-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant36-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,73:149:99:1695,0,1811:39,37,40,33 chr1 169678024 . T C 1686.59 PASS AC=1;AF=0.68;AN=2;DP=1140;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant18-variant20-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant34-variant36-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,23:44:99:609,0,518:7,14,6,17 chr1 169679472 . G GCT 1364.22 PASS AC=1;AF=0.646;AN=2;DP=825;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant18-variant20-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant36-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,10:24:99:403,0,534:13,1,10,0 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 0/1:73,65:138:99:1466,0,1717:41,32,36,29 chr1 169692132 . T C 3819.36 PASS AC=1;AF=0.673;AN=2;DP=2748;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant18-variant20-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant34-variant36-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,47:75:99:1361,0,772:7,21,17,30 chr1 169692522 . T C 9989.02 PASS AC=1;AF=0.594;AN=2;DP=5222;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant13-variant14-variant16-variant18-variant23-variant24-variant27-variant31-variant32-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:142,165:307:99:4496,0,3741:72,70,82,83 chr1 169695870 . G A 1362.18 PASS AC=1;AF=0.5;AN=2;DP=1040;FractionInformativeReads=1;MQ=60;set=variant8-variant16-variant18-variant23-variant24-variant27-variant31-variant36 GT:AD:DP:GQ:PL:SB 0/1:52,62:114:99:1509,0,1207:30,22,36,26 chr1 169697117 . A T 1589.12 PASS AC=1;AF=0.5;AN=2;DP=1048;MQ=60;set=variant8-variant16-variant18-variant23-variant24-variant27-variant31-variant36 GT:AD:DP:GQ:PL:SB 0/1:78,60:138:99:1456,0,2001:35,43,29,31 chr1 169697444 . C T 1565.23 PASS AC=1;AF=0.588;AN=2;DP=1216;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant13-variant14-variant16-variant18-variant23-variant24-variant27-variant31-variant32-variant36-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:41,29:70:99:746,0,1190:11,30,8,21 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 1/1:0,106:106:99:3304,318,0:0,0,49,57 chr1 169698921 . C T 938.93 PASS AC=1;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 0/1:30,35:65:99:930,0,799:10,20,12,23 chr1 169699466 . CA C 1201.9 PASS AC=1;AF=0.673;AN=2;DP=1290;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant18-variant20-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant34-variant36-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,20:43:99:422,0,528:17,6,16,4 chr1 169699819 . G A 342.57 PASS AC=1;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 0/1:39,21:60:99:618,0,1056:13,26,4,17 chr1 169699839 . GT GTT,G 397.5 PASS AC=1,0;AF=0.45,0.05;AN=2;DP=446;MQ=60;set=variant8-filterInvariant16-variant18-variant23-variant24-variant27-filterInvariant29-variant31-variant36-filterInvariant39 GT:DP:GQ:SB 0/1:28:99:2,10,3,13 chr1 169702705 . G A 3269.84 PASS AC=1;AF=0.64;AN=2;DP=3249;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant12-variant13-variant14-variant16-variant18-variant20-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant36-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,48:116:99:985,0,1696:33,35,23,25 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 0/1:64:99:12,38,4,10 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 1/1:0,11:11:33:422,33,0:0,0,2,9 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 1/1:0,50:50:99:1541,150,0:0,0,25,25 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 1/1:0,70:70:99:2805,211,0:0,0,23,47 chr1 169765052 . C G 679.71 PASS AC=2;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 1/1:0,66:66:99:2048,198,0:0,0,27,39 chr1 169765139 . T C 58.69 PASS AC=1;AF=0.5;AN=2;DP=186;FractionInformativeReads=1;MQ=60;set=variant8-variant18-variant23-variant24-variant27-variant31 GT:AD:DP:GQ:PL:SB 0/1:18,12:30:99:290,0,469:8,10,3,9 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 1/1:0,132:132:99:3958,394,0:0,0,72,60 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 1/1:0,180:180:99:5300,539,0:0,0,91,89 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 1/1:0,29:29:87:869,87,0:0,0,9,20 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 1/1:0,7:7:21:256,21,0:0,0,1,6 chr1 169817023 . T C 124.46 PASS AC=1;AF=0.5;AN=2;DP=27;FS=0;FractionInformativeReads=1;MQ=60;set=variant8-variant18-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:124,0,117:0,3,0,4 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 1/1:0,42:42:99:1381,126,0:0,0,14,28 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 0/1:18:99:2,5,7,4 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 0/1:57,47:104:99:1165,0,1470:34,23,22,25 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 1/1:0,112:112:99:3625,336,0:0,0,61,51 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 0/1:51,41:92:99:1559,0,2766:34,17,25,16 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 1/1:0,23:23:69:829,69,0:0,0,7,16 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 1/1:0,19:19:57:703,57,0:0,0,3,16 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 0/1:21,31:52:99:682,0,559:7,14,10,21 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 1/1:0,10:10:30:380,30,0:0,0,9,1 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 1/1:1,178:179:99:5300,526,0:1,0,100,78 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 1/1:0,50:50:99:1555,150,0:0,0,18,32 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 1/1:0,3:3:9:86,9,0:0,0,0,3 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 1/1:0,13:13:39:445,39,0:0,0,3,10 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 1/1:33:94:1,0,23,9 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 1/1:0,10:10:30:281,30,0:0,0,6,4 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 1/1:0,18:18:54:658,54,0:0,0,15,3 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 0/1:31,29:60:99:1105,0,3008:9,22,12,17 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 0/1:4,4:8:99:116,0,123:4,0,3,1 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 0/1:13,5:18:96:96,0,379:10,3,4,1 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 0/1:93,97:190:99:2433,0,2355:45,48,46,51 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 0/1:72,51:123:99:1170,0,1932:45,27,26,25 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 0/1:13,6:19:99:132,0,285:6,7,2,4 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 0/1:26,33:59:99:741,0,625:15,11,19,14 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 1/1:0,13:13:39:546,39,0:0,0,13,0 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 0/1:62,62:124:99:1487,0,1603:32,30,34,28 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 0/1:66,65:131:99:2534,0,3475:31,35,34,31 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 0/1:66,66:132:99:2561,0,3536:31,35,35,31 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 0/1:2,3:5:43:75,0,43:1,1,0,3 chr1 170501167 . T C 489.75 PASS AC=1;AF=0.6;AN=2;DP=284;MQ=60;set=variant3-variant4-variant10-variant11-variant12-variant13-variant15-variant23-variant31-variant32 GT:AD:DP:GQ:PL:SB 0/1:9,17:26:99:434,0,204:6,3,11,6 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 1/1:0,145:145:99:4283,434,0:0,0,76,69 chr1 170501456 . C T 2940.5 PASS AC=1;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 0/1:60,58:118:99:1369,0,1471:25,35,29,29 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 1/1:0,7:7:21:266,21,0:0,0,6,1 chr1 170508755 . G GT 822.37 PASS AC=1;AF=0.625;AN=2;DP=338;MQ=60;set=variant3-variant4-variant10-variant11-variant12-variant15-variant23-variant32 GT:AD:DP:GQ:PL:SB 0/1:11,13:24:99:324,0,271:1,10,4,9 chr1 170511604 . T C 675.27 PASS AC=1;AF=0.577;AN=2;DP=570;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant15-variant23-variant31-variant32-variant34 GT:AD:DP:GQ:PL:SB 0/1:17,20:37:99:591,0,419:13,4,16,4 chr1 170514229 . G A 1819.13 PASS AC=1;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 0/1:31,22:53:99:532,0,817:21,10,15,7 chr1 170521376 . G A 1121.05 PASS AC=1;AF=0.65;AN=2;DP=2554;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,42:96:99:1030,0,1392:27,27,24,18 chr1 170632384 . A G 337.39 PASS AC=2;AF=0.563;AN=2;DP=672;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant10-variant11-variant18-variant23-variant30-variant31-variant32-variant33-variant36-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1329,132,0:0,0,24,20 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 1/1:0,26:26:78:891,78,0:0,0,10,16 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 1/1:14:42:0,0,2,12 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 1/1:0,49:49:99:1491,147,0:0,0,24,25 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 1/1:0,38:38:99:1690,114,0:0,0,19,19 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 1/1:0,38:38:99:1735,117,0:0,0,18,20 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 1/1:0,40:40:99:1699,120,0:0,0,18,22 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 1/1:0,34:34:99:1440,102,0:0,0,14,20 chr1 170633186 . AT A,ATT 370.38 PASS AC=2,0;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 1/1:31:96:0,0,15,16 chr1 170696240 . G T 320.39 PASS AC=1;AF=0.5;AN=2;DP=73;FractionInformativeReads=1;MQ=60;set=variant7-variant17-variant23-variant24-variant39 GT:AD:DP:GQ:PL:SB 0/1:3,8:11:53:259,0,53:2,1,4,4 chr1 170696474 . A C 2175.62 PASS AC=2;AF=0.886;AN=2;DP=3190;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1689,162,0:0,0,25,29 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 1/1:0,39:39:99:1205,117,0:0,0,16,23 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 2/2:7:22:0,0,2,5 chr1 170705899 . G GT 521.98 PASS AC=1;AF=0.521;AN=2;DP=1187;MQ=60;set=variant-variant2-variant4-variant7-variant8-variant10-variant11-variant13-variant17-variant19-variant20-variant21-variant23-variant24-variant28-variant30-variant31-variant34-variant36-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,22:47:99:585,0,652:13,12,13,9 chr1 170707675 . T C 6477.62 PASS AC=1;AF=0.523;AN=2;DP=8708;MQ=60;set=variant-variant2-variant4-variant7-variant8-variant10-variant11-variant17-variant19-variant20-variant21-variant23-variant24-variant28-variant30-variant31-variant34-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:189,166:355:99:4147,0,4876:91,98,86,80 chr1 170708637 . C G 901.64 PASS AC=2;AF=0.886;AN=2;DP=1132;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,31:31:93:1089,93,0:0,0,7,24 chr1 170708668 . T G 285.2 PASS AC=1;AF=0.5;AN=2;DP=37;FS=0;FractionInformativeReads=1;MQ=60;set=variant7-variant17-variant23 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:309,0,262:1,7,1,7 chr1 170916646 . G T 2281.96 PASS AC=1;AF=0.607;AN=2;DP=2138;MQ=60;set=variant4-variant6-variant9-variant11-variant14-variant17-variant18-variant23-variant27-variant29-variant30-variant36-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:70,43:113:99:1034,0,1830:33,37,19,24 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 0/1:92:99:20,26,20,26 chr1 170927572 . T TC 873.55 PASS AC=1;AF=0.5;AN=2;DP=1375;set=variant4-variant8-variant14-variant16-variant17-variant23-variant27-variant28-variant33-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:53,42:95:99:1140,0,1860:22,31,18,24 chr1 170928671 . T C 1642.67 PASS AC=1;AF=0.5;AN=2;DP=1424;MQ=60;set=variant4-variant8-variant14-variant16-variant17-variant23-variant27-variant28-variant33-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:55,38:93:99:891,0,1306:28,27,20,18 chr1 170928973 . T C 550.24 PASS AC=1;AF=0.5;AN=2;DP=424;FractionInformativeReads=1;MQ=60;set=variant4-variant8-variant14-variant16-variant17-variant23-variant27-variant28-variant33-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:15,20:35:99:554,0,339:6,9,6,14 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 0/1:57,44:101:99:1041,0,1322:32,25,29,15 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 0/1:11:0:1,0,8,2 chr1 171061990 . A G 1110.12 PASS AC=1;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 0/1:26,38:64:99:1048,0,680:10,16,13,25 chr1 171069959 . A G 43.52 PASS AC=1;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 0/1:2,3:5:77:102,0,77:2,0,3,0 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 0/1:20,29:49:99:689,0,474:11,9,17,12 chr1 171076966 . G A 1534.38 PASS AC=1;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 0/1:43,47:90:99:1136,0,1111:18,25,23,24 chr1 171077198 . G A 2219.64 PASS AC=1;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 0/1:68,74:142:99:1843,0,1712:37,31,43,31 chr1 171077372 . C G 1697.4 PASS AC=1;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 0/1:70,70:140:99:1818,0,1849:33,37,31,39 chr1 171112490 . C T 578.15 PASS AC=1;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 0/1:16,21:37:99:601,0,472:5,11,5,16 chr1 171130598 . CACACA C 836.45 PASS AC=1;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 0/1:22,19:41:99:713,0,1465:2,20,2,17 chr1 171227216 . T C 1699.75 PASS AC=1;AF=0.558;AN=2;DP=2836;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant34-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:50,44:94:99:1143,0,1362:25,25,22,22 chr1 171227487 . A G 1159.94 PASS AC=1;AF=0.5;AN=2;DP=1021;MQ=60;set=variant4-variant5-variant7-variant11-variant13-variant14-variant15-variant17-variant23-variant25-variant26-variant34-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:34,41:75:99:1033,0,773:12,22,14,27 chr1 171250044 . C T 1055.92 PASS AC=1;AF=0.5;AN=2;DP=1714;MQ=60;set=variant4-variant5-variant7-variant11-variant13-variant14-variant15-variant17-variant23-variant26-variant34-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:69,38:107:99:782,0,1657:39,30,21,17 chr1 171251509 . G T 394.29 PASS AC=1;AF=0.5;AN=2;DP=516;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant7-variant11-variant13-variant14-variant15-variant17-variant23-variant26-variant34-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:11,15:26:99:327,0,324:3,8,6,9 chr1 171252287 . A G 678.84 PASS AC=1;AF=0.5;AN=2;DP=914;MQ=60;set=variant4-variant5-variant7-variant11-variant14-variant15-variant17-variant23-variant26-variant34-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:30,28:58:99:600,0,640:14,16,14,14 chr1 171254890 . C T 3029.75 PASS AC=1;AF=0.538;AN=2;DP=4009;set=variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant34-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:77,69:146:99:1955,0,2169:53,24,49,20 chr1 171283477 . T TA,TAA 1397.48 PASS AC=1,0;AF=0.462,0.038;AN=2;DP=1847;MQ=60;set=variant4-variant5-variant7-variant11-variant14-variant15-variant17-variant23-variant26-variant34-variant37-variant38-variant39 GT:DP:GQ:SB 0/1:125:99:27,28,31,39 chr1 171292017 . A G 626.28 PASS AC=1;AF=0.5;AN=2;DP=719;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant7-variant11-variant14-variant15-variant17-variant23-variant26-variant34-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:27,23:50:99:590,0,773:19,8,19,4 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 0/1:27,21:48:99:715,0,1084:10,17,7,14 chr1 171301043 . GA GAA,G 899.31 PASS AC=1,0;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 0/1:41:99:8,15,5,13 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 0/1:47,51:98:99:1385,0,1092:20,27,17,34 chr1 171311003 . A C 1248.56 PASS AC=1;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 0/1:58,78:136:99:1768,0,1334:25,33,37,41 chr1 171487092 . TG T 329.5 PASS AC=2;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 1/1:0,18:18:54:674,54,0:0,0,3,15 chr1 171491264 . T A 517.88 PASS AC=2;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 1/1:0,9:9:27:298,27,0:0,0,8,1 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 1/1:0,17:17:51:632,51,0:0,0,13,4 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 1/1:0,24:24:72:851,72,0:0,0,18,6 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 1/1:2,96:98:99:2935,272,0:0,2,47,49 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 1/1:0,93:93:99:3025,278,0:0,0,45,48 chr1 171511442 . A G 769.53 PASS AC=2;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 1/1:1,25:26:42:907,42,0:0,1,5,20 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 1/1:0,38:38:99:1238,114,0:0,0,11,27 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 1/1:0,27:27:81:985,81,0:0,0,7,20 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 1/1:0,192:192:99:5736,574,0:0,0,94,98 chr1 171526910 . G A 3477.82 PASS AC=1;AF=0.553;AN=2;DP=1746;MQ=60;set=variant3-variant6-variant8-variant13-variant15-variant19-variant20-variant23-variant25-variant30-variant31-variant32-variant33-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,37:63:99:839,0,610:9,17,15,22 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 1/1:0,25:25:75:975,75,0:0,0,3,22 chr1 171546833 . C A 1232.98 PASS AC=2;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 1/1:0,24:24:72:906,72,0:0,0,5,19 chr1 171548617 . G A 1511.37 PASS AC=2;AF=0.607;AN=2;DP=4195;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,143:143:99:4231,429,0:0,0,60,83 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 1/1:0,21:21:63:680,63,0:0,0,12,9 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 1/1:0,141:141:99:4076,421,0:0,0,75,66 chr1 171558447 . GTT GT,GTTT,G 139.99 PASS AC=1,0,1;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 3/1:18:77:2,1,13,2 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 1/1:0,55:55:99:1784,165,0:0,0,29,26 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 1/1:0,116:116:99:3695,346,0:0,0,52,64 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 1/1:0,95:95:99:3221,284,0:0,0,46,49 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 1/1:0,77:77:99:2956,231,0:0,0,47,30 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 1/1:0,108:108:99:3129,323,0:0,0,58,50 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 0/1:89,88:177:99:2367,0,2162:50,39,50,38 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 0/1:18,21:39:99:521,0,537:3,15,7,14 chr1 171669823 . G A 2733.21 PASS AC=1;AF=0.529;AN=2;DP=2969;MQ=60;set=variant-variant4-variant7-variant8-variant10-variant13-variant14-variant16-variant17-variant23-variant27-variant28-variant29-variant30-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:99,84:183:99:2197,0,2620:44,55,28,56 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 0/1:151,125:276:99:3153,0,4280:65,86,58,67 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 1/1:0,26:26:78:863,78,0:0,0,19,7 chr1 171675296 . A G 417.63 PASS AC=1;AF=0.529;AN=2;DP=448;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant7-variant8-variant10-variant13-variant14-variant16-variant17-variant23-variant27-variant28-variant29-variant30-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:186,0,197:5,3,3,4 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 1/1:0,5:5:15:200,15,0:0,0,4,1 chr1 171766580 . T G 2382.15 PASS AC=2;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 1/1:0,116:116:99:4025,348,0:0,0,78,38 chr1 171956803 . C T 1468.48 PASS AC=1;AF=0.536;AN=2;DP=1340;MQ=60;set=variant3-variant11-variant12-variant13-variant16-variant18-variant21-variant23-variant26-variant33-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:60,47:107:99:1076,0,1415:34,26,25,22 chr1 172001666 . CTTTTTTTTTT CTTTTTTTT,CTT,CT,CTTT,CTTTTTT,CTTTTTTTTT,C,CTTTTTTTTTTT 62.53 PASS AC=0,1,0,0,0,0,0,0;AF=0.086,0.138,0.138,0.069,0.017,0.017,0.052,0.034;AN=2;DP=1281;set=variant2-variant3-filterInvariant4-variant5-variant9-variant11-variant12-variant13-filterInvariant14-variant15-variant16-filterInvariant17-variant18-variant22-variant23-variant25-filterInvariant26-variant27-variant28-variant29-variant31-variant32-variant34-variant36-variant39-variant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/2:18:99:3,6,2,7 chr1 172011059 . G A 913.76 PASS AC=1;AF=0.63;AN=2;DP=757;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant9-variant10-variant11-variant12-variant16-variant18-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,19:27:99:562,0,186:6,2,13,6 chr1 172038079 . T C 1020.73 PASS AC=1;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 0/1:51,61:112:99:1469,0,1179:19,32,31,30 chr1 172100831 . G A 1237.68 PASS AC=1;AF=0.588;AN=2;DP=1476;FractionInformativeReads=1;MQ=60;set=variant11-variant12-variant13-variant14-variant16-variant18-variant23-variant25-variant27-variant29-variant30-variant31-variant32-variant34-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:36,49:85:99:1242,0,870:23,13,32,17 chr1 172222629 . TCTCTCCTCTCCTCTCCTCTC TCTCTC,TCTCTCCTCTC,T,TCTCTCCTCTCCTCTC 508.02 PASS AC=1,0,0,0;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 0/1:8:19:1,0,5,2 chr1 172279909 . G A 585.61 PASS AC=1;AF=0.6;AN=2;DP=907;MQ=60;set=variant2-variant7-variant9-variant12-variant14-variant15-variant16-variant23-variant24-variant29-variant32-variant33-variant34-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:30,33:63:99:1012,0,914:22,8,24,9 chr1 172280452 . ATG A,ATGTGTGTG,ATGTG,ATGTGTGTGTG,ATGTGTG 68.53 PASS AC=0,1,0,0,0;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 0/2:78:99:13,39,7,19 chr1 172292355 . C CTCA 989.17 PASS AC=1;AF=0.6;AN=2;DP=258;MQ=60;set=variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant23-variant24-variant29-variant32-variant33-variant34-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:117,0,141:2,1,2,1 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 0/1:77,51:128:99:1177,0,1865:37,40,25,26 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 1/1:0,73:73:99:2275,219,0:0,0,28,45 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 0/2:244:99:108,98,21,17 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 1/1:1,405:406:99:12099,1207,0:1,0,192,213 chr1 172381157 . C G 4691.11 PASS AC=1;AF=0.5;AN=2;DP=1372;MQ=60;set=variant9-variant23-variant24-variant27 GT:AD:DP:GQ:PL:SB 0/1:146,142:288:99:3764,0,3556:74,72,67,75 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 0/1:174,188:362:99:4854,0,4658:108,66,104,84 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 1/1:0,15:15:45:535,45,0:0,0,12,3 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 2/3:9:99:0,0,8,1 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 1/1:0,145:145:99:4471,433,0:0,0,82,63 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 1/1:0,19:19:57:764,57,0:0,0,9,10 chr1 172412891 . G A 1364.38 PASS AC=1;AF=0.5;AN=2;DP=129;FS=5.426;FractionInformativeReads=0.992;MQ=60;MQRankSum=-1.287;QD=10.58;ReadPosRankSum=0.91;SOR=0.418;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:65,63:128:99:1393,0,1553:26,39,32,31 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 1/1:0,92:92:99:2935,276,0:0,0,41,51 chr1 172417781 . A G 79.71 PASS AC=1;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 0/1:2,9:11:16:264,0,16:1,1,2,7 chr1 172425529 . C G 1572.2 PASS AC=2;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 1/1:0,157:157:99:4575,469,0:0,0,76,81 chr1 172425640 . G A 828.35 PASS AC=1;AF=0.5;AN=2;DP=396;FractionInformativeReads=1;MQ=60;set=variant12-variant16-variant18-variant23-variant39 GT:AD:DP:GQ:PL:SB 0/1:21,32:53:99:955,0,591:5,16,10,22 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 1/1:0,13:13:39:499,39,0:0,0,12,1 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 1/1:0,20:20:60:670,60,0:0,0,16,4 chr1 172434812 . C T 1084.98 PASS AC=2;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 1/1:0,90:90:99:2640,269,0:0,0,40,50 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 1/1:1,80:81:99:2432,233,0:1,0,46,34 chr1 172501617 . G C 1587.02 PASS AC=1;AF=0.5;AN=2;DP=146;FS=0.617;FractionInformativeReads=1;MQ=60;MQRankSum=-0.476;QD=10.87;ReadPosRankSum=0.48;SOR=0.76;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:81,65:146:99:1615,0,1998:46,35,38,27 chr1 172502479 . T C 1220.4 PASS AC=1;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 0/1:49,50:99:99:1378,0,1399:35,14,29,21 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 0/1:2,3:5:76:120,0,76:2,0,3,0 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 0/1:4,4:8:99:153,0,159:0,4,0,4 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 0/1:67,34:101:99:664,0,1766:31,36,18,16 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 0/1:1,6:7:13:157,0,13:1,0,5,1 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 0/1:37,10:47:91:91,0,774:21,16,4,6 chr1 172633611 . G C 1418.56 PASS AC=1;AF=0.5;AN=2;DP=128;FS=0.651;FractionInformativeReads=1;MQ=60;MQRankSum=-1.569;QD=11.08;ReadPosRankSum=-0.193;SOR=0.768;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:68,60:128:99:1447,0,1640:33,35,28,32 chr1 172634589 . TG T 529.37 PASS AC=1;AF=0.5;AN=2;DP=479;MQ=60;set=variant8-variant10-variant15-variant23-variant30-variant31-variant34-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:19,12:31:99:373,0,674:13,6,8,4 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 1/1:0,97:97:99:2964,291,0:0,0,52,45 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 0/2:17:99:5,4,6,2 chr1 173153665 . CT C 24120.7 PASS AC=1;AF=0.536;AN=2;DP=6497;MQ=60;set=variant3-variant5-variant8-variant11-variant14-variant18-variant19-variant20-variant23-variant25-variant27-variant29-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:226,173:399:99:5302,0,7194:116,110,81,92 chr1 173153841 . TAC T 1516.21 PASS AC=1;AF=0.538;AN=2;DP=550;MQ=60;set=variant3-variant5-variant8-variant11-variant14-variant18-variant19-variant20-variant23-variant25-variant27-variant29-variant41 GT:AD:DP:GQ:PL:SB 0/1:18,10:28:99:270,0,555:4,14,4,6 chr1 173154304 . G T 5150.08 PASS AC=1;AF=0.591;AN=2;DP=2260;MQ=60;set=variant3-variant5-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant23-variant25-variant27-variant28-variant29-variant30-variant36-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:47,54:101:99:1547,0,1423:22,25,28,26 chr1 173154354 . A C 6694.05 PASS AC=1;AF=0.533;AN=2;DP=2067;MQ=60;set=variant3-variant5-variant8-variant11-variant14-variant15-variant18-variant19-variant20-variant23-variant25-variant27-variant29-variant30-variant41 GT:AD:DP:GQ:PL:SB 0/1:64,75:139:99:1895,0,1669:30,34,45,30 chr1 173154539 . T C 9801.02 PASS AC=1;AF=0.533;AN=2;DP=3759;MQ=60;set=variant3-variant5-variant8-variant11-variant14-variant15-variant18-variant19-variant20-variant23-variant25-variant27-variant29-variant30-variant41 GT:AD:DP:GQ:PL:SB 0/1:123,108:231:99:2869,0,3265:67,56,50,58 chr1 173155022 . G GA 2701.18 PASS AC=1;AF=0.533;AN=2;DP=1089;MQ=60;set=variant3-variant5-variant8-variant11-variant14-variant15-variant18-variant19-variant20-variant23-variant25-variant27-variant29-variant30-variant41 GT:AD:DP:GQ:PL:SB 0/1:39,23:62:99:510,0,1006:15,24,11,12 chr1 173457017 . C T 1362.57 PASS AC=1;AF=0.526;AN=2;DP=1965;set=variant2-variant5-variant6-variant8-variant11-variant14-variant16-variant17-variant20-variant21-variant23-variant26-variant27-variant29-variant33-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,43:96:99:1192,0,1459:36,17,27,16 chr1 173457599 . A G 3232.88 PASS AC=1;AF=0.525;AN=2;DP=4760;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant11-variant14-variant16-variant17-variant20-variant21-variant23-variant26-variant27-variant29-variant33-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:121,101:222:99:2479,0,2969:59,62,44,57 chr1 173470105 . A G 1048.32 PASS AC=1;AF=0.5;AN=2;DP=1479;MQ=60;set=variant5-variant6-variant8-variant11-variant14-variant16-variant17-variant20-variant21-variant23-variant26-variant27-variant29-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,28:61:99:845,0,948:17,16,10,18 chr1 173493312 . A G 244.53 PASS AC=1;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 0/1:2,3:5:76:113,0,76:0,2,1,2 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 1/1:0,15:15:45:538,45,0:0,0,13,2 chr1 173606179 . A T 166.16 PASS AC=1;AF=0.5;AN=2;DP=501;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant22-variant23-variant26-variant27-variant29-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,13:21:99:509,0,176:3,5,0,13 chr1 173606207 . T A 197.13 PASS AC=1;AF=0.595;AN=2;DP=294;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant8-variant10-variant11-variant14-variant16-variant17-variant22-variant23-variant26-variant27-variant29-variant33-variant34-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:99:273,0,106:0,3,0,7 chr1 173683954 . C T 47.78 PASS AC=2;AF=0.804;AN=2;DP=164;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant22-variant23-variant26-variant29-variant32-variant33-variant34-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:316,24,0:0,0,6,2 chr1 173702764 . C T 506.38 PASS AC=2;AF=0.625;AN=2;DP=688;MQ=60;set=variant2-variant3-variant6-variant8-variant11-variant14-variant16-variant17-variant22-variant23-variant26-variant27-variant29-variant32-variant34-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1181,105,0:0,0,26,9 chr1 173724942 . A G 310.19 PASS AC=2;AF=0.632;AN=2;DP=297;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant8-variant11-variant14-variant16-variant17-variant22-variant23-variant27-variant29-variant32-variant34-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:660,45,0:0,0,15,0 chr1 173797451 . T C 1242.78 PASS AC=2;AF=0.611;AN=2;DP=2411;MQ=60;set=variant2-variant6-filterInvariant8-variant11-variant14-variant16-variant17-filterInvariant22-variant23-variant26-variant27-variant29-variant32-variant34-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:12,79:91:56:1647,56,0:10,2,23,56 chr1 173802433 . GA G 66.14 PASS AC=2;AF=0.75;AN=2;DP=54;FS=0;FractionInformativeReads=1;MQ=60;set=variant14-variant16-variant17-variant22-variant23-variant26-variant27-variant36-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:103,9,0:0,0,3,0 chr1 173825692 . T G 280.43 PASS AC=2;AF=0.688;AN=2;DP=158;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant8-variant14-variant16-variant22-variant23-variant26-variant29-variant32-variant34-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:361,27,0:0,0,8,1 chr1 173835211 . C T 568.74 PASS AC=2;AF=0.632;AN=2;DP=790;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant8-variant14-variant16-variant17-variant22-variant23-variant26-variant27-variant29-variant32-variant34-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1298,108,0:0,0,11,25 chr1 173836194 . G A 767.76 PASS AC=1;AF=0.545;AN=2;DP=677;MQ=60;set=variant2-variant3-variant14-variant16-variant22-variant23-variant27-variant32-variant34-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:38,19:57:99:587,0,1094:15,23,3,16 chr1 173836247 . T TA 362.41 PASS AC=2;AF=0.632;AN=2;DP=668;MQ=60;set=variant2-variant3-variant6-variant8-variant14-variant16-variant17-variant22-variant23-variant26-variant27-variant29-variant32-variant34-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:758,75,0:0,0,9,16 chr1 173836602 . G A 353.3 PASS AC=2;AF=0.658;AN=2;DP=278;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant8-variant14-variant16-variant17-variant22-variant23-variant26-variant27-variant29-variant32-variant34-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,19:20:50:569,50,0:1,0,13,6 chr1 173837306 . T C 1816.6 PASS AC=2;AF=0.632;AN=2;DP=2643;MQ=60;set=variant2-variant3-variant6-variant8-variant14-variant16-variant17-variant22-variant23-variant26-variant27-variant29-variant32-variant34-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:3291,305,0:0,0,50,52 chr1 173839240 . C T 106.7 PASS AC=2;AF=0.667;AN=2;DP=222;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant8-variant14-variant16-variant22-variant23-variant26-variant27-variant29-variant32-variant34-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:121,12,0:0,0,3,1 chr1 173842467 . A G 718.91 PASS AC=2;AF=0.804;AN=2;DP=325;MQ=60;set=variant2-variant3-variant6-variant8-variant10-variant13-variant14-variant16-variant17-variant22-variant23-variant26-variant27-variant29-variant32-variant33-variant34-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:356,27,0:0,0,7,2 chr1 173854659 . C T 169.82 PASS AC=1;AF=0.5;AN=2;DP=171;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant14-variant16-variant17-variant22-variant23-variant26-variant36-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,10:13:84:404,0,84:3,0,10,0 chr1 173855298 . A T 1164.62 PASS AC=2;AF=0.804;AN=2;DP=1433;MQ=60;set=variant2-variant3-variant6-variant8-variant10-variant13-variant14-variant16-variant17-variant22-variant23-variant26-variant27-variant29-variant32-variant33-variant34-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1762,158,0:0,0,24,29 chr1 173876561 . C G 710.09 PASS AC=1;AF=0.5;AN=2;DP=603;FractionInformativeReads=1;MQ=60;set=variant6-variant14-variant16-variant17-variant22-variant23-variant26-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,30:60:99:738,0,805:19,11,15,15 chr1 173878832 . T C 5845.9 PASS AC=2;AF=0.783;AN=2;DP=4816;MQ=60;set=variant2-variant3-variant6-variant8-variant10-variant13-variant14-variant16-variant17-variant22-variant23-variant26-variant27-variant29-variant32-variant33-variant34-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,187:187:99:5822,561,0:0,0,105,82 chr1 173878862 . T C 6368.63 PASS AC=2;AF=0.783;AN=2;DP=4865;MQ=60;set=variant2-variant3-variant6-variant8-variant10-variant13-variant14-variant16-variant17-variant22-variant23-variant26-variant27-variant29-variant32-variant33-variant34-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,190:190:99:5899,569,0:0,0,93,97 chr1 173900706 . CCTA C 3673.48 PASS AC=1;AF=0.5;AN=2;DP=2783;MQ=60;set=variant6-variant10-variant13-variant14-variant16-variant17-variant22-variant23-variant26-variant36-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,102:178:99:4018,0,3299:37,39,44,58 chr1 173901373 . T TA 504.38 PASS AC=1;AF=0.5;AN=2;DP=544;MQ=60;set=variant6-variant14-variant16-variant17-variant22-variant23-variant26-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,28:45:99:678,0,372:8,9,14,14 chr1 173903300 . G A 4713.76 PASS AC=1;AF=0.5;AN=2;DP=4747;MQ=60;set=variant6-variant10-variant13-variant14-variant16-variant17-variant22-variant23-variant26-variant36-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:188,175:363:99:4081,0,4686:85,103,85,90 chr1 173903737 . G A 3858.42 PASS AC=1;AF=0.5;AN=2;DP=4399;MQ=60;set=variant6-variant10-variant13-variant14-variant16-variant17-variant22-variant23-variant26-variant36-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:150,163:313:99:3888,0,3771:64,86,68,95 chr1 173904809 . T C 4237.64 PASS AC=1;AF=0.5;AN=2;DP=4068;MQ=60;set=variant6-variant10-variant13-variant14-variant16-variant17-variant22-variant23-variant26-variant36-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:127,111:238:99:2728,0,3089:72,55,68,43 chr1 173904959 . A G 3852.82 PASS AC=1;AF=0.5;AN=2;DP=4117;MQ=60;set=variant6-variant10-variant13-variant14-variant16-variant17-variant22-variant23-variant26-variant36-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:113,119:232:99:3076,0,2617:48,65,54,65 chr1 173905237 . A G 4281.68 PASS AC=1;AF=0.5;AN=2;DP=4530;MQ=60;set=variant6-variant10-variant13-variant14-variant16-variant17-variant22-variant23-variant26-variant36-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:135,141:276:99:3264,0,3220:60,75,68,73 chr1 173905652 . CAAAA CAAAAAA,CAAAAAAA,CAAAAA,CAAAAAAAAAA,CAAA,CAA,CA,C 190.89 PASS AC=0,0,0,0,0,0,1,0;AF=0.05,0.025,0.1,0.025,0.15,0.075,0.05,0.025;AN=2;DP=785;set=variant2-filterInvariant6-filterInvariant9-variant10-variant12-filterInvariant13-filterInvariant15-variant21-variant22-variant23-variant24-variant29-variant32-variant33-variant34-variant36-variant37-variant38-filterInvariant39-variant44 GT:DP:GQ:SB 0/7:47:99:15,17,10,5 chr1 173905846 . C CA,CAA 262.9 PASS AC=1,0;AF=0.389,0.222;AN=2;DP=324;MQ=60;set=variant8-variant10-variant13-variant16-variant22-variant23-variant26-variant37-variant42 GT:DP:GQ:SB 0/1:19:99:2,6,4,7 chr1 173906530 . GA G 3456.21 PASS AC=1;AF=0.5;AN=2;DP=3485;MQ=60;set=variant6-variant10-variant13-variant14-variant16-variant17-variant22-variant23-variant26-variant36-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:102,120:222:99:3069,0,2500:63,39,70,50 chr1 173906656 . TA TAA,T 66.28 PASS AC=1,0;AF=0.463,0.037;AN=2;DP=6908;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant8-filterInvariant12-filterInvariant15-filterInvariant16-filterInvariant19-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant25-filterInvariant26-filterInvariant27-variant29-filterInvariant30-filterInvariant32-filterInvariant34-filterInvariant36-filterInvariant38-filterInvariant39-variant40-filterInvariant42-filterInvariant43 GT:DP:GQ:SB 0/1:219:99:83,95,21,20 chr1 173907812 . C T 1961.03 PASS AC=1;AF=0.5;AN=2;DP=1570;MQ=60;set=variant6-variant10-variant13-variant14-variant16-variant17-variant22-variant23-variant26-variant36-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,38:90:99:938,0,1245:20,32,14,24 chr1 173952539 . T A 921.72 PASS AC=1;AF=0.611;AN=2;DP=1269;MQ=60;set=variant2-variant6-variant8-variant10-variant13-variant14-variant16-variant17-variant22-variant23-variant26-variant29-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,33:70:99:751,0,869:23,14,21,12 chr1 173952836 . A G 675.42 PASS AC=1;AF=0.5;AN=2;DP=592;MQ=60;set=variant6-variant14-variant16-variant17-variant22-variant23-variant26-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,22:52:99:582,0,821:11,19,8,14 chr1 173953860 . G C 382.09 PASS AC=1;AF=0.5;AN=2;DP=349;FractionInformativeReads=1;MQ=60;set=variant6-variant14-variant16-variant17-variant22-variant23-variant26-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,21:37:99:607,0,445:4,12,5,16 chr1 173961807 . AAC A,AACAC,AACACAC,AACACACAC 198.08 PASS AC=0,1,0,0;AF=0.159,0.295,0.068,0.023;AN=2;DP=675;set=variant3-variant5-filterInvariant6-variant12-variant14-variant16-filterInvariant17-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant29-variant30-variant31-variant36-variant37-variant38-variant40-variant42-variant44 GT:DP:GQ:SB 0/2:26:99:14,5,4,3 chr1 174128457 . G T 452.49 PASS AC=1;AF=0.5;AN=2;DP=107;FractionInformativeReads=1;MQ=60;set=variant6-variant16-variant17-variant23-variant26-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,10:17:99:204,0,215:6,1,6,4 chr1 174188285 . G A 819.78 PASS AC=1;AF=0.618;AN=2;DP=1160;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant13-variant14-variant16-variant19-variant22-variant23-variant27-variant29-variant32-variant33-variant34-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,28:64:99:665,0,813:17,19,16,12 chr1 174210540 . A T 486.89 PASS AC=1;AF=0.5;AN=2;DP=25;FS=4.465;FractionInformativeReads=1;MQ=60;MQRankSum=-0.638;QD=19.48;ReadPosRankSum=0.971;SOR=1.863;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:10,15:25:99:515,0,279:7,3,13,2 chr1 174219799 . G T 1478.41 PASS AC=1;AF=0.5;AN=2;DP=563;MQ=60;set=variant6-variant14-variant16-variant17-variant23-variant26-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,33:75:99:828,0,900:18,24,11,22 chr1 174221887 . GT G 128.96 PASS AC=2;AF=0.76;AN=2;DP=439;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant10-variant13-variant14-variant16-variant17-variant19-variant22-variant23-variant26-variant27-variant29-variant32-variant33-variant34-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:286,24,0:0,0,0,8 chr1 174274062 . A G 306.55 PASS AC=1;AF=0.633;AN=2;DP=449;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant13-variant14-variant16-variant19-variant22-variant23-variant27-variant32-variant33-variant34-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:21,14:35:99:363,0,492:12,9,9,5 chr1 174274349 . T G 390.96 PASS AC=1;AF=0.633;AN=2;DP=914;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant13-variant14-variant16-variant19-variant22-variant23-variant27-variant32-variant33-variant34-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,22:47:99:552,0,686:8,17,7,15 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 1/1:1,122:123:99:3513,357,0:1,0,73,49 chr1 174516999 . C T 742.66 PASS AC=1;AF=0.6;AN=2;DP=685;MQ=60;set=variant-variant2-variant3-variant13-variant14-variant16-variant19-variant22-variant23-variant27-variant32-variant33-variant34-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:22,15:37:99:361,0,589:15,7,10,5 chr1 174769068 . GCACACACACACACACACACACACA G,GCACACACACA,GCACACACACACA,GCA,GCACA,GCACACACACACACACACA,GCACACACA,GCACACACACACACA,GCACACA,GCACACACACACACACACACACACACA,GCACACACACACACACACACA 666.74 PASS AC=0,0,0,1,0,0,0,1,0,0,0;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 4/8:13:99:0,0,10,3 chr1 174769080 . A G 67.64 PASS AC=1;AF=0.5;AN=2;DP=13;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.592;QD=5.2;ReadPosRankSum=1.099;SOR=0.223;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:10,3:13:96:96,0,411:8,2,2,1 chr1 174843716 . CTTTTTTTTTTTTTT CTTTTTTTT,CTTTTTTTTTTTT,CTTTTT,CTTTTTTTTT,CTTTTTTTTTTT,CTTTTTTTTTT,CTTTTTTTTTTTTT,CT,C 143.61 PASS AC=0,0,0,0,0,0,2,0,0;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 7/7:13:15:1,0,0,12 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 1/1:0,26:26:78:1021,78,0:0,0,2,24 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 0/1:77,63:140:99:1462,0,1980:45,32,39,24 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 0/1:231:99:63,60,43,65 chr1 174961987 . C T 8789.82 PASS AC=2;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 1/1:0,302:302:99:9224,904,0:0,0,169,133 chr1 174962071 . A G 2962.5 PASS AC=1;AF=0.5;AN=2;DP=2124;MQ=60;set=variant6-variant14-variant16-variant17-variant23-variant26-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:146,138:284:99:3286,0,3758:68,78,69,69 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 1/1:0,38:38:99:1408,114,0:0,0,20,18 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 0/1:101,108:209:99:2380,0,2503:50,51,58,50 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 0/1:82:99:27,15,28,12 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 0/1:145,131:276:99:3273,0,3573:90,55,81,50 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 0/1:163,120:283:99:2662,0,3902:77,86,64,56 chr1 174984074 . CT C,TT 91.01 PASS AC=1,0;AF=0.5,0.25;AN=2;DP=73;set=variant23-variant26 GT:DP:GQ:SB 0/1:22:99:3,10,1,8 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 0/1:60,36:96:99:788,0,1484:37,23,23,13 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 0/1:52,41:93:99:1212,0,1408:27,25,25,16 chr1 175053098 . T C 3119.6 PASS AC=1;AF=0.563;AN=2;DP=2265;MQ=60;set=variant6-variant9-variant12-variant15-variant19-variant20-variant21-variant22-variant23-variant28-variant29-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,44:137:99:1491,0,5560:32,61,12,32 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 0/1:91,44:135:99:1494,0,5539:30,61,12,32 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 0/1:28,27:55:99:711,0,658:17,11,18,9 chr1 175063571 . A G 197.43 PASS AC=1;AF=0.567;AN=2;DP=153;FractionInformativeReads=1;MQ=60;set=variant9-variant12-variant15-variant19-variant20-variant21-variant22-variant23-variant28-variant29-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:73:73,0,158:0,4,1,2 chr1 175092674 . C T 3771.42 PASS AC=2;AF=0.75;AN=2;DP=6597;set=variant-variant2-variant3-variant4-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-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,173:173:99:5399,515,0:0,0,91,82 chr1 175092707 . C T 1265.3 PASS AC=1;AF=0.66;AN=2;DP=4361;MQ=60;set=variant-variant4-variant9-variant10-variant12-variant14-variant15-variant18-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant34-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:90,100:190:99:2532,0,2395:47,43,47,53 chr1 175092840 . T C 2394.04 PASS AC=2;AF=0.75;AN=2;DP=5094;MQ=60;set=variant-variant2-variant3-variant4-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-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,147:147:99:4473,440,0:0,0,56,91 chr1 175092992 . GGAGT G 367.87 PASS AC=2;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 1/1:0,17:17:51:765,51,0:0,0,5,12 chr1 175095936 . C T 147.1 PASS AC=1;AF=0.654;AN=2;DP=541;MQ=60;set=variant-variant4-variant9-variant10-variant12-variant14-variant15-variant18-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,13:25:99:419,0,306:8,4,11,2 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 0/1:16,27:43:99:894,0,408:4,12,5,22 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 0/1:56,51:107:99:1193,0,1310:27,29,25,26 chr1 175097349 . C T 2585.37 PASS AC=2;AF=0.763;AN=2;DP=4371;MQ=60;set=variant-variant2-variant3-variant4-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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,106:106:99:2958,314,0:0,0,50,56 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 0/1:5,15:20:85:372,0,85:3,2,6,9 chr1 175104790 . T C 276.08 PASS AC=1;AF=0.568;AN=2;DP=493;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant11-variant13-variant14-variant16-variant17-variant19-variant20-variant23-variant26-variant27-variant29-variant31-variant32-variant33-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:283,0,227:7,0,8,1 chr1 175104796 . G T 934.74 PASS AC=2;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 1/1:0,23:23:69:903,69,0:0,0,21,2 chr1 175105880 . G A 2346.78 PASS AC=2;AF=0.784;AN=2;DP=2690;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1662,159,0:0,0,32,21 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 1/1:0,65:65:99:2075,193,0:0,0,35,30 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 1/1:0,113:113:99:3326,339,0:0,0,63,50 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 0/1:57:99:12,9,22,14 chr1 175116252 . C G 1678.13 PASS AC=2;AF=0.864;AN=2;DP=3562;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2230,224,0:0,0,41,34 chr1 175126223 . T A 1584.34 PASS AC=1;AF=0.603;AN=2;DP=5780;MQ=60;set=variant2-variant4-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:100,101:201:99:2187,0,2227:52,48,52,49 chr1 175126423 . A G 832.01 PASS AC=1;AF=0.593;AN=2;DP=1813;MQ=60;set=variant2-variant4-variant7-variant9-variant12-variant14-variant15-variant18-variant19-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,21:49:99:542,0,774:14,14,10,11 chr1 175126524 . T C 1036.72 PASS AC=1;AF=0.593;AN=2;DP=2395;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant9-variant12-variant14-variant15-variant18-variant19-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,34:80:99:897,0,1170:25,21,21,13 chr1 175126644 . G A 4210.13 PASS AC=2;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 1/1:0,133:133:99:3807,397,0:0,0,66,67 chr1 175126721 . T C 1665.72 PASS AC=1;AF=0.596;AN=2;DP=4190;MQ=60;set=variant2-variant4-variant7-variant9-variant12-variant15-variant18-variant19-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,79:156:99:1788,0,1918:43,34,41,38 chr1 175127534 . G C 337.13 PASS AC=1;AF=0.597;AN=2;DP=1165;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-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,16:33:99:438,0,493:9,8,7,9 chr1 175127771 . C T 240.08 PASS AC=1;AF=0.597;AN=2;DP=1295;FractionInformativeReads=1;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-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,18:46:99:380,0,624:13,15,10,8 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 0/1:29,21:50:99:774,0,2418:12,17,9,12 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 0/1:29,20:49:99:796,0,2415:12,17,8,12 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 0/1:29,21:50:99:796,0,2415:12,17,8,13 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 0/1:27,24:51:99:629,0,1063:16,11,13,11 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 0/1:26,28:54:99:669,0,977:14,12,17,11 chr1 175129691 . G T 1979.11 PASS AC=1;AF=0.586;AN=2;DP=1370;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,23:49:99:589,0,694:16,10,10,13 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 0/1:26,29:55:99:1100,0,993:16,10,13,16 chr1 175129946 . C T 998.38 PASS AC=1;AF=0.603;AN=2;DP=1621;set=variant-variant3-variant5-variant6-variant8-variant10-variant11-variant13-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,26:55:99:784,0,1120:13,16,16,10 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 0/1:29,29:58:99:1091,0,1069:17,12,13,16 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 0/1:34,35:69:99:858,0,921:16,18,16,19 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 1/1:0,58:58:99:1790,173,0:0,0,24,34 chr1 175135829 . G A 952.55 PASS AC=1;AF=0.591;AN=2;DP=1123;MQ=60;set=variant-variant3-variant6-variant8-variant11-variant13-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,25:40:99:619,0,357:7,8,10,15 chr1 175161849 . G T 581.59 PASS AC=1;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 0/1:29,26:55:99:539,0,594:12,17,11,15 chr1 175161930 . C G 274.57 PASS AC=1;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 0/1:12,8:20:99:167,0,404:2,10,3,5 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 1/1:0,18:18:54:641,54,0:0,0,14,4 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 1/1:0,84:84:99:2499,252,0:0,0,46,38 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 1/1:0,72:72:99:3250,219,0:0,0,48,24 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 1/1:0,73:73:99:3250,219,0:0,0,49,24 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 1/1:0,135:135:99:4196,404,0:0,0,64,71 chr1 175324711 . G A 1189.38 PASS AC=1;AF=0.5;AN=2;DP=948;MQ=60;set=variant12-variant20-variant23-variant29-variant30-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:62,48:110:99:1075,0,1581:27,35,21,27 chr1 175329083 . A C,T 336.22 PASS AC=1,1;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 1/2:6:76:0,0,3,3 chr1 175331617 . C A 276.22 PASS AC=1;AF=0.5;AN=2;DP=176;MQ=60;set=variant12-variant20-variant23-variant29-variant30-variant36-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:153,0,154:4,2,4,2 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 1/1:0,24:24:72:920,72,0:0,0,4,20 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 1/1:0,55:55:99:1778,165,0:0,0,23,32 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 1/1:0,22:22:66:802,66,0:0,0,5,17 chr1 175348543 . T C 648.67 PASS AC=1;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 0/1:13,12:25:99:341,0,328:9,4,7,5 chr1 175348723 . C T 1050.17 PASS AC=1;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 0/1:37,44:81:99:1111,0,1007:20,17,25,19 chr1 175355128 . C G 168.92 PASS AC=1;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 0/1:22,29:51:99:801,0,475:12,10,21,8 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 1/1:0,75:75:99:2456,225,0:0,0,35,40 chr1 175355618 . T C 615.88 PASS AC=1;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 0/1:18,12:30:99:366,0,603:5,13,2,10 chr1 175360690 . C T 997.02 PASS AC=1;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 0/1:41,31:72:99:758,0,1242:14,27,11,20 chr1 175362736 . G A 358.52 PASS AC=1;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 0/1:4,13:17:99:480,0,128:4,0,11,2 chr1 175365663 . G A 943.7 PASS AC=1;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 0/1:52,54:106:99:1284,0,1282:28,24,30,24 chr1 175375334 . C T 68.16 PASS AC=1;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 0/1:21,17:38:99:459,0,620:15,6,12,5 chr1 175375469 . C A 1680.17 PASS AC=1;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 0/1:84,83:167:99:1941,0,1949:44,40,45,38 chr1 175375683 . T C 2035.15 PASS AC=1;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 0/1:100,108:208:99:3053,0,2435:50,50,60,48 chr1 175375802 . T C 2680.88 PASS AC=1;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 0/1:80,122:202:99:3142,0,2177:38,42,53,69 chr1 175376019 . AG A,AGG 85.03 PASS AC=1,0;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 0/1:24:99:2,11,1,10 chr1 175712765 . GTCTCTCTCTCTCTCTCTCTCTCTC GTCTCTCTCTCTCTCTCTC,GTCTCTCTCTCTC,GTCTCTCTCTCTCTCTCTCTCTCTCTC,GTCTCTCTCTCTCTC,GTCTCTCTC,GTCTC,GTCTCTCTCTCTCTCTCTCTCTC,GTCTCTCTCTC,GTCTCTCTCTCTCTCTC,GTCTCTCTCTCTCTCTCTCTC,GTCTCTCTCTCTCTCTCTCTCTCTCTCTC,G 584.99 PASS AC=0,0,0,0,0,0,0,0,0,1,0,0;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 0/10:8:9:1,1,4,2 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 1/1:0,96:96:99:3159,288,0:0,0,51,45 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 1/1:0,97:97:99:2745,290,0:0,0,50,47 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 1/1:0,79:79:99:2287,236,0:0,0,36,43 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 1/1:0,34:34:99:1100,102,0:0,0,24,10 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 0/1:50:99:12,22,7,9 chr1 176103053 . TAC T 677.16 PASS AC=2;AF=0.625;AN=2;DP=1830;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant34-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1779,120,0:0,0,14,26 chr1 176118219 . G A 650.28 PASS AC=1;AF=0.596;AN=2;DP=1010;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant21-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,21:33:99:441,0,387:5,7,10,11 chr1 176129391 . CTTTTT CTTT,CTTTT,CT,CTT,C,CTTTTTTT 168.88 PASS AC=0,1,0,0,1,0;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 5/2:15:78:2,0,4,9 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 1/1:0,39:39:99:1167,117,0:0,0,14,25 chr1 176153658 . T C 435.8 PASS AC=2;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 1/1:0,19:19:57:633,57,0:0,0,14,5 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 1/1:0,31:31:92:1034,92,0:0,0,8,23 chr1 176563534 . G GATGCC 1177.27 PASS AC=1;AF=0.5;AN=2;DP=117;FractionInformativeReads=1;MQ=60;set=variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:14,28:42:99:1215,0,2473:8,6,20,8 chr1 176563537 . G A 1177.31 PASS AC=1;AF=0.5;AN=2;DP=132;FractionInformativeReads=1;MQ=60;set=variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:15,30:45:99:1206,0,2626:10,5,22,8 chr1 176563538 . C CCT 1159.27 PASS AC=1;AF=0.5;AN=2;DP=134;FractionInformativeReads=1;MQ=60;set=variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:15,30:45:99:1197,0,2709:10,5,22,8 chr1 176563542 . C T 1201.51 PASS AC=1;AF=0.5;AN=2;DP=147;FractionInformativeReads=1;MQ=60;set=variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:21,30:51:99:1230,0,2693:14,7,22,8 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 1/2:60:89:8,6,22,24 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 1/1:0,217:217:99:6481,650,0:0,0,103,114 chr1 176665102 . ATGTGTGTGTGTGTGTGTGTG ATGTGTGTGTGTGTGTGTGTGTG,A,ATGTGTGTGTGTGTGTGTG,ATGTGTGTGTGTGTGTG,ATGTGTGTGTGTGTG,ATGTGTGTGTGTGTGTGTGTGTGTG,ATGTGTGTGTGTGTGTGTGTGTGTGTG 53.55 PASS AC=0,0,2,0,0,0,0;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 3/3:9:26:0,0,3,6 chr1 176671912 . TGAGAGAGA T,TGA,TGAGA,TGAGAGA,TGAGAGAGAGA 744.16 PASS AC=0,0,0,1,0;AF=0.318,0.136,0.045,0.091,0.023;AN=2;DP=1349;set=variant4-variant9-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant21-filterInvariant22-variant23-variant25-filterInvariant26-filterInvariant27-variant29-variant33-variant37-variant38-variant40-filterInvariant41-variant44 GT:DP:GQ:SB 0/4:26:99:4,12,3,7 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 1/1:0,128:128:99:4194,384,0:0,0,51,77 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 1/1:0,29:29:87:1003,87,0:0,0,17,12 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 1/1:0,31:31:93:887,93,0:0,0,16,15 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 1/1:0,25:25:75:1125,75,0:0,0,18,7 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 1/1:0,284:284:99:8498,850,0:0,0,125,159 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 1/1:0,41:41:99:1216,122,0:0,0,22,19 chr1 176832552 . G A 570.9 PASS AC=2;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 1/1:0,52:52:99:1810,156,0:0,0,15,37 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 1/1:0,44:44:99:1478,132,0:0,0,21,23 chr1 176837817 . A G 281.17 PASS AC=2;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 1/1:0,13:13:39:420,39,0:0,0,8,5 chr1 176845386 . C T 219.12 PASS AC=2;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 1/1:0,14:14:42:453,42,0:0,0,8,6 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 1/1:0,17:17:51:528,51,0:0,0,11,6 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 1/1:0,42:42:99:1247,126,0:0,0,25,17 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 1/1:0,47:47:99:1574,141,0:0,0,24,23 chr1 176857498 . G A 356.64 PASS AC=2;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 1/1:0,37:37:99:1157,111,0:0,0,13,24 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 1/1:0,76:76:99:2535,228,0:0,0,38,38 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 1/1:0,89:89:99:2880,267,0:0,0,46,43 chr1 176913215 . AT A,ATT 247.8 PASS AC=1,0;AF=0.571,0.036;AN=2;DP=887;set=variant2-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-filterInvariant23-filterInvariant24-filterInvariant25-variant29-filterInvariant31-variant32-variant33-variant34-variant37-filterInvariant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:33:92:4,21,1,7 chr1 177198818 . G T 285.13 PASS AC=2;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 1/1:0,5:5:15:196,15,0:0,0,5,0 chr1 177198998 . T C 1620.78 PASS AC=2;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 1/1:0,151:151:99:4553,453,0:0,0,90,61 chr1 177199426 . G A 346.59 PASS AC=2;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 1/1:0,21:21:63:739,63,0:0,0,7,14 chr1 177199560 . A G 255.13 PASS AC=2;AF=1;AN=2;DP=24;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant25-variant27-variant37 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:283,27,0:0,0,3,6 chr1 177250670 . G A 1713.49 PASS AC=2;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 1/1:0,113:113:99:3412,338,0:0,0,53,60 chr1 177902388 . G A 1204.9 PASS AC=1;AF=0.529;AN=2;DP=2676;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant11-variant13-variant17-variant21-variant23-variant25-variant26-variant29-variant32-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,79:146:99:2043,0,1594:36,31,52,27 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 0/1:64,66:130:99:1586,0,1534:35,29,36,30 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 1/1:0,4:4:12:174,12,0:0,0,0,4 chr1 177914725 . C T 2943 PASS AC=1;AF=0.6;AN=2;DP=1443;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant11-variant13-variant21-variant23-variant26-variant29-variant32-variant33-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,32:59:99:895,0,756:17,10,18,14 chr1 177914728 . A G 972.19 PASS AC=2;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 1/1:0,64:64:99:2521,192,0:0,0,39,25 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 1/1:0,103:103:99:3053,309,0:0,0,54,49 chr1 177921434 . T A 691.15 PASS AC=2;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 1/1:0,49:49:99:1453,146,0:0,0,19,30 chr1 177923440 . T G 3436.75 PASS AC=1;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 0/1:70,69:139:99:1506,0,1709:41,29,37,32 chr1 177929379 . C T 401.97 PASS AC=1;AF=0.531;AN=2;DP=461;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant11-variant13-variant21-variant23-variant26-variant29-variant32-variant33-variant36-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:14,15:29:99:416,0,427:11,3,10,5 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 0/1:55,42:97:99:995,0,1315:26,29,19,23 chr1 177929940 . G A 1093.75 PASS AC=1;AF=0.605;AN=2;DP=1271;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant21-variant23-variant25-variant26-variant29-variant32-variant33-variant36-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,25:59:99:721,0,953:22,12,17,8 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 1/1:0,107:107:99:3345,321,0:0,0,60,47 chr1 177930096 . T C 4704.69 PASS AC=1;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 0/1:67,73:140:99:1730,0,1510:32,35,32,41 chr1 177930642 . G A 1447.51 PASS AC=1;AF=0.677;AN=2;DP=2337;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,28:64:99:584,0,942:21,15,17,11 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 1/1:0,52:52:99:1657,155,0:0,0,23,29 chr1 177931086 . C T 298.19 PASS AC=1;AF=0.683;AN=2;DP=638;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant20-variant21-variant23-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:187,0,114:1,3,1,4 chr1 177933443 . G A 456.31 PASS AC=1;AF=0.683;AN=2;DP=3676;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,58:99:99:1390,0,1032:15,26,27,31 chr1 177934467 . T C 106.77 PASS AC=1;AF=0.7;AN=2;DP=312;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,2:7:69:69,0,147:1,4,2,0 chr1 177935203 . A G 466.35 PASS AC=1;AF=0.677;AN=2;DP=1809;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,32:60:99:770,0,671:15,13,13,19 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 1/1:0,37:37:99:1099,111,0:0,0,15,22 chr1 177935344 . T C 48.22 PASS AC=1;AF=0.583;AN=2;DP=55;FractionInformativeReads=1;MQ=60;set=variant12-variant16-variant23-variant24-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:97:241,0,97:1,2,1,6 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 0/1:102,113:215:99:2712,0,2325:47,55,50,63 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 1/1:0,45:45:99:1472,135,0:0,0,19,26 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 0/1:10,8:18:99:262,0,302:2,8,2,6 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 0/1:25,24:49:99:640,0,574:10,15,12,12 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 0/1:42,26:68:99:627,0,969:24,18,14,12 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 0/1:73,53:126:99:1155,0,1832:41,32,29,24 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 0/1:17,18:35:99:432,0,454:9,8,8,10 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 0/1:78,51:129:99:1361,0,1992:45,33,28,23 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 0/1:49,30:79:99:1057,0,1972:24,25,13,17 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 0/1:46,37:83:99:996,0,1443:14,32,11,26 chr1 178483231 . G A 627.96 PASS AC=1;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 0/1:33,36:69:99:798,0,811:17,16,19,17 chr1 178484834 . A G 1436.14 PASS AC=1;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 0/1:16,32:48:99:843,0,371:12,4,20,12 chr1 178489903 . C G 1580.87 PASS AC=1;AF=0.5;AN=2;DP=114;FS=0;FractionInformativeReads=0.991;MQ=60;MQRankSum=-1.124;QD=13.87;ReadPosRankSum=0.795;SOR=0.648;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:50,63:113:99:1609,0,1254:24,26,31,32 chr1 178489978 . T G 1511.29 PASS AC=1;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 0/1:54,48:102:99:1189,0,1189:28,26,26,22 chr1 178491785 . C CT,CTT 143.93 PASS AC=1,0;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 0/1:35:99:4,11,6,14 chr1 178492447 . T A 1164.28 PASS AC=1;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 0/1:36,22:58:99:675,0,1137:27,9,16,6 chr1 178492635 . T C 4060.39 PASS AC=1;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 0/1:116,119:235:99:2719,0,2707:49,67,56,63 chr1 178494428 . C T 260.52 PASS AC=1;AF=0.536;AN=2;DP=705;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant11-variant12-variant14-variant18-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:220,0,153:3,1,6,0 chr1 178499068 . T A 271.03 PASS AC=1;AF=0.517;AN=2;DP=960;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant11-variant12-variant14-variant18-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,11:27:99:252,0,466:10,6,6,5 chr1 178511825 . A G 598.35 PASS AC=2;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 1/1:0,48:48:99:1594,144,0:0,0,32,16 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 0/1:62,47:109:99:1142,0,1395:35,27,29,18 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 0/1:70,58:128:99:1303,0,1558:39,31,33,25 chr1 178511941 . A C 1786.6 PASS AC=1;AF=0.517;AN=2;DP=4317;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant11-variant12-variant14-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,68:140:99:1515,0,1511:39,33,37,31 chr1 178513895 . T G 1061.26 PASS AC=1;AF=0.586;AN=2;DP=1110;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,19:31:99:466,0,340:11,1,13,6 chr1 178514165 . C T 959.55 PASS AC=1;AF=0.517;AN=2;DP=2708;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant11-variant12-variant14-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,47:109:99:1028,0,1573:26,36,21,26 chr1 178514560 . A AT 4042.69 PASS AC=1;AF=0.586;AN=2;DP=5107;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,75:142:99:2015,0,1754:31,36,35,40 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 0/1:62,62:124:99:1397,0,1660:27,35,33,29 chr1 178515135 . A T 1662.77 PASS AC=1;AF=0.586;AN=2;DP=1948;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,23:41:99:525,0,480:8,10,11,12 chr1 178515187 . A G 1297.55 PASS AC=1;AF=0.586;AN=2;DP=1768;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,15:39:99:367,0,654:11,13,6,9 chr1 178516901 . C T 172.72 PASS AC=1;AF=0.521;AN=2;DP=271;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant11-variant14-variant17-variant18-variant21-variant22-variant23-variant26-variant30-variant31-variant32-variant33-variant34-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,8:15:99:226,0,188:6,1,6,2 chr1 178517316 . C T 1684.7 PASS AC=1;AF=0.586;AN=2;DP=2137;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant14-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,33:53:99:828,0,531:11,9,15,18 chr1 178517365 . A G 519.12 PASS AC=1;AF=0.517;AN=2;DP=1603;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant11-variant12-variant14-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,30:51:99:744,0,493:10,11,15,15 chr1 178517591 . A G 3745.81 PASS AC=2;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 1/1:0,94:94:99:2887,282,0:0,0,53,41 chr1 178518008 . A G 9211.03 PASS AC=2;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 1/1:1,211:212:99:6244,590,0:1,0,88,123 chr1 178646748 . A T 580.2 PASS AC=2;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 1/1:0,36:36:99:1662,111,0:0,0,20,16 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 1/1:0,37:37:99:1662,111,0:0,0,21,16 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 1/1:0,32:32:96:1190,96,0:0,0,25,7 chr1 178694402 . G GGCA 11199.8 PASS AC=2;AF=0.966;AN=2;DP=11222;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,207:207:99:9197,644,0:0,0,111,96 chr1 178745798 . CTT CT,C 176.18 PASS AC=1,1;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 2/1:60:99:1,1,38,20 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 0/1:40,42:82:99:942,0,970:14,26,18,24 chr1 178746031 . C T 185.86 PASS AC=1;AF=0.625;AN=2;DP=526;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant12-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant30-variant32-variant36-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,8:28:99:269,0,618:4,16,0,8 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 1/1:0,7:7:21:231,21,0:0,0,4,3 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 1/1:0,25:25:74:719,74,0:0,0,9,16 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 0/1:24,26:50:99:574,0,650:12,12,13,13 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 1/1:0,94:94:99:3011,282,0:0,0,50,44 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 0/1:43,39:82:99:947,0,1030:17,26,16,23 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 1/1:0,19:19:57:600,57,0:0,0,13,6 chr1 178858624 . A T 112.84 PASS AC=1;AF=0.667;AN=2;DP=131;FS=0;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant7-variant8-variant9-variant12-variant15-variant19-variant23-variant24-variant30-variant32-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,2:8:66:66,0,251:6,0,2,0 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 1/1:0,45:45:99:1320,134,0:0,0,27,18 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 1/1:0,78:78:99:2333,234,0:0,0,39,39 chr1 178866674 . A G 118.66 PASS AC=1;AF=0.625;AN=2;DP=282;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant12-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant30-variant32-variant36-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:267,0,280:7,2,7,0 chr1 178871217 . G A 793.98 PASS AC=1;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 0/1:30,34:64:99:881,0,891:23,7,25,9 chr1 178886918 . T C 2917.39 PASS AC=1;AF=0.5;AN=2;DP=481;FractionInformativeReads=1;MQ=60;set=variant9-variant23 GT:AD:DP:GQ:PL:SB 0/1:133,87:220:99:1929,0,3305:66,67,42,45 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 0/1:79,48:127:99:1298,0,2104:28,51,14,34 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 1/1:0,136:136:99:4260,408,0:0,0,80,56 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 1/1:0,274:274:99:8459,821,0:0,0,137,137 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 0/1:5,9:14:99:259,0,121:1,4,3,6 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 0/1:13,4:17:99:129,0,441:11,2,4,0 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 0/1:43,25:68:99:550,0,984:22,21,15,10 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 0/1:30,23:53:99:671,0,740:13,17,10,13 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 0/1:42,58:100:99:1312,0,823:27,15,37,21 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 0/1:32,30:62:99:806,0,847:13,19,10,20 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 0/1:22,14:36:99:376,0,640:7,15,5,9 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 0/1:3,3:6:74:74,0,74:1,2,1,2 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 0/1:57,76:133:99:2339,0,1743:29,28,36,40 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 0/1:3,13:16:90:360,0,90:2,1,8,5 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 0/1:45,33:78:99:889,0,1205:25,20,21,12 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 0/1:42,40:82:99:1067,0,1185:16,26,17,23 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 0/1:130,143:273:99:3269,0,3083:64,66,75,68 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 0/1:13,11:24:99:339,0,398:5,8,6,5 chr1 179068851 . A G 323.91 PASS AC=1;AF=0.643;AN=2;DP=1499;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,18:27:99:567,0,285:5,4,6,12 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 0/1:32,32:64:99:824,0,920:18,14,18,14 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 0/1:17,18:35:99:452,0,492:8,9,10,8 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 0/1:24,26:50:99:619,0,612:13,11,15,11 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 0/1:15,13:28:99:326,0,467:6,9,5,8 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 0/1:8,3:11:61:61,0,207:3,5,1,2 chr1 179072728 . T C 3877.52 PASS AC=1;AF=0.643;AN=2;DP=9194;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:97,100:197:99:2636,0,2262:44,53,41,59 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 0/1:17,13:30:99:443,0,434:7,10,5,8 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 0/1:13,8:21:99:208,0,424:5,8,6,2 chr1 179073799 . T C 1840.17 PASS AC=1;AF=0.5;AN=2;DP=157;FS=0.591;FractionInformativeReads=0.987;MQ=60;MQRankSum=0.192;QD=11.72;ReadPosRankSum=-0.206;SOR=0.761;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:75,80:155:99:1868,0,1936:40,35,44,36 chr1 179074869 . T G 465.92 PASS AC=1;AF=0.643;AN=2;DP=2083;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,33:68:99:778,0,831:18,17,14,19 chr1 179075755 . A G 390.56 PASS AC=2;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 1/1:0,38:38:99:1254,113,0:0,0,16,22 chr1 179080115 . CTTTT CTT,CT,CTTT,C 982.21 PASS AC=0,1,0,0;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 0/2:27:99:3,9,3,12 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 0/1:20,23:43:99:655,0,595:6,14,6,17 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 0/1:10,15:25:99:373,0,256:7,3,10,5 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 0/1:11,9:20:99:252,0,273:4,7,2,7 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 0/1:8,6:14:99:147,0,197:3,5,2,4 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 0/1:4,4:8:99:115,0,117:1,3,1,3 chr1 179198653 . T C 1336.7 PASS AC=1;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 0/1:41,43:84:99:984,0,1009:25,16,25,18 chr1 179198767 . ACGCCGCCGC ACGCCGCCGCCGCCGCCGC,ACGCCGCCGCCGCCGC,ACGCCGC,A,ACGCCGCCGCCGCCGCCGCCGC 1617.13 PASS AC=0,1,1,0,0;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 3/2:60:99:1,1,18,40 chr1 179263003 . G A 1423.11 PASS AC=1;AF=0.536;AN=2;DP=2175;MQ=60;set=variant8-variant9-variant11-variant15-variant16-variant17-variant21-variant23-variant27-variant32-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,59:138:99:1281,0,1917:39,40,30,29 chr1 179292442 . G A 218.24 PASS AC=2;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 1/1:0,34:34:99:987,102,0:0,0,20,14 chr1 179304892 . T C 468.23 PASS AC=2;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 1/1:0,28:28:84:909,84,0:0,0,9,19 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 0/1:18,8:26:99:239,0,566:3,15,1,7 chr1 179310262 . C T 2246.35 PASS AC=1;AF=0.536;AN=2;DP=2147;MQ=60;set=variant8-variant9-variant11-variant15-variant16-variant17-variant21-variant23-variant27-variant32-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,72:137:99:1881,0,1684:38,27,33,39 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 0/1:53,64:117:99:1551,0,1213:23,30,25,39 chr1 179312102 . T C 1540.37 PASS AC=2;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 1/1:0,115:115:99:3295,344,0:0,0,54,61 chr1 179312249 . AT A 404.92 PASS AC=2;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 1/1:0,17:17:51:635,51,0:0,0,3,14 chr1 179317895 . ATGTGTGTGTGTGTGTGTGTGTGTGTG ATGTGTGTGTGTGTG,ATGTGTGTGTGTGTGTG,A,ATGTGTGTGTGTGTGTGTGTGTG,ATG,ATGTGTGTGTGTGTGTGTGTG,ATGTG,AAGTGTGTGTGTGTGTGTGTGTGTGTGTG 932.01 PASS AC=0,0,2,0,0,0,0,0;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 3/3:20:62:0,0,15,5 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 1/1:0,88:88:99:2555,263,0:0,0,37,51 chr1 179320665 . A G 511.47 PASS AC=2;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 1/1:0,50:50:99:1712,150,0:0,0,14,36 chr1 179322810 . G T 3994.6 PASS AC=1;AF=0.667;AN=2;DP=372;FractionInformativeReads=1;MQ=60;set=variant14-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:67,48:115:99:1060,0,1814:34,33,23,25 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 1/1:0,182:182:99:5459,545,0:0,0,98,84 chr1 179323919 . A G 7878.38 PASS AC=2;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 1/1:0,259:259:99:8181,776,0:0,0,144,115 chr1 179325506 . A G 2603.82 PASS AC=2;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 1/1:0,148:148:99:4748,443,0:0,0,53,95 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 1/1:0,12:12:36:517,36,0:0,0,0,12 chr1 179325657 . GT G 249.13 PASS AC=2;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 1/1:0,5:5:15:145,15,0:0,0,0,5 chr1 179326065 . A C 690.08 PASS AC=2;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 1/1:0,46:46:99:1686,136,0:0,0,38,8 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 1/1:1,130:131:99:4222,354,0:1,0,36,94 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 1/1:0,24:24:72:924,72,0:0,0,8,16 chr1 179326708 . TAC T 5277.59 PASS AC=2;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 1/1:0,230:230:99:10234,692,0:0,0,97,133 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 1/1:0,164:164:99:4985,491,0:0,0,58,106 chr1 179327017 . A G 1042.29 PASS AC=2;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 1/1:0,79:79:99:2730,237,0:0,0,52,27 chr1 179334801 . C A 284.46 PASS AC=2;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 1/1:0,4:4:12:113,12,0:0,0,3,1 chr1 179334840 . C T 325.96 PASS AC=2;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 1/1:0,9:9:27:268,27,0:0,0,6,3 chr1 179334917 . G C 675.12 PASS AC=2;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 1/1:0,33:33:99:1104,99,0:0,0,21,12 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 1/1:0,58:58:99:1729,174,0:0,0,34,24 chr1 179335058 . C T 528.99 PASS AC=2;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 1/1:0,52:52:99:1577,156,0:0,0,25,27 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 0/1:15,22:37:99:592,0,424:7,8,8,14 chr1 179335158 . C T 490.56 PASS AC=2;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 1/1:0,31:31:93:1364,93,0:0,0,12,19 chr1 179335162 . G C 493.55 PASS AC=2;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 1/1:0,29:29:87:1294,87,0:0,0,12,17 chr1 179335366 . C T 61.77 PASS AC=2;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 1/1:0,7:7:21:308,21,0:0,0,4,3 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 0/1:15:89:3,3,5,4 chr1 179339334 . G A 500.32 PASS AC=2;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 1/1:0,20:20:60:787,60,0:0,0,4,16 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 1/1:0,116:116:99:3021,347,0:0,0,55,61 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 1/1:0,5:5:15:171,15,0:0,0,4,1 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 1/1:0,28:28:83:935,83,0:0,0,21,7 chr1 179364391 . A G 519.57 PASS AC=2;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 1/1:0,61:61:99:1903,183,0:0,0,22,39 chr1 179380472 . GT G 1312.14 PASS AC=2;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 1/1:0,40:40:99:1211,120,0:0,0,12,28 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 1/1:0,7:7:21:315,21,0:0,0,7,0 chr1 179398573 . C T 221.5 PASS AC=1;AF=0.667;AN=2;DP=23;FS=0;FractionInformativeReads=1;MQ=60;set=variant14-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:99:111,0,124:4,0,3,0 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 1/1:2,42:44:82:1052,82,0:1,1,16,26 chr1 179401896 . G A 502.42 PASS AC=2;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 1/1:0,10:10:30:328,30,0:0,0,5,5 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 0/1:26,39:65:99:1559,0,1183:11,15,19,20 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 0/1:19,27:46:99:672,0,447:8,11,12,15 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 1/1:0,11:11:33:407,33,0:0,0,3,8 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 1/1:0,11:11:33:479,33,0:0,0,11,0 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 0/1:44,34:78:99:697,0,1062:27,17,18,16 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 1/1:0,6:6:18:226,18,0:0,0,2,4 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 1/1:0,26:26:78:949,78,0:0,0,5,21 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 1/1:0,7:7:21:234,21,0:0,0,2,5 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 1/1:0,16:16:48:545,48,0:0,0,11,5 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 0/1:9,6:15:99:136,0,279:7,2,4,2 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 0/1:79:99:22,20,23,14 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 0/1:49,46:95:99:1619,0,3200:24,25,27,19 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 0/1:51,57:108:99:1294,0,1153:23,28,22,35 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 0/1:15,21:36:99:578,0,424:11,4,15,6 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 1/1:1,68:69:99:2673,162,0:1,0,28,40 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 0/1:90,116:206:99:2838,0,2182:44,46,63,53 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 0/1:124,80:204:99:1885,0,3113:59,65,41,39 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 1/1:0,182:182:99:5503,544,0:0,0,87,95 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 0/1:71,65:136:99:1664,0,2069:35,36,31,34 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 0/1:54,55:109:99:1449,0,1554:20,34,23,32 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 0/1:46,44:90:99:1051,0,1262:17,29,19,25 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 1/1:0,120:120:99:3529,359,0:0,0,56,64 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 0/1:17,14:31:99:308,0,425:7,10,6,8 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 1/1:0,30:30:90:1105,90,0:0,0,24,6 chr1 179560718 . T C 759.96 PASS AC=1;AF=0.675;AN=2;DP=2071;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant10-variant13-variant14-variant15-variant16-variant19-variant22-variant23-variant27-variant32-variant34-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:59,38:97:99:844,0,1198:31,28,22,16 chr1 179561154 . C T 722.05 PASS AC=1;AF=0.675;AN=2;DP=1072;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant10-variant13-variant14-variant15-variant16-variant19-variant22-variant23-variant27-variant32-variant34-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,25:48:99:582,0,446:11,12,15,10 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 1/1:0,39:39:99:1217,117,0:0,0,22,17 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 1/1:2,37:39:60:952,60,0:1,1,23,14 chr1 179562143 . G A 241.61 PASS AC=1;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 0/1:14,7:21:99:171,0,354:6,8,2,5 chr1 179562707 . G A 2128.21 PASS AC=1;AF=0.5;AN=2;DP=1510;MQ=60;set=variant2-variant4-variant11-variant21-variant23-variant26-variant29-variant30-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:65,56:121:99:1252,0,1498:37,28,29,27 chr1 179562740 . G C 1849.32 PASS AC=1;AF=0.673;AN=2;DP=4075;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant22-variant23-variant24-variant27-variant32-variant33-variant34-variant36-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,70:125:99:1599,0,1196:27,28,36,34 chr1 179563033 . A G 707.71 PASS AC=1;AF=0.5;AN=2;DP=516;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant11-variant21-variant23-variant26-variant29-variant30-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:25,23:48:99:819,0,1423:8,17,10,13 chr1 179563041 . T C 716.73 PASS AC=1;AF=0.5;AN=2;DP=425;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant11-variant21-variant23-variant26-variant29-variant30-variant38 GT:AD:DP:GQ:PL:SB 0/1:24,22:46:99:800,0,1384:8,16,9,13 chr1 179563058 . A G 265.98 PASS AC=1;AF=0.5;AN=2;DP=400;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant11-variant21-variant23-variant26-variant29-variant30-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:21,14:35:99:322,0,600:6,15,7,7 chr1 179563152 . GT G 48.13 PASS AC=1;AF=0.5;AN=2;DP=59;MQ=60;set=variant11-variant21-variant23-variant26-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:145,0,107:1,3,0,5 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 0/1:2,7:9:64:260,0,64:2,0,7,0 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 0/1:17,11:28:99:281,0,442:11,6,8,3 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 0/1:23,22:45:99:481,0,558:15,8,13,9 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 0/1:20,19:39:99:454,0,481:8,12,7,12 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 0/1:42,34:76:99:745,0,1039:21,21,19,15 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 1/1:0,92:92:99:2575,274,0:0,0,46,46 chr1 179605058 . G A 123.08 PASS AC=2;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 1/1:0,13:13:39:477,39,0:0,0,2,11 chr1 179620253 . G A 997.59 PASS AC=1;AF=0.648;AN=2;DP=1659;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant22-variant23-variant24-variant27-variant30-variant32-variant33-variant34-variant36-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,34:59:99:897,0,711:6,19,9,25 chr1 179632347 . A C 42.64 PASS AC=1;AF=0.66;AN=2;DP=248;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant19-variant23-variant24-variant27-variant30-variant32-variant33-variant34-variant36-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,2:8:66:66,0,166:4,2,2,0 chr1 179632727 . G A 122.47 PASS AC=2;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 1/1:0,12:12:36:507,36,0:0,0,0,12 chr1 179712223 . A C 596.86 PASS AC=1;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 0/1:24,20:44:99:458,0,546:14,10,13,7 chr1 179712480 . T G 215.02 PASS AC=1;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 0/1:14,16:30:99:401,0,411:3,11,6,10 chr1 179712616 . G T 152.64 PASS AC=1;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 0/1:9,6:15:99:109,0,178:5,4,2,4 chr1 179776841 . A G 106.19 PASS AC=1;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 0/1:7,11:18:99:342,0,206:6,1,9,2 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 1/1:0,93:93:99:2873,278,0:0,0,45,48 chr1 179784071 . C T 889.68 PASS AC=1;AF=0.5;AN=2;DP=386;MQ=60;set=variant15-variant23-variant31-variant33-variant36 GT:AD:DP:GQ:PL:SB 0/1:28,33:61:99:929,0,664:12,16,12,21 chr1 179784230 . ACGCGCG ACG,A,ACGCG 75.55 PASS AC=0,1,0;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 0/2:26:37:1,3,9,13 chr1 179784244 . G A 547.08 PASS AC=1;AF=0.5;AN=2;DP=163;set=variant18-filterInvariant23-variant24-variant28-variant29-variant40 GT:AD:DP:GQ:PL:SB 0/1:12,5:17:69:69,0,345:4,8,2,3 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 0/1:6,15:21:99:415,0,128:2,4,7,8 chr1 179811337 . CA CAA,C 275.69 PASS AC=0,1;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 0/2:27:78:15,6,4,2 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 1/1:0,3:3:9:135,9,0:0,0,3,0 chr1 179813613 . T C 5944.45 PASS AC=1;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 0/1:192,151:343:99:3861,0,5136:100,92,73,78 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 1/1:0,45:45:99:1604,135,0:0,0,32,13 chr1 179852074 . T C 1014.94 PASS AC=2;AF=0.763;AN=2;DP=4948;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-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,114:114:99:3537,342,0:0,0,49,65 chr1 179852552 . T G 328.94 PASS AC=2;AF=0.763;AN=2;DP=977;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-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:62:676,62,0:0,0,16,5 chr1 179858333 . C T 163.57 PASS AC=2;AF=0.784;AN=2;DP=586;FractionInformativeReads=1;MQ=60;set=variant-variant2-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-variant36-variant37-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:358,27,0:0,0,8,1 chr1 179858444 . G A 946.95 PASS AC=2;AF=0.782;AN=2;DP=3261;MQ=60;set=variant-variant2-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-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2094,204,0:0,0,41,27 chr1 179876988 . C G 1496.98 PASS AC=2;AF=0.763;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-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,58:60:99:1664,129,0:1,1,22,36 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 1/1:0,110:110:99:3440,328,0:0,0,55,55 chr1 179887681 . G C 3150.48 PASS AC=2;AF=0.738;AN=2;DP=7318;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-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,217:217:99:7064,648,0:0,0,103,114 chr1 179887788 . C T 4521.92 PASS AC=1;AF=0.711;AN=2;DP=10469;MQ=60;set=variant-variant2-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-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:144,117:261:99:2942,0,3644:78,66,64,53 chr1 179888228 . G C 539.78 PASS AC=2;AF=0.788;AN=2;DP=704;FractionInformativeReads=1;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-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:527,39,0:0,0,1,12 chr1 179983665 . G A 704.08 PASS AC=1;AF=0.737;AN=2;DP=2309;MQ=60;set=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-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,32:60:99:855,0,715:10,18,9,23 chr1 179989584 . G C 1743.16 PASS AC=1;AF=0.5;AN=2;DP=648;FractionInformativeReads=1;MQ=60;set=variant6-variant23-variant31-variant33-variant36 GT:AD:DP:GQ:PL:SB 0/1:66,59:125:99:1536,0,1834:32,34,29,30 chr1 179989742 . G C 1581.68 PASS AC=1;AF=0.737;AN=2;DP=5415;MQ=60;set=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-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,77:139:99:2001,0,1516:31,31,41,36 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 1/1:0,15:15:45:631,45,0:0,0,1,14 chr1 180010702 . T C 148.54 PASS AC=1;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 0/1:3,6:9:68:240,0,68:2,1,6,0 chr1 180010911 . A G 1643.37 PASS AC=1;AF=0.5;AN=2;DP=1050;FractionInformativeReads=1;MQ=60;set=variant6-variant14-variant23-variant31-variant33-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:68,57:125:99:1399,0,1722:32,36,25,32 chr1 180022343 . T G 498.71 PASS AC=1;AF=0.737;AN=2;DP=2911;MQ=60;set=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-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,24:58:99:639,0,1025:9,25,6,18 chr1 180059736 . GACATACCT G 277.58 PASS AC=1;AF=0.737;AN=2;DP=1004;set=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-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:192,0,216:5,1,5,0 chr1 180059811 . A C 1790.14 PASS AC=1;AF=0.737;AN=2;DP=3558;MQ=60;set=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-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,37:75:99:975,0,880:24,14,26,11 chr1 180080115 . T G 432.3 PASS AC=1;AF=0.737;AN=2;DP=1612;MQ=60;set=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-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,14:28:99:329,0,421:11,3,9,5 chr1 180082703 . C CA 1924.9 PASS AC=1;AF=0.737;AN=2;DP=5888;set=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-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,55:114:99:1224,0,1330:27,32,27,28 chr1 180124379 . T C 255.13 PASS AC=1;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 0/1:10,4:14:98:98,0,309:4,6,1,3 chr1 180135757 . TG T 890.42 PASS AC=1;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 0/1:22,53:75:99:1645,0,557:10,12,23,30 chr1 180144291 . CAA CAAA,C 849 PASS AC=1,0;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 0/1:31:22:5,1,17,8 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 0/1:14,30:44:99:882,0,347:4,10,8,22 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 1/1:0,55:55:99:1735,165,0:0,0,30,25 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 1/1:0,8:8:24:360,24,0:0,0,2,6 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 1/1:0,8:8:24:360,24,0:0,0,2,6 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 1/1:0,7:7:21:239,21,0:0,0,2,5 chr1 180163569 . G A 855.03 PASS AC=1;AF=0.5;AN=2;DP=58;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.842;QD=14.74;ReadPosRankSum=-0.156;SOR=0.628;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:31,27:58:99:883,0,1795:11,20,10,17 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 0/1:29,22:51:99:785,0,1761:10,19,6,16 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 0/1:8,11:19:99:295,0,221:6,2,8,3 chr1 180167357 . G C 1208.7 PASS AC=1;AF=0.5;AN=2;DP=204;FractionInformativeReads=1;MQ=60;set=variant6-variant23 GT:AD:DP:GQ:PL:SB 0/1:54,44:98:99:1178,0,1385:27,27,19,25 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 0/1:50,38:88:99:1070,0,1264:25,25,19,19 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 1/1:0,65:65:99:2018,194,0:0,0,34,31 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 0/1:17,13:30:99:327,0,496:8,9,6,7 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 1/1:0,72:72:99:2369,215,0:0,0,37,35 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 1/1:0,77:77:99:2500,231,0:0,0,38,39 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 1/1:0,104:104:99:2833,310,0:0,0,54,50 chr1 180171810 . CAA C,CA,CCAAAA,CAAA,CAAAA,CAAAAA 2053.67 PASS AC=0,1,0,0,0,0;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 0/2:50:99:16,21,6,7 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 1/1:0,70:70:99:3057,213,0:0,0,30,40 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 1/1:0,65:65:99:2858,196,0:0,0,28,37 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 1/1:99:99:2,2,39,56 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 1/1:1,71:72:99:2053,206,0:0,1,35,36 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 0/1:12,15:27:99:341,0,328:3,9,6,9 chr1 180199384 . A AAG,AG 567.9 PASS AC=1,0;AF=0.58,0.02;AN=2;DP=407;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant14-variant15-variant19-variant21-variant23-variant24-variant26-variant27-variant31-variant32-variant33-variant36-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:15:99:6,1,7,1 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 1/1:0,13:13:39:465,39,0:0,0,4,9 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 1/1:0,91:91:99:2976,273,0:0,0,39,52 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 1/1:0,37:37:99:1315,111,0:0,0,16,21 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 1/1:0,17:17:51:724,51,0:0,0,8,9 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 1/1:0,32:32:96:1210,96,0:0,0,11,21 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 1/1:0,27:27:81:1208,81,0:0,0,11,16 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 1/1:0,31:31:93:1017,93,0:0,0,18,13 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 1/1:0,33:33:99:992,99,0:0,0,18,15 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 1/1:117:99:0,0,77,40 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 1/1:0,21:21:63:779,63,0:0,0,13,8 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 1/1:0,8:8:24:262,24,0:0,0,2,6 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 1/1:0,32:32:96:942,96,0:0,0,15,17 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 1/1:0,8:8:24:276,24,0:0,0,5,3 chr1 180471054 . C A 43.97 PASS AC=2;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 1/1:0,21:21:63:711,63,0:0,0,16,5 chr1 180757056 . A G 332.98 PASS AC=1;AF=0.524;AN=2;DP=987;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant12-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant27-variant29-variant32-variant34-variant36-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,9:32:99:201,0,521:9,14,2,7 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 1/1:0,12:12:36:463,36,0:0,0,3,9 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 0/1:7,5:12:99:176,0,192:5,2,5,0 chr1 180803922 . T C 269.69 PASS AC=1;AF=0.545;AN=2;DP=365;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant12-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant27-variant29-variant32-variant34-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,11:20:99:297,0,226:6,3,8,3 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 0/1:6,13:19:99:492,0,194:0,6,1,12 chr1 180853719 . C T 305.5 PASS AC=1;AF=0.525;AN=2;DP=918;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant27-variant29-variant32-variant34-variant36-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,21:46:99:554,0,766:14,11,13,8 chr1 180853815 . T C 898.14 PASS AC=1;AF=0.525;AN=2;DP=2101;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant27-variant29-variant32-variant34-variant36-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,43:92:99:1030,0,1054:26,23,23,20 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 1/1:0,229:229:99:6942,685,0:0,0,133,96 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 0/1:137,172:309:99:4623,0,3533:73,64,98,74 chr1 180857538 . C A 50.58 PASS AC=1;AF=0.5;AN=2;DP=925;FractionInformativeReads=1;set=filterInvariant3-variant15-filterInvariant21-filterInvariant23-variant24-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:103,10:113:99:125,0,7170:52,51,10,0 chr1 180857541 . T A 176.55 PASS AC=1;AF=0.5;AN=2;DP=1169;FractionInformativeReads=1;set=filterInvariant3-filterInvariant4-variant15-filterInvariant21-filterInvariant23-filterInvariant24-filterInvariant36-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:103,12:115:99:173,0,6864:51,52,12,0 chr1 180857542 . T A 216.49 PASS AC=1;AF=0.5;AN=2;DP=1160;FractionInformativeReads=1;set=filterInvariant3-filterInvariant4-variant15-filterInvariant21-filterInvariant23-filterInvariant24-variant36-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:102,12:114:99:213,0,6728:50,52,12,0 chr1 180857543 . G A 222.51 PASS AC=1;AF=0.5;AN=2;DP=1163;FractionInformativeReads=1;set=filterInvariant3-filterInvariant4-variant15-filterInvariant21-filterInvariant23-filterInvariant24-variant36-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:104,12:116:99:210,0,6770:51,53,12,0 chr1 180857544 . AGTTTT A 225.94 PASS AC=1;AF=0.5;AN=2;DP=1174;FractionInformativeReads=1;set=filterInvariant3-filterInvariant4-variant15-filterInvariant21-filterInvariant23-variant24-variant36-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:108,13:121:99:207,0,6721:52,56,13,0 chr1 180859368 . T G 4721.09 PASS AC=1;AF=0.521;AN=2;DP=10512;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant10-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant27-variant29-variant32-variant34-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:221,185:406:99:4074,0,5164:104,117,84,101 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 1/1:1,139:140:99:4580,378,0:1,0,66,73 chr1 180886810 . C G 673.06 PASS AC=1;AF=0.522;AN=2;DP=982;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant14-variant15-variant21-variant22-variant23-variant24-variant29-variant30-variant33-variant34-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,27:44:99:729,0,546:15,2,18,9 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 1/1:0,90:90:99:2638,269,0:0,0,50,40 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 0/1:52,57:109:99:1266,0,1187:28,24,29,28 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 0/1:16,11:27:99:404,0,669:3,13,2,9 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 0/1:130,125:255:99:3126,0,3271:69,61,67,58 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 0/1:124,133:257:99:3259,0,3150:58,66,60,73 chr1 180905694 . C T 7409.32 PASS AC=1;AF=0.568;AN=2;DP=4714;MQ=60;set=variant3-variant4-variant7-variant8-variant12-variant14-variant15-variant19-variant23-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant36-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:124,87:211:99:1911,0,3113:50,74,36,51 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 1/1:0,94:94:99:2983,282,0:0,0,45,49 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 1/1:0,23:23:68:633,68,0:0,0,14,9 chr1 180914966 . C T 300.13 PASS AC=1;AF=0.559;AN=2;DP=248;MQ=60;set=variant2-variant5-variant8-variant9-variant11-variant12-variant15-variant17-variant20-variant21-variant23-variant25-variant31-variant36-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,5:14:99:180,0,202:4,5,1,4 chr1 180915244 . GA G 545.13 PASS AC=2;AF=0.932;AN=2;DP=1010;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:448,48,0:0,0,11,5 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 0/1:22,28:50:99:765,0,492:9,13,16,12 chr1 180916130 . G T 3555.36 PASS AC=1;AF=0.583;AN=2;DP=2853;MQ=60;set=variant2-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant15-variant17-variant20-variant21-variant23-variant24-variant25-variant26-variant31-variant32-variant36-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:53,54:107:99:1380,0,1422:19,34,23,31 chr1 180917788 . C T 2570.75 PASS AC=1;AF=0.583;AN=2;DP=1683;MQ=60;set=variant2-variant5-variant8-variant9-variant11-variant12-variant15-variant17-variant21-variant23-variant24-variant25-variant31-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:51,38:89:99:852,0,1213:24,27,15,23 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 1/1:0,71:71:99:2334,213,0:0,0,35,36 chr1 180918365 . C T 1274.42 PASS AC=1;AF=0.556;AN=2;DP=1930;MQ=60;set=variant-variant2-variant5-variant8-variant10-variant11-variant12-variant17-variant23-variant24-variant25-variant31-variant36-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,25:60:99:695,0,1015:17,18,12,13 chr1 180918705 . C G 2472.2 PASS AC=2;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 1/1:0,61:61:99:1708,183,0:0,0,31,30 chr1 180919255 . C T 4205.56 PASS AC=1;AF=0.556;AN=2;DP=2958;MQ=60;set=variant2-variant5-variant8-variant9-variant11-variant15-variant17-variant18-variant21-variant23-variant24-variant25-variant31-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:66,73:139:99:1785,0,1630:31,35,37,36 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 0/1:39,30:69:99:686,0,1071:22,17,13,17 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 0/1:73,36:109:99:670,0,1832:31,42,16,20 chr1 180920340 . AAACAAC A 2629.71 PASS AC=1;AF=0.556;AN=2;DP=1174;MQ=60;set=variant2-variant5-variant8-variant9-variant11-variant15-variant17-variant18-variant21-variant23-variant24-variant25-variant31-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:38,23:61:99:852,0,2532:21,17,10,13 chr1 180943529 . C T 7448.33 PASS AC=2;AF=0.763;AN=2;DP=7325;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-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,146:146:99:4393,438,0:0,0,78,68 chr1 180944532 . T TAA 13783.8 PASS AC=2;AF=0.756;AN=2;DP=10890;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-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,244:244:99:10635,746,0:0,0,128,116 chr1 180953853 . A G 4226.74 PASS AC=2;AF=0.763;AN=2;DP=4922;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-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,124:124:99:3657,328,0:0,0,63,61 chr1 180957130 . C A 374.75 PASS AC=2;AF=0.878;AN=2;DP=292;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-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:177,12,0:0,0,4,0 chr1 180962282 . A G 601.88 PASS AC=2;AF=0.763;AN=2;DP=550;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-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:575,54,0:0,0,13,5 chr1 180962526 . C T 732.82 PASS AC=1;AF=0.5;AN=2;DP=267;MQ=60;set=variant2-variant5-variant23 GT:AD:DP:GQ:PL:SB 0/1:58,38:96:99:931,0,1516:24,34,18,20 chr1 180991665 . C G 2984.01 PASS AC=1;AF=0.636;AN=2;DP=3690;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant33-variant34-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,66:126:99:1464,0,1403:32,28,42,24 chr1 181003340 . A AG 1025.85 PASS AC=1;AF=0.553;AN=2;DP=1514;MQ=60;set=variant2-variant3-variant4-variant5-variant12-variant13-variant14-variant15-variant21-variant23-variant26-variant28-variant30-variant32-variant33-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:39,23:62:99:672,0,1274:17,22,9,14 chr1 181018440 . A G 697.78 PASS AC=1;AF=0.5;AN=2;DP=58;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.322;QD=12.03;ReadPosRankSum=-0.109;SOR=0.693;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:29,29:58:99:726,0,664:12,17,12,17 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 1/1:0,22:22:66:740,66,0:0,0,12,10 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 0/1:3,9:12:55:276,0,55:1,2,3,6 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 0/2:22:99:10,2,6,4 chr1 181548341 . A G 2248.12 PASS AC=2;AF=0.542;AN=2;DP=1707;set=variant-variant2-variant8-variant11-variant19-variant22-variant23-variant26-variant27-variant28-variant32-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3481,353,0:0,0,56,62 chr1 181549677 . A G 1971.34 PASS AC=1;AF=0.5;AN=2;DP=154;FS=2.066;FractionInformativeReads=1;MQ=60;MQRankSum=0.154;QD=12.8;ReadPosRankSum=0.527;SOR=0.506;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:72,82:154:99:2000,0,1685:45,27,47,35 chr1 181684605 . A G 731.08 PASS AC=1;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 0/1:35,22:57:99:602,0,894:15,20,6,16 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 0/2:7:28:0,2,1,4 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 0/1:66,59:125:99:1443,0,1667:40,26,35,24 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 0/1:34,29:63:99:557,0,844:16,18,13,16 chr1 181726413 . G A 246.92 PASS AC=1;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 0/1:14,17:31:99:418,0,413:3,11,5,12 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 0/1:34,31:65:99:805,0,926:13,21,12,19 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 0/1:30,13:43:99:303,0,860:17,13,5,8 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 0/1:63:99:14,13,21,15 chr1 181752923 . AAGCTT A 1318.59 PASS AC=1;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 0/1:30,42:72:99:1660,0,1863:14,16,17,25 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 0/1:69,58:127:99:1333,0,1773:28,41,26,32 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 1/1:0,40:40:99:1785,120,0:0,0,20,20 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 1/1:0,45:45:99:1504,134,0:0,0,22,23 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 0/1:18,11:29:99:246,0,531:10,8,7,4 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 0/1:30,34:64:99:728,0,818:14,16,15,19 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 1/1:0,82:82:99:2597,246,0:0,0,41,41 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 0/1:49,34:83:99:793,0,1454:29,20,20,14 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 0/1:83,98:181:99:2646,0,1895:35,48,36,62 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 0/1:61,58:119:99:1579,0,1809:29,32,30,28 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 1/1:0,77:77:99:2713,230,0:0,0,27,50 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 1/1:0,125:125:99:3982,375,0:0,0,76,49 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 1/1:0,36:36:99:1048,108,0:0,0,18,18 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 1/1:0,33:33:99:1220,99,0:0,0,11,22 chr1 181776264 . TA TAA,T,TAAA 191.68 PASS AC=0,1,0;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 0/2:28:74:13,9,3,3 chr1 182350896 . C G 3103.69 PASS AC=2;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 1/1:0,140:140:99:4666,419,0:0,0,98,42 chr1 182350909 . C T 3434.27 PASS AC=2;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 1/1:2,162:164:99:5318,441,0:1,1,113,49 chr1 182351233 . G A 4006.98 PASS AC=2;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 1/1:0,246:246:99:7511,736,0:0,0,117,129 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 1/1:0,66:66:99:2173,197,0:0,0,29,37 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 1/1:0,81:81:99:3635,247,0:0,0,46,35 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 1/1:0,80:80:99:3673,252,0:0,0,46,34 chr1 182352621 . T C 817.14 PASS AC=2;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 1/1:0,57:57:99:1770,170,0:0,0,25,32 chr1 182353198 . A T 95.61 PASS AC=2;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 1/1:0,33:33:95:818,95,0:0,0,17,16 chr1 182354850 . A G 330.57 PASS AC=2;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 1/1:0,23:23:69:953,69,0:0,0,9,14 chr1 182355046 . A G 823.87 PASS AC=2;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 1/1:0,153:153:99:4314,459,0:0,0,79,74 chr1 182356399 . A G 1466.96 PASS AC=2;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 1/1:0,93:93:99:2698,278,0:0,0,47,46 chr1 182359578 . A C 95.31 PASS AC=2;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 1/1:0,12:12:36:407,36,0:0,0,9,3 chr1 182360169 . T G 543.31 PASS AC=2;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 1/1:0,48:48:99:1441,143,0:0,0,26,22 chr1 182360202 . A C 861.93 PASS AC=2;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 1/1:0,64:64:99:2064,192,0:0,0,37,27 chr1 182360223 . G T 868.51 PASS AC=2;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 1/1:0,74:74:99:2212,220,0:0,0,44,30 chr1 182360315 . C T 1359.08 PASS AC=2;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 1/1:0,169:169:99:5013,506,0:0,0,98,71 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 1/1:0,121:121:99:3834,363,0:0,0,58,63 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 1/1:0,82:82:99:2359,246,0:0,0,38,44 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 1/1:0,52:52:99:1540,156,0:0,0,22,30 chr1 182361150 . G C 236.31 PASS AC=1;AF=0.5;AN=2;DP=19;FS=2.199;FractionInformativeReads=1;MQ=60;MQRankSum=1.479;QD=12.44;ReadPosRankSum=1.986;SOR=0.235;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:7,12:19:99:265,0,154:6,1,8,4 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 1/1:0,11:11:33:373,33,0:0,0,3,8 chr1 182367548 . G A 1928.73 PASS AC=2;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 1/1:1,106:107:99:3266,275,0:0,1,43,63 chr1 182367643 . A G 634.2 PASS AC=2;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 1/1:0,38:38:99:1344,114,0:0,0,15,23 chr1 182367893 . A G 2267.5 PASS AC=2;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 1/1:0,204:204:99:5921,610,0:0,0,94,110 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 1/1:0,169:169:99:5412,505,0:0,0,97,72 chr1 182369233 . A G 2847.08 PASS AC=2;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 1/1:0,257:257:99:7717,770,0:0,0,117,140 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 1/1:0,28:28:84:839,84,0:0,0,11,17 chr1 182419624 . T C 166.15 PASS AC=1;AF=0.558;AN=2;DP=318;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant13-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant36-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:77:93,0,77:1,2,1,2 chr1 182429295 . CTG C,CTGTG 605.61 PASS AC=1,1;AF=0.706,0.015;AN=2;DP=2190;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-filterInvariant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant42-variant44 GT:DP:GQ:SB 1/2:35:99:0,1,10,24 chr1 182429728 . T C 694.02 PASS AC=1;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 0/1:26,24:50:99:506,0,713:18,8,14,10 chr1 182491107 . A C 1107.38 PASS AC=2;AF=0.886;AN=2;DP=1261;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:83:948,83,0:0,0,22,6 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 0/1:45,44:89:99:1084,0,1072:17,28,17,27 chr1 182501933 . C A 5592.27 PASS AC=2;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 1/1:0,113:113:99:3328,338,0:0,0,54,59 chr1 182502033 . G T 3237.63 PASS AC=2;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 1/1:0,47:47:99:1455,140,0:0,0,19,28 chr1 182509269 . G A 1588.09 PASS AC=2;AF=0.875;AN=2;DP=1728;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1019,90,0:0,0,21,9 chr1 182509292 . A G 652.15 PASS AC=2;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 1/1:0,53:53:99:1639,159,0:0,0,36,17 chr1 182509617 . C A 192.1 PASS AC=2;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 1/1:0,11:11:33:447,33,0:0,0,1,10 chr1 182517238 . C A 103.54 PASS AC=2;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 1/1:0,4:4:12:172,12,0:0,0,4,0 chr1 182517357 . G C 376.07 PASS AC=2;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 1/1:0,28:28:84:997,84,0:0,0,21,7 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 1/1:0,183:183:99:5636,548,0:0,0,104,79 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 1/1:0,166:166:99:5641,496,0:0,0,61,105 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 0/1:88,65:153:99:1536,0,2006:45,43,29,36 chr1 182551337 . A C 1698.25 PASS AC=1;AF=0.645;AN=2;DP=4273;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,85:145:99:2094,0,1287:27,33,40,45 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 1/1:0,38:38:99:1205,114,0:0,0,13,25 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 1/1:0,41:41:99:1360,122,0:0,0,25,16 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 1/1:0,58:58:99:1808,174,0:0,0,30,28 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 1/1:0,85:85:99:2471,254,0:0,0,38,47 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 1/1:0,17:17:51:596,51,0:0,0,12,5 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 1/1:0,123:123:99:4008,369,0:0,0,80,43 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 1/1:0,69:69:99:2016,207,0:0,0,32,37 chr1 182784022 . T C 1376.18 PASS AC=2;AF=0.652;AN=2;DP=3429;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant33-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2883,270,0:0,0,34,56 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 1/1:0,77:77:99:2632,231,0:0,0,27,50 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 1/1:0,57:57:99:1916,171,0:0,0,30,27 chr1 183100563 . GGT GTGTGTGTGT,GGTGT,GTGTGTGTGTGTGT,GTGTGTGTGTGT,GTGTGTGTGTGTGTGT,GTGTGTGT,GTGTGTGTGTGTGTGTGTGT,GTGTGTGTGTGTGTGTGT,GGTGTGT,G 649.43 PASS AC=0,1,0,0,0,0,0,0,0,0;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 0/2:25:99:1,13,1,10 chr1 183102632 . G A 436.13 PASS AC=1;AF=0.5;AN=2;DP=51;FS=1.118;FractionInformativeReads=1;MQ=60;MQRankSum=1.847;QD=8.55;ReadPosRankSum=-0.124;SOR=0.475;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:30,21:51:99:464,0,851:11,19,9,12 chr1 183218026 . AGTGTGTGT AGTGT,AGTGTGT,AGTGTGTGTGTGT,AGTGTGTGTGT,A,AGT 461.76 PASS AC=0,1,0,1,0,0;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 2/4:11:99:0,0,10,1 chr1 183253213 . G A 1200.94 PASS AC=1;AF=0.633;AN=2;DP=1052;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,21:38:99:480,0,446:6,11,9,12 chr1 183253959 . T G 727.26 PASS AC=1;AF=0.662;AN=2;DP=1041;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,13:32:99:367,0,570:4,15,5,8 chr1 183261710 . A G 149.07 PASS AC=1;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 0/1:9,19:28:99:557,0,234:6,3,13,6 chr1 183441977 . C T 420.19 PASS AC=1;AF=0.682;AN=2;DP=1048;MQ=60;set=variant2-variant3-variant5-variant8-variant10-variant11-variant15-variant16-variant17-variant18-variant21-variant23-variant26-variant28-variant29-variant32-variant33-variant34-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,23:47:99:694,0,697:5,19,6,17 chr1 183471295 . G T 412.66 PASS AC=2;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 1/1:0,10:10:30:406,30,0:0,0,9,1 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 0/1:37:99:13,12,5,7 chr1 183486859 . G A 3569.45 PASS AC=2;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 1/1:0,103:103:99:3252,309,0:0,0,55,48 chr1 183496658 . A G 196.45 PASS AC=1;AF=0.711;AN=2;DP=277;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant8-variant10-variant11-variant15-variant16-variant17-variant21-variant23-variant26-variant28-variant29-variant32-variant33-variant34-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:99:186,0,110:3,0,5,1 chr1 183516100 . G C 571.96 PASS AC=1;AF=0.633;AN=2;DP=554;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,14:25:99:375,0,382:10,1,11,3 chr1 183516440 . G A 2569.81 PASS AC=1;AF=0.587;AN=2;DP=1641;MQ=60;set=variant-variant4-variant6-variant7-variant9-variant12-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant36-variant37-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,31:58:99:879,0,632:11,16,11,20 chr1 183521283 . C T 725.95 PASS AC=1;AF=0.621;AN=2;DP=1411;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant36-variant37-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:17,30:47:99:771,0,382:8,9,15,15 chr1 183522743 . G GCC,GC,GCCC,GCCGGCCCC,GCCCCCC,GCCCCCCCCCCCCCCCCC 396.97 PASS AC=1,0,0,0,0,0;AF=0.3,0.05,0.1,0.05,0.1,0.05;AN=2;DP=260;set=variant-variant3-variant7-variant9-variant20-variant23-variant29-variant31-variant32-variant38 GT:DP:GQ:SB 0/1:25:99:6,11,2,6 chr1 183522752 . G C 490.99 PASS AC=1;AF=0.633;AN=2;DP=345;set=variant-variant3-variant4-variant6-variant7-variant9-variant17-variant20-variant23-filterInvariant24-variant29-variant31-variant32-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:19,10:29:99:314,0,1024:8,11,2,8 chr1 183524850 . A AGAT 3773.56 PASS AC=1;AF=0.69;AN=2;DP=5868;MQ=60;set=variant2-variant3-variant5-variant8-variant10-variant11-variant15-variant16-variant17-variant18-variant21-variant23-variant26-variant28-variant29-variant32-variant33-variant34-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:97,95:192:99:3675,0,3774:42,55,43,52 chr1 183524855 . C A 9375.79 PASS AC=2;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 1/1:0,208:208:99:7866,634,0:0,0,95,113 chr1 183525452 . T G 4670.67 PASS AC=2;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 1/1:0,128:128:99:3776,383,0:0,0,53,75 chr1 183534935 . C T 1186.13 PASS AC=1;AF=0.621;AN=2;DP=1906;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant36-variant37-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:32,24:56:99:637,0,760:18,14,16,8 chr1 183542387 . T C 2784.61 PASS AC=1;AF=0.621;AN=2;DP=2442;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant36-variant37-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:35,31:66:99:758,0,885:20,15,19,12 chr1 183617706 . G A 1117.5 PASS AC=1;AF=0.5;AN=2;DP=85;FS=1.764;FractionInformativeReads=1;MQ=60;MQRankSum=0.031;QD=13.15;ReadPosRankSum=-1.51;SOR=0.685;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:45,40:85:99:1146,0,1261:21,24,21,19 chr1 183711483 . C T 2625.17 PASS AC=1;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 0/1:35,30:65:99:752,0,871:14,21,13,17 chr1 183852914 . G C 3734.1 PASS AC=1;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 0/1:49,40:89:99:1057,0,1265:23,26,21,19 chr1 183857394 . A G 279.58 PASS AC=1;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 0/1:10,5:15:99:99,0,277:7,3,3,2 chr1 183867085 . C T 412.01 PASS AC=1;AF=0.579;AN=2;DP=850;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant10-variant13-variant14-variant16-variant18-variant19-variant22-variant23-variant28-variant36-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:23,20:43:99:602,0,710:5,18,4,16 chr1 183871637 . G A 2621.69 PASS AC=1;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 0/1:16,36:52:99:987,0,378:12,4,23,13 chr1 183873898 . A G 412.49 PASS AC=1;AF=0.528;AN=2;DP=448;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant10-variant13-variant14-variant16-variant18-variant19-variant22-variant23-variant28-variant36-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:17,19:36:99:453,0,450:13,4,13,6 chr1 183876287 . T C 850.24 PASS AC=1;AF=0.556;AN=2;DP=1272;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant10-variant14-variant16-variant18-variant19-variant22-variant23-variant28-variant36-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:43,26:69:99:589,0,1151:18,25,12,14 chr1 183876489 . C A 163.71 PASS AC=1;AF=0.529;AN=2;DP=164;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant10-variant13-variant14-variant16-variant22-variant23-variant28-variant36-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:79:228,0,79:1,2,1,6 chr1 183891159 . C G 388.95 PASS AC=1;AF=0.58;AN=2;DP=794;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant10-variant13-variant14-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant28-variant32-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,10:23:99:366,0,461:12,1,10,0 chr1 183895178 . G A 1844.96 PASS AC=1;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 0/1:33,19:52:99:474,0,902:21,12,14,5 chr1 183895721 . C A 3886.16 PASS AC=1;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 0/1:69,64:133:99:1413,0,1719:33,36,32,32 chr1 183896961 . T C 9289.99 PASS AC=1;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 0/1:123,112:235:99:2771,0,3110:59,64,49,63 chr1 183897297 . TA TAA,T 848.37 PASS AC=0,1;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 0/2:35:82:14,14,3,4 chr1 183905073 . C T 554.27 PASS AC=1;AF=0.565;AN=2;DP=1411;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant10-variant13-variant14-variant16-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,29:55:99:629,0,612:16,10,16,13 chr1 183905188 . G C 419.26 PASS AC=1;AF=0.565;AN=2;DP=1330;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant10-variant13-variant14-variant16-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:28,22:50:99:525,0,737:14,14,11,11 chr1 183906009 . A G 1105.37 PASS AC=1;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 0/1:20,13:33:99:301,0,581:9,11,8,5 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 0/1:24,18:42:99:397,0,610:12,12,10,8 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 0/1:26,22:48:99:501,0,725:11,15,10,12 chr1 183906829 . C T 468.61 PASS AC=1;AF=0.565;AN=2;DP=1256;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant10-variant13-variant14-variant16-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:37,26:63:99:616,0,915:21,16,13,13 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 0/1:40,20:60:99:433,0,977:19,21,10,10 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 0/1:40,40:80:99:991,0,949:21,19,20,20 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 0/1:34,27:61:99:781,0,990:17,17,14,13 chr1 183907344 . A T 138.09 PASS AC=1;AF=0.588;AN=2;DP=3716;set=filterInvariant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-filterInvariant31-variant32-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,41:80:99:1675,0,1603:22,17,24,17 chr1 183907345 . A T 138.05 PASS AC=1;AF=0.536;AN=2;DP=3003;set=filterInvariant-variant2-variant3-variant5-variant7-variant8-variant10-variant13-variant14-variant16-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-filterInvariant31-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:39,43:82:99:1675,0,1604:22,17,26,17 chr1 183907346 . A T,ATTTT,ATT 4020.25 PASS AC=1,0,0;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 0/1:82:99:22,18,25,17 chr1 183907670 . A G 8872.21 PASS AC=1;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 0/1:144,113:257:99:2720,0,3624:69,75,57,56 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 1/1:0,9:9:27:348,27,0:0,0,2,7 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 1/1:0,14:14:42:492,42,0:0,0,11,3 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 1/1:0,8:8:24:316,24,0:0,0,1,7 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 1/1:0,16:16:48:458,48,0:0,0,2,14 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 0/2:30:99:4,14,5,7 chr1 184041629 . C CA 77.05 PASS AC=1;AF=0.5;AN=2;DP=89;FS=0;MQ=60;set=variant-variant4-variant18-variant23-variant31-variant32-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:88:88,0,89:0,4,0,4 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 0/1:4,3:7:99:111,0,120:3,1,3,0 chr1 184591008 . A G 786.68 PASS AC=1;AF=0.5;AN=2;DP=63;FS=3.506;FractionInformativeReads=1;MQ=60;MQRankSum=1.493;QD=12.49;ReadPosRankSum=-2.057;SOR=1.246;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:33,30:63:99:815,0,823:17,16,19,11 chr1 184596584 . C A 737.31 PASS AC=1;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 0/1:33,25:58:99:615,0,861:19,14,14,11 chr1 184596806 . C G 797.92 PASS AC=1;AF=0.5;AN=2;DP=1220;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant8-variant10-variant12-variant15-variant16-variant17-variant19-variant23-variant24-variant26-variant27-variant29-variant31-variant33-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,26:40:99:814,0,305:5,9,9,17 chr1 184596854 . C T 238.78 PASS AC=1;AF=0.5;AN=2;DP=23;FS=0;FractionInformativeReads=0.913;MQ=60;MQRankSum=-0.88;QD=10.38;ReadPosRankSum=1.232;SOR=0.495;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:10,11:21:99:267,0,260:3,7,4,7 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 0/1:19,13:32:99:249,0,450:10,9,5,8 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 0/1:40,30:70:99:633,0,1096:22,18,16,14 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 0/1:52,42:94:99:964,0,1253:23,29,22,20 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 0/1:17,19:36:99:471,0,477:9,8,13,6 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 0/1:30,26:56:99:562,0,676:15,15,14,12 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 0/1:186,173:359:99:4432,0,4794:86,100,72,101 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 0/1:72,70:142:99:2044,0,2101:22,50,22,48 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 0/1:220,219:439:99:5463,0,5108:101,119,94,125 chr1 184661932 . A AG 706.56 PASS AC=1;AF=0.587;AN=2;DP=2800;set=variant2-variant4-variant7-variant8-variant9-variant10-variant11-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant26-variant29-variant31-variant32-variant33-variant34-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,36:103:99:558,0,1304:42,25,25,11 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 0/1:157,131:288:99:3154,0,4015:79,78,65,66 chr1 184663537 . A C 1181.61 PASS AC=1;AF=0.596;AN=2;DP=2173;MQ=60;set=variant2-variant4-variant7-variant8-variant9-variant10-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,30:63:99:793,0,806:12,21,12,18 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 0/1:16,20:36:99:577,0,431:4,12,9,11 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 0/1:3,11:14:37:301,0,37:1,2,2,9 chr1 184675814 . G A 1199.09 PASS AC=1;AF=0.577;AN=2;DP=4353;MQ=60;set=variant2-variant4-variant7-variant8-variant9-variant10-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,68:129:99:1716,0,1486:28,33,35,33 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 0/1:38,49:87:99:1194,0,1082:13,25,20,29 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 0/1:7,6:13:99:184,0,226:1,6,1,5 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 0/1:11,8:19:99:219,0,421:0,11,2,6 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 0/1:18,50:68:99:1638,0,469:7,11,21,29 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 0/2:16:99:3,8,1,4 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 0/1:79,92:171:99:2399,0,2000:36,43,46,46 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 0/1:141,86:227:99:1938,0,3510:77,64,51,35 chr1 184760624 . CTT CT,C,CTTT 429.46 PASS AC=0,1,0;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 0/2:155:99:31,37,38,49 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 2/1:77:99:0,1,19,57 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 0/1:5,2:7:69:69,0,153:4,1,1,1 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 0/1:25,39:64:99:1016,0,626:11,14,18,21 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 0/1:17,40:57:99:1206,0,394:8,9,21,19 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 0/1:62,54:116:99:1331,0,1732:29,33,29,25 chr1 184777079 . G A 766.68 PASS AC=1;AF=0.525;AN=2;DP=768;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant8-variant10-variant13-variant15-variant16-variant17-variant18-variant23-variant26-variant28-variant29-variant31-variant33-variant34-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,15:27:99:513,0,418:10,2,14,1 chr1 184777101 . G A 881.37 PASS AC=1;AF=0.525;AN=2;DP=1238;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant8-variant10-variant13-variant15-variant16-variant17-variant18-variant23-variant26-variant28-variant29-variant31-variant33-variant34-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,22:44:99:738,0,673:18,4,20,2 chr1 184777177 . C A 1837.14 PASS AC=1;AF=0.531;AN=2;DP=2653;MQ=60;set=variant2-variant3-variant4-variant8-variant10-variant15-variant16-variant17-variant23-variant26-variant29-variant31-variant33-variant34-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:77,65:142:99:1457,0,1765:44,33,39,26 chr1 184777467 . A T 201.67 PASS AC=1;AF=0.542;AN=2;DP=659;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant8-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant23-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:392,0,335:4,8,2,10 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 1/1:0,14:14:42:471,42,0:0,0,11,3 chr1 185014562 . C CCTCG 309.63 PASS AC=1;AF=0.5;AN=2;DP=96;MQ=60;set=variant12-variant23 GT:AD:DP:GQ:PL:SB 0/1:20,17:37:99:653,0,749:11,9,5,12 chr1 185070964 . GTT GTTTTT,GT,G,GTTTTTTTT,GTTT,GTTTTTT,GTTTT 167.51 PASS AC=0,1,0,0,0,0,0;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 0/2:40:99:12,14,1,13 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 1/1:0,10:10:30:371,30,0:0,0,1,9 chr1 185277169 . G T 563.67 PASS AC=1;AF=0.5;AN=2;DP=91;FractionInformativeReads=1;MQ=60;set=variant12-variant23 GT:AD:DP:GQ:PL:SB 0/1:24,21:45:99:499,0,630:8,16,7,14 chr1 185984517 . T C 2246.23 PASS AC=1;AF=0.581;AN=2;DP=3962;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,41:116:99:1049,0,1893:33,42,17,24 chr1 186022032 . T G 365.74 PASS AC=1;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 0/1:9,8:17:99:228,0,259:7,2,6,2 chr1 186026474 . T C 1787.88 PASS AC=1;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 0/1:69,57:126:99:1295,0,1674:34,35,29,28 chr1 186030902 . G T 62.08 PASS AC=1;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 0/1:9,7:16:99:267,0,331:9,0,6,1 chr1 186031041 . C T 752.68 PASS AC=1;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 0/1:39,44:83:99:1022,0,967:16,23,20,24 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 0/1:6,3:9:67:67,0,240:4,2,2,1 chr1 186106861 . C T 1434.45 PASS AC=1;AF=0.5;AN=2;DP=533;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant12-variant23-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:64,47:111:99:1182,0,1669:32,32,23,24 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 1/1:0,103:103:99:3217,309,0:0,0,36,67 chr1 186265948 . T A 1719.76 PASS AC=2;AF=0.742;AN=2;DP=2410;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2121,212,0:0,0,42,29 chr1 186274133 . C T 347.1 PASS AC=1;AF=0.5;AN=2;DP=123;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant17-variant22-variant23-variant28-variant31-variant36 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:151,0,198:1,5,1,4 chr1 186274157 . G T 127.69 PASS AC=1;AF=0.5;AN=2;DP=62;FS=0;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant17-variant22-variant23-variant31-variant36 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:117,0,233:0,3,0,3 chr1 186274159 . G A 127.69 PASS AC=1;AF=0.5;AN=2;DP=57;FS=0;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant17-variant22-variant23-variant31-variant36 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:117,0,233:0,3,0,3 chr1 186275760 . G A 1094.04 PASS AC=1;AF=0.5;AN=2;DP=680;MQ=60;set=variant8-variant9-variant17-variant22-variant23-variant28-variant31-variant36 GT:AD:DP:GQ:PL:SB 0/1:40,50:90:99:1380,0,1033:22,18,24,26 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 1/1:1,507:508:99:15049,1482,0:1,0,261,246 chr1 186283425 . G A 1710.63 PASS AC=1;AF=0.5;AN=2;DP=1041;set=variant8-variant9-variant17-variant22-variant23-variant28-variant31-variant36 GT:AD:DP:GQ:PL:SB 0/1:62,69:131:99:1854,0,1491:24,38,21,48 chr1 186286782 . A G 181.37 PASS AC=1;AF=0.5;AN=2;DP=129;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant17-variant22-variant23-variant28-variant31-variant36 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:192,0,199:1,5,0,5 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 0/1:3,5:8:71:201,0,71:2,1,5,0 chr1 186295021 . A G 878.33 PASS AC=1;AF=0.5;AN=2;DP=483;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant17-variant22-variant23-variant28-variant31-variant36 GT:AD:DP:GQ:PL:SB 0/1:17,38:55:99:917,0,445:7,10,16,22 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 0/1:30,27:57:99:676,0,730:10,20,14,13 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 1/1:0,27:27:80:894,80,0:0,0,7,20 chr1 186313293 . G A 319.45 PASS AC=1;AF=0.5;AN=2;DP=125;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant17-variant22-variant23-variant28-variant31-variant36 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:99:267,0,105:1,2,0,7 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 0/1:9,12:21:99:346,0,266:2,7,3,9 chr1 186316488 . C T 1025.15 PASS AC=1;AF=0.5;AN=2;DP=987;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant17-variant22-variant23-variant28-variant31-variant36 GT:AD:DP:GQ:PL:SB 0/1:72,57:129:99:1161,0,1887:36,36,31,26 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 0/1:12,10:22:99:259,0,315:8,4,7,3 chr1 186319580 . C A 91.72 PASS AC=1;AF=0.5;AN=2;DP=70;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant17-variant22-variant23-variant28-variant31-variant36 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:234,0,114:1,4,0,6 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 0/1:6,17:23:99:485,0,126:1,5,4,13 chr1 186329869 . C G 3129.35 PASS AC=2;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 1/1:0,108:108:99:3255,324,0:0,0,68,40 chr1 186330643 . T C 587.79 PASS AC=2;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 1/1:0,13:13:39:544,39,0:0,0,12,1 chr1 186330700 . A AG 913.98 PASS AC=2;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 1/1:0,56:56:99:2132,168,0:0,0,41,15 chr1 186343759 . G A 94.73 PASS AC=1;AF=0.6;AN=2;DP=39;FS=0;FractionInformativeReads=1;MQ=60;set=variant9-variant17-variant23-variant28-variant31 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:99:202,0,102:2,1,5,1 chr1 186344876 . A AG 822.17 PASS AC=1;AF=0.5;AN=2;DP=617;MQ=60;set=variant8-variant9-variant17-variant18-variant21-variant22-variant23-variant28-variant31-variant36 GT:AD:DP:GQ:PL:SB 0/1:18,27:45:99:678,0,398:10,8,14,13 chr1 186345125 . AGTGT AGTGTGTGTGTGT,AGTGTGTGTGTGTGTGT,AGTGTGTGT,AGTGTGTGTGT,AGTGTGTGTGTGTGT,AGTGTGT,A 316.69 PASS AC=0,0,0,2,0,0,0;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 4/4:8:23:0,0,3,5 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 1/1:0,27:27:81:940,81,0:0,0,21,6 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 0/1:28,41:69:99:905,0,647:16,12,22,19 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 0/1:11,17:28:99:480,0,233:4,7,5,12 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 0/1:26,17:43:99:465,0,712:8,18,4,13 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 0/1:28:99:6,13,1,8 chr1 186370598 . T TTCTG 945.06 PASS AC=2;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 1/1:0,20:20:59:754,59,0:0,0,8,12 chr1 186390303 . A C 10458.4 PASS AC=2;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 1/1:0,291:291:99:8488,870,0:0,0,138,153 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 0/1:3,6:9:68:240,0,68:1,2,1,5 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 0/1:157,120:277:99:2718,0,3885:83,74,69,51 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 0/1:66,56:122:99:1299,0,1621:35,31,30,26 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 0/1:24,20:44:99:443,0,663:8,16,7,13 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 0/1:12,7:19:99:194,0,316:5,7,2,5 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 1/1:0,87:87:99:2701,261,0:0,0,39,48 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 0/1:32,40:72:99:1043,0,857:17,15,16,24 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 1/1:1,194:195:99:6113,545,0:1,0,84,110 chr1 186643058 . A G 1980.98 PASS AC=2;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 1/1:0,155:155:99:4549,464,0:0,0,86,69 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 0/1:1,8:9:10:276,0,10:1,0,6,2 chr1 186649221 . A G 748.73 PASS AC=2;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 1/1:0,47:47:99:1366,140,0:0,0,24,23 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 0/1:11,7:18:99:208,0,329:2,9,2,5 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 0/1:19,27:46:99:1075,0,760:8,11,8,19 chr1 186876244 . A C 166.53 PASS AC=1;AF=0.5;AN=2;DP=10;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.58;QD=16.65;ReadPosRankSum=0.546;SOR=0.223;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:94:195,0,94:0,3,2,5 chr1 186901738 . TTCTTCTTTTAAAA T 520.96 PASS AC=1;AF=0.717;AN=2;DP=623;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant30-variant31-variant32-variant33-variant36-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,9:14:99:363,0,547:5,0,9,0 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 1/1:0,10:10:30:399,30,0:0,0,9,1 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 1/1:0,57:57:99:2006,170,0:0,0,11,46 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 1/1:0,10:10:30:425,30,0:0,0,9,1 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 1/1:0,18:18:54:677,54,0:0,0,14,4 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 1/1:0,28:28:84:1018,84,0:0,0,6,22 chr1 186946638 . C T 445.54 PASS AC=1;AF=0.533;AN=2;DP=292;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant9-variant11-variant19-variant23-variant24-variant25-variant27-variant33-variant34-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,8:11:99:327,0,205:3,0,8,0 chr1 186946641 . C G 445.54 PASS AC=1;AF=0.533;AN=2;DP=309;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant9-variant11-variant19-variant23-variant24-variant25-variant27-variant33-variant34-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,8:11:99:327,0,205:3,0,8,0 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 1/1:0,85:85:99:2674,255,0:0,0,29,56 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 1/1:1,63:64:99:2051,165,0:0,1,25,38 chr1 187610698 . C A 3224.98 PASS AC=2;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 1/1:0,121:121:99:3578,360,0:0,0,68,53 chr1 187610777 . C G 1459.08 PASS AC=2;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 1/1:0,140:140:99:4244,418,0:0,0,70,70 chr1 187610852 . A T,C 538.32 PASS AC=0,2;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 2/2:133:99:0,0,59,74 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 0/1:35,36:71:99:1102,0,998:25,10,29,7 chr1 190446806 . G C 119.43 PASS AC=1;AF=0.625;AN=2;DP=100;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant12-variant14-variant15-variant17-variant23-variant32-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:70:70,0,159:1,4,1,2 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 1/1:0,32:32:96:982,96,0:0,0,19,13 chr1 190760788 . C T 177.17 PASS AC=1;AF=0.55;AN=2;DP=112;FractionInformativeReads=1;MQ=60;set=variant-variant10-variant13-variant15-variant18-variant19-variant23-variant28-variant32-variant41 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:71:198,0,71:1,2,1,4 chr1 190769033 . T C 267.8 PASS AC=1;AF=0.5;AN=2;DP=350;MQ=60;set=variant-variant13-variant15-variant19-variant23-variant28-variant32-variant41 GT:AD:DP:GQ:PL:SB 0/1:23,29:52:99:594,0,464:10,13,13,16 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 0/1:4:14:0,2,0,2 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 0/1:84,65:149:99:1432,0,1910:37,47,30,35 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 0/1:12,9:21:99:250,0,273:8,4,6,3 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 0/1:5,5:10:99:187,0,157:4,1,5,0 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 1/1:0,10:10:30:267,30,0:0,0,10,0 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 1/1:0,26:26:78:966,78,0:0,0,22,4 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 1/1:0,27:27:81:1093,81,0:0,0,3,24 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 0/1:133,138:271:99:3431,0,3261:72,61,71,67 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 0/1:36,40:76:99:1118,0,1006:9,27,10,30 chr1 192606617 . A C 689.04 PASS AC=1;AF=0.531;AN=2;DP=487;MQ=60;set=variant-variant2-variant4-variant5-variant10-variant13-variant18-variant19-variant20-variant23-variant29-variant31-variant32-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:5,9:14:99:316,0,187:5,0,8,1 chr1 192629379 . A T 449.08 PASS AC=1;AF=0.5;AN=2;DP=60;FractionInformativeReads=1;MQ=60;set=variant5-variant23 GT:AD:DP:GQ:PL:SB 0/1:20,10:30:99:238,0,550:6,14,5,5 chr1 192779227 . T A 275.3 PASS AC=1;AF=0.647;AN=2;DP=180;FractionInformativeReads=1;MQ=60;set=variant3-variant12-variant13-variant15-variant16-variant20-variant21-variant22-variant23-variant28-variant29-variant33-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:114,0,140:4,0,3,2 chr1 192780088 . GCT G 6791.32 PASS AC=1;AF=0.625;AN=2;DP=2275;set=variant3-variant12-variant13-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant33-variant34-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,52:101:99:1917,0,1803:28,21,29,23 chr1 192780337 . CAA C 862.91 PASS AC=1;AF=0.632;AN=2;DP=214;MQ=60;set=variant3-variant12-variant13-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant33-variant34-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:117,0,124:0,3,1,2 chr1 192781172 . C G 18104 PASS AC=1;AF=0.625;AN=2;DP=9977;MQ=60;set=variant3-variant12-variant13-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant28-variant29-variant30-variant33-variant34-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:222,202:424:99:5034,0,5344:102,120,99,103 chr1 193045198 . 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=0.406;SOR=0.693;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:117,0,119:0,3,0,3 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 1/1:0,17:17:51:556,51,0:0,0,11,6 chr1 193054154 . G A 1900.18 PASS AC=1;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 0/1:42,38:80:99:885,0,1063:19,23,16,22 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 1/1:0,412:412:99:12210,1232,0:0,0,232,180 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 1/1:0,25:25:75:852,75,0:0,0,7,18 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 1/1:4,71:75:99:1847,112,0:3,1,35,36 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 1/1:0,118:118:99:4066,352,0:0,0,56,62 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 1/1:0,7:7:21:215,21,0:0,0,5,2 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 1/1:0,79:79:99:2523,236,0:0,0,40,39 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 1/1:0,242:242:99:10558,746,0:0,0,120,122 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 1/1:0,240:240:99:9970,759,0:0,0,117,123 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 1/1:0,205:205:99:6098,612,0:0,0,104,101 chr1 193091319 . A AG 1350.25 PASS AC=1;AF=0.5;AN=2;DP=155;FS=2.963;FractionInformativeReads=0.948;MQ=60;MQRankSum=-0.002;QD=8.71;ReadPosRankSum=-0.295;SOR=0.949;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:83,64:147:99:1388,0,2032:41,42,36,28 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 1/1:0,25:25:75:1078,75,0:0,0,3,22 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 1/1:0,5:5:15:216,15,0:0,0,0,5 chr1 193111228 . TGA T 164.7 PASS AC=1;AF=0.5;AN=2;DP=478;MQ=60;set=filterInvariant4-variant12-filterInvariant15-filterInvariant23-variant25-filterInvariant31-filterInvariant39 GT:AD:DP:GQ:PL:SB 0/1:42,7:49:99:113,0,1360:7,35,3,4 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 1/1:0,3:3:9:132,9,0:0,0,1,2 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 1/1:0,84:84:99:2574,251,0:0,0,53,31 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 0/1:10,17:27:99:506,0,248:7,3,12,5 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 1/1:0,83:83:99:2492,248,0:0,0,34,49 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 1/1:0,36:36:99:1126,108,0:0,0,11,25 chr1 196251522 . T C 171.18 PASS AC=2;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 1/1:0,29:29:87:896,87,0:0,0,10,19 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 1/1:0,26:26:78:1032,78,0:0,0,3,23 chr1 196397208 . A G 1217.88 PASS AC=1;AF=0.5;AN=2;DP=104;FS=1.685;FractionInformativeReads=1;MQ=60;MQRankSum=-1.245;QD=11.71;ReadPosRankSum=-0.79;SOR=0.476;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:52,52:104:99:1246,0,1401:36,16,33,19 chr1 196398619 . T C 299.27 PASS AC=1;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 0/1:12,11:23:99:419,0,480:12,0,11,0 chr1 196398974 . T A 146.83 PASS AC=1;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 0/1:11,7:18:99:220,0,334:2,9,1,6 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 1/1:0,13:13:39:557,39,0:0,0,0,13 chr1 196642072 . C T 957.22 PASS AC=1;AF=0.571;AN=2;DP=1321;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant10-variant14-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant27-variant28-variant29-variant32-variant34-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:28,26:54:99:640,0,813:19,9,16,10 chr1 196642233 . G A 2320.35 PASS AC=1;AF=0.571;AN=2;DP=2723;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant10-variant14-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant27-variant28-variant29-variant32-variant34-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:83,56:139:99:1164,0,1985:38,45,24,32 chr1 196642969 . C CTT 2365.56 PASS AC=1;AF=0.526;AN=2;DP=2007;MQ=60;set=variant4-variant7-variant10-variant14-variant16-variant17-variant20-variant23-variant24-variant25-variant27-variant28-variant29-variant32-variant34-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:71,53:124:99:1657,0,2179:40,31,32,21 chr1 196654324 . A C 2151.96 PASS AC=1;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 0/1:123,109:232:99:2585,0,2975:63,60,51,58 chr1 196658497 . G T 62.35 PASS AC=1;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 0/1:4,10:14:95:286,0,95:3,1,7,3 chr1 196658905 . G A 280.9 PASS AC=1;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 0/1:3,3:6:58:109,0,58:1,2,0,3 chr1 196659237 . C T 527.58 PASS AC=1;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 0/1:49,35:84:99:753,0,1436:33,16,20,15 chr1 196670757 . C T 125.25 PASS AC=1;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 0/1:2,4:6:63:118,0,63:0,2,1,3 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 0/1:43,38:81:99:856,0,977:23,20,23,15 chr1 196684625 . G T 395.07 PASS AC=1;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 0/1:16,14:30:99:412,0,545:14,2,11,3 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 0/1:96,19:115:99:542,0,5417:58,38,13,6 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 0/1:108,25:133:99:623,0,5703:64,44,16,9 chr1 196794519 . C T 377.93 PASS AC=1;AF=0.795;AN=2;DP=141;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant27-variant28-variant31-variant32-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:76:76,0,119:3,0,2,1 chr1 196795849 . A G 611.51 PASS AC=1;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 0/1:14,12:26:99:352,0,334:7,7,10,2 chr1 196796184 . G A 998.15 PASS AC=1;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 0/1:45,28:73:99:633,0,1042:17,28,15,13 chr1 196796240 . T A 532.27 PASS AC=1;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 0/1:16,21:37:99:497,0,450:3,13,8,13 chr1 196797123 . C T 409.13 PASS AC=1;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 0/1:18,16:34:99:345,0,397:12,6,10,6 chr1 196797238 . C T 366.36 PASS AC=1;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 0/1:50,5:55:59:59,0,2892:28,22,0,5 chr1 196801042 . G T 1276.34 PASS AC=1;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 0/1:79,70:149:99:1541,0,2015:45,34,34,36 chr1 196801078 . A T 1107.45 PASS AC=1;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 0/1:79,65:144:99:1385,0,1931:39,40,30,35 chr1 196801190 . C A 319.26 PASS AC=1;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 0/1:34,15:49:99:335,0,1061:8,26,4,11 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 1/1:0,79:79:99:2398,237,0:0,0,47,32 chr1 196876458 . A G 1659.8 PASS AC=2;AF=0.694;AN=2;DP=6190;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,159:160:99:4790,443,0:1,0,103,56 chr1 196887457 . G A 2382.92 PASS AC=1;AF=0.5;AN=2;DP=1178;set=variant9-variant12-variant13-variant20-variant23-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,72:153:99:1686,0,2054:42,39,39,33 chr1 196920148 . C T 1077.64 PASS AC=1;AF=0.528;AN=2;DP=1318;set=variant4-variant7-variant10-variant14-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant28-variant29-variant31-variant32-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,30:73:99:678,0,973:20,23,13,17 chr1 196967458 . G T 775.76 PASS AC=1;AF=0.5;AN=2;DP=716;FractionInformativeReads=1;MQ=60;set=variant4-variant14-variant17-variant19-variant21-variant23-variant25-variant28-variant29-variant31-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,28:49:99:737,0,540:7,14,10,18 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 0/1:93,100:193:99:2348,0,2363:43,50,47,53 chr1 197008597 . A C 1046.95 PASS AC=2;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 1/1:0,86:86:99:2636,258,0:0,0,36,50 chr1 197009798 . A G 865.92 PASS AC=2;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 1/1:0,70:70:99:2122,210,0:0,0,36,34 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 1/1:0,6:6:18:259,18,0:0,0,0,6 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 1/1:0,33:33:99:1064,99,0:0,0,10,23 chr1 197030237 . CT C 75.73 PASS AC=2;AF=0.731;AN=2;DP=75;MQ=60;set=variant4-variant10-variant12-variant16-variant17-variant19-variant20-variant21-variant23-variant29-variant31-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:128,12,0:0,0,1,3 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 1/1:0,80:80:99:2291,240,0:0,0,39,41 chr1 197053141 . T C 46.27 PASS AC=1;AF=0.563;AN=2;DP=41;FS=0;FractionInformativeReads=1;MQ=60;set=variant4-variant19-variant21-variant23-variant25-variant29-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:156,0,116:3,0,4,0 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 1/1:0,83:83:99:2465,249,0:0,0,45,38 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 1/1:0,79:79:99:2314,236,0:0,0,43,36 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 1/1:0,10:10:30:444,30,0:0,0,10,0 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 1/1:0,13:13:39:520,39,0:0,0,12,1 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 1/1:0,31:31:92:955,92,0:0,0,22,9 chr1 197070521 . C G 1035.93 PASS AC=1;AF=0.5;AN=2;DP=389;FractionInformativeReads=1;MQ=60;set=variant4-variant14-variant19-variant23-variant25-variant29 GT:AD:DP:GQ:PL:SB 0/1:29,26:55:99:711,0,728:12,17,14,12 chr1 197070776 . C T 2243 PASS AC=1;AF=0.5;AN=2;DP=2047;FractionInformativeReads=1;MQ=60;set=variant4-variant14-variant17-variant19-variant21-variant23-variant25-variant28-variant29-variant31-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,54:127:99:1481,0,1801:37,36,33,21 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 1/1:0,134:134:99:4248,401,0:0,0,65,69 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 1/1:0,105:105:99:3514,314,0:0,0,43,62 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 1/1:1,124:125:99:3816,333,0:1,0,70,54 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 0/1:26,28:54:99:723,0,660:18,8,18,10 chr1 197101621 . T C 136.65 PASS AC=2;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 1/1:0,6:6:18:249,18,0:0,0,0,6 chr1 197102745 . A G 3269.82 PASS AC=1;AF=0.5;AN=2;DP=3048;MQ=60;set=variant4-variant14-variant17-variant19-variant21-variant23-variant25-variant28-variant29-variant31-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:102,82:184:99:2057,0,2644:46,56,31,51 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 1/1:0,77:77:99:2428,229,0:0,0,25,52 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 1/1:0,4:4:12:143,12,0:0,0,3,1 chr1 197108946 . A G 689.6 PASS AC=1;AF=0.5;AN=2;DP=187;MQ=60;set=variant9-variant12-variant23 GT:AD:DP:GQ:PL:SB 0/1:36,38:74:99:883,0,905:17,19,16,22 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 1/1:0,17:17:51:718,51,0:0,0,1,16 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 1/1:2,170:172:99:5264,467,0:1,1,76,94 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 1/1:0,33:33:99:1029,99,0:0,0,19,14 chr1 197128726 . G A 3221.53 PASS AC=1;AF=0.5;AN=2;DP=2913;MQ=60;set=variant4-variant14-variant17-variant19-variant21-variant23-variant25-variant28-variant29-variant31-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:131,107:238:99:2417,0,3139:67,64,56,51 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 1/1:0,32:32:96:1160,96,0:0,0,19,13 chr1 197141253 . A C 206.37 PASS AC=1;AF=0.5;AN=2;DP=369;MQ=60;set=variant4-variant14-variant17-variant19-variant23-variant25-variant28-variant29-variant31-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:18,16:34:99:371,0,453:10,8,9,7 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 0/1:6,9:15:99:316,0,229:4,2,8,1 chr1 197316435 . T C 4138.84 PASS AC=1;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 0/1:60,52:112:99:1425,0,1433:36,24,37,15 chr1 197325908 . T G 3496.87 PASS AC=1;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 0/1:53,34:87:99:837,0,1355:32,21,18,16 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 1/1:0,115:115:99:3447,344,0:0,0,62,53 chr1 197398086 . A G 1035.61 PASS AC=1;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 0/1:25,32:57:99:822,0,546:13,12,18,14 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 1/1:0,211:211:99:6446,631,0:0,0,99,112 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 1/1:0,241:241:99:7477,722,0:0,0,116,125 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 1/1:0,291:291:99:9280,872,0:0,0,150,141 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 1/1:0,52:52:99:1906,156,0:0,0,16,36 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 1/1:0,215:215:99:6576,644,0:0,0,108,107 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 1/1:0,209:209:99:6607,626,0:0,0,113,96 chr1 197410789 . CTTTTTT CTTTTTTT,CTTTTT,CTTTT,CTTTTTTTTTTTTTTTTTTTTTT,CTTTTTTTT,C 32.5 PASS AC=1,0,0,0,0,0;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 0/1:12:15:0,4,3,5 chr1 197412029 . C T 810.22 PASS AC=1;AF=0.638;AN=2;DP=1192;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant11-variant15-variant16-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,16:27:99:614,0,418:1,10,0,16 chr1 197412251 . TAA TA,T 127.49 PASS AC=2,0;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 1/1:15:1:2,0,12,1 chr1 197412976 . C T 1918.1 PASS AC=1;AF=0.633;AN=2;DP=3504;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant15-variant16-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,49:102:99:1269,0,1424:37,16,36,13 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 1/1:0,346:346:99:10698,1036,0:0,0,184,162 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 1/1:9:29:0,0,1,8 chr1 197446702 . G T 604.15 PASS AC=1;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 0/1:34,34:68:99:784,0,927:20,14,19,15 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 1/1:0,127:127:99:3378,379,0:0,0,63,64 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 1/1:1,155:156:99:5427,432,0:1,0,67,88 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 1/1:2,196:198:99:6501,556,0:2,0,92,104 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 1/1:0,176:176:99:7908,535,0:0,0,87,89 chr1 197475055 . CAATCT C 4967.96 PASS AC=2;AF=0.977;AN=2;DP=5619;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:4188,284,0:0,0,35,59 chr1 197475085 . T C 3400.05 PASS AC=2;AF=0.977;AN=2;DP=4691;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:3031,269,0:0,0,37,53 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 1/1:0,214:214:99:6396,641,0:0,0,94,120 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 1/1:2,420:422:99:12620,1214,0:1,1,211,209 chr1 197477448 . C T 4626.98 PASS AC=1;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 0/1:180,139:319:99:3172,0,4450:85,95,55,84 chr1 197477498 . G A 2530.83 PASS AC=1;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 0/1:111,95:206:99:2169,0,2876:48,63,37,58 chr1 197478756 . ATT AT,A 371.25 PASS AC=2,0;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 1/1:42:48:2,2,26,12 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 1/1:0,274:274:99:8333,819,0:0,0,115,159 chr1 197480927 . C T 1041.95 PASS AC=1;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 0/1:50,34:84:99:697,0,1228:28,22,20,14 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 1/1:0,9:9:27:384,27,0:0,0,1,8 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 1/1:0,23:23:69:870,69,0:0,0,16,7 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 1/1:0,8:8:24:354,24,0:0,0,0,8 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 1/1:0,4:4:13:181,13,0:0,0,0,4 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 1/1:0,9:9:27:338,27,0:0,0,8,1 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 1/1:0,40:40:99:1279,120,0:0,0,28,12 chr1 197515981 . T C 567.57 PASS AC=1;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 0/1:13,14:27:99:398,0,386:3,10,4,10 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 1/1:2,325:327:99:9557,943,0:1,1,177,148 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 1/1:0,57:57:99:2044,171,0:0,0,19,38 chr1 197704717 . C T 1443.03 PASS AC=1;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 0/1:79,49:128:99:1229,0,2180:51,28,31,18 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 1/1:0,64:64:99:1696,192,0:0,0,41,23 chr1 197742171 . C T 621.07 PASS AC=1;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 0/1:10,11:21:99:344,0,335:1,9,2,9 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 0/1:57,57:114:99:1431,0,1585:20,37,21,36 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 0/1:59,51:110:99:1159,0,1236:31,28,28,23 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 1/1:0,186:186:99:5474,558,0:0,0,95,91 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 0/1:23,31:54:99:939,0,653:15,8,18,13 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 0/1:30,33:63:99:1003,0,774:11,19,14,19 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 0/1:22,34:56:99:998,0,668:18,4,25,9 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 0/1:12,9:21:99:209,0,410:10,2,5,4 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 1/1:0,304:304:99:9295,910,0:0,0,142,162 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 0/1:105,103:208:99:2672,0,2711:44,61,44,59 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 0/1:80,102:182:99:2758,0,2027:30,50,36,66 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 0/1:171,160:331:99:3824,0,3991:98,73,96,64 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 0/1:47,50:97:99:1459,0,1288:17,30,18,32 chr1 197902871 . CAAA CA,C,CAA,CAAAAA 110.71 PASS AC=1,0,1,0;AF=0.693,0.08,0.068,0.011;AN=2;DP=1778;set=Intersection GT:DP:GQ:SB 1/3:29:99:1,1,10,17 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 0/1:91,75:166:99:1869,0,2285:49,42,41,34 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 0/1:97,77:174:99:1873,0,2486:54,43,39,38 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 0/1:33,33:66:99:782,0,757:7,26,10,23 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 0/1:18,14:32:99:372,0,558:3,15,4,10 chr1 198701289 . T C 106.77 PASS AC=2;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 1/1:0,2:2:6:90,6,0:0,0,1,1 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 0/1:32:99:4,6,9,13 chr1 200080462 . A AT 264.5 PASS AC=1;AF=0.5;AN=2;DP=759;set=variant4-variant6-filterInvariant8-variant14-filterInvariant16-variant18-variant22-variant23-filterInvariant24-variant25-variant26-filterInvariant28-variant37-filterInvariant38-variant39-variant40-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:23,17:40:99:277,0,404:11,12,6,11 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 0/1:17,21:38:99:331,0,284:6,11,11,10 chr1 200080464 . C A,CAA 531.3 PASS AC=1,0;AF=0.417,0.125;AN=2;DP=974;set=variant4-variant6-variant8-variant12-variant14-filterInvariant15-variant16-variant17-variant18-variant21-variant22-variant23-filterInvariant24-variant25-variant26-filterInvariant28-variant36-variant37-filterInvariant38-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:42:99:8,9,11,14 chr1 200089872 . C T 434.79 PASS AC=2;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 1/1:0,61:61:99:2140,183,0:0,0,46,15 chr1 200090120 . G A 659.77 PASS AC=2;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 1/1:0,71:71:99:2265,213,0:0,0,26,45 chr1 200090219 . C T 179.63 PASS AC=2;AF=0.633;AN=2;DP=457;FractionInformativeReads=1;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-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:753,51,0:0,0,0,17 chr1 200143064 . CTTTTT CTTTT,CT,CTTT,C 107.95 PASS AC=1,0,0,0;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 0/1:16:75:6,3,5,2 chr1 200143281 . C T 1027.05 PASS AC=2;AF=0.571;AN=2;DP=2929;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant11-variant13-variant14-variant16-variant18-variant19-variant23-variant24-variant25-variant26-variant33-variant36-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,110:110:99:3454,330,0:0,0,56,54 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 1/1:0,29:29:93:1317,93,0:0,0,19,10 chr1 200182664 . C T 402.72 PASS AC=2;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 1/1:0,34:34:99:1408,102,0:0,0,22,12 chr1 200182703 . GGAGGACGCCGGAGAGGAGGCCGGA G 1354.23 PASS AC=2;AF=0.588;AN=2;DP=1065;MQ=60;set=variant2-variant7-variant8-variant10-variant13-variant15-variant16-variant20-variant23-variant25-variant29-variant32-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1715,117,0:0,0,28,10 chr1 200182834 . A G 538.45 PASS AC=2;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 1/1:0,118:118:99:3669,354,0:0,0,67,51 chr1 200183398 . C A 460.73 PASS AC=2;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 1/1:0,78:78:99:2560,234,0:0,0,29,49 chr1 200183460 . C T 175.33 PASS AC=2;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 1/1:0,43:43:99:1411,127,0:0,0,12,31 chr1 200311674 . C A 294.97 PASS AC=2;AF=0.635;AN=2;DP=988;set=variant2-variant5-variant6-variant7-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant27-variant29-variant30-variant32-variant33-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,41:41:99:1207,123,0:0,0,26,15 chr1 200311868 . C G 1136.92 PASS AC=2;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 1/1:0,85:85:99:2619,254,0:0,0,39,46 chr1 200311910 . T A 840.98 PASS AC=2;AF=0.583;AN=2;DP=2079;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant27-variant29-variant30-variant32-variant33-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2177,209,0:0,0,30,40 chr1 200312546 . CAA CA,C 254 PASS AC=2,0;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 1/1:16:47:0,0,3,13 chr1 200342484 . T TA,TAA 106.64 PASS AC=2,0;AF=0.776,0.034;AN=2;DP=287;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant18-variant19-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant36-variant37-variant38-variant41-variant43 GT:DP:GQ:SB 1/1:5:15:0,0,1,4 chr1 200342825 . C A 443.99 PASS AC=2;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 1/1:0,36:36:99:1076,108,0:0,0,23,13 chr1 200343081 . A G 214.46 PASS AC=2;AF=0.605;AN=2;DP=239;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant11-variant12-variant13-variant16-variant17-variant20-variant21-variant22-variant23-variant29-variant32-variant33-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:513,36,0:0,0,6,6 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 1/1:0,259:259:99:7604,775,0:0,0,130,129 chr1 200521291 . TTTC T 2272.78 PASS AC=2;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 1/1:0,113:113:99:4865,340,0:0,0,48,65 chr1 200521412 . G A 1512.57 PASS AC=2;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 1/1:0,101:101:99:3324,303,0:0,0,53,48 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 1/1:0,18:18:55:700,55,0:0,0,2,16 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 1/1:13:42:0,0,1,12 chr1 200522269 . G A 228.07 PASS AC=2;AF=0.743;AN=2;DP=563;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:570,39,0:0,0,13,0 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 1/1:0,51:51:99:1572,152,0:0,0,34,17 chr1 200522566 . G C 1447.42 PASS AC=2;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 1/1:0,113:113:99:3430,338,0:0,0,58,55 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 1/1:0,6:6:18:213,18,0:0,0,5,1 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 1/1:0,124:124:99:3612,371,0:0,0,71,53 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 1/1:0,22:22:65:616,65,0:0,0,15,7 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 1/1:0,12:12:36:447,36,0:0,0,2,10 chr1 200550243 . GAAAAAAA GAAAAAAAAAA,GAAAAAAAAA,GAAAAAAAAAAAAAAAAAA,GAAAAAAAA,G,GAAAAAAAAAAAAA,GAAAAAAAAAAAAAA,GAAAAAAAAAAAA 184.51 PASS AC=2,0,0,0,0,0,0,0;AF=0.25,0.182,0.023,0.068,0.091,0.023,0.068,0.023;AN=2;DP=151;FS=0;set=variant-variant4-variant5-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant28-variant33-variant36-variant37-variant39-variant41-variant42 GT:DP:GQ:SB 1/1:3:12:0,0,3,0 chr1 200555482 . C T 80.65 PASS AC=2;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 1/1:0,16:16:48:592,48,0:0,0,3,13 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 1/1:0,92:92:99:2738,275,0:0,0,44,48 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 1/1:0,56:56:99:1838,167,0:0,0,32,24 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 1/1:0,42:42:99:1377,126,0:0,0,13,29 chr1 200589813 . C A 383.39 PASS AC=2;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 1/1:0,48:48:99:1498,143,0:0,0,21,27 chr1 200593402 . A G 491.07 PASS AC=2;AF=0.583;AN=2;DP=246;FractionInformativeReads=1;MQ=60;set=variant11-variant15-variant19-variant23-variant29-variant33 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:634,72,0:0,0,12,12 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 1/1:0,35:35:99:1319,105,0:0,0,5,30 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 1/1:0,39:39:99:1171,117,0:0,0,23,16 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 1/1:0,13:13:39:579,39,0:0,0,13,0 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 1/1:0,43:43:99:1442,129,0:0,0,32,11 chr1 200638847 . A G 334.7 PASS AC=2;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 1/1:0,38:38:99:1156,114,0:0,0,23,15 chr1 200639040 . CGGAGCGTAGA C 355.37 PASS AC=2;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 1/1:0,64:64:99:2852,193,0:0,0,32,32 chr1 200639156 . G A 96.25 PASS AC=2;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 1/1:0,15:15:45:558,45,0:0,0,7,8 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 1/1:0,23:23:69:800,69,0:0,0,6,17 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 1/1:0,18:18:54:766,54,0:0,0,14,4 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 0/1:24,26:50:99:577,0,516:8,16,10,16 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 0/1:11,4:15:99:135,0,1167:9,2,3,1 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 0/1:11,4:15:99:135,0,1167:9,2,3,1 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 0/1:11,4:15:99:135,0,1167:9,2,3,1 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 0/1:9,24:33:99:933,0,573:7,2,16,8 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 0/1:9,24:33:99:933,0,573:7,2,16,8 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 0/1:51,47:98:99:1303,0,1599:15,36,19,28 chr1 200864267 . T C 773.09 PASS AC=2;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 1/1:0,9:9:26:209,26,0:0,0,5,4 chr1 200868493 . GTGTGTGTGCA G 631.85 PASS AC=2;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 1/1:0,18:18:54:776,54,0:0,0,9,9 chr1 200876788 . T TA,TAA 355.64 PASS AC=1,1;AF=0.147,0.471;AN=2;DP=405;MQ=60;set=variant2-variant5-variant7-variant11-variant12-variant14-variant16-variant20-variant22-variant23-variant29-filterInvariant32-variant33-variant34-variant38-variant43-variant44 GT:DP:GQ:SB 1/2:23:99:0,0,16,7 chr1 200877850 . T G 249.53 PASS AC=2;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 1/1:0,23:23:69:778,69,0:0,0,13,10 chr1 200878727 . G A 368.9 PASS AC=2;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 1/1:0,9:9:27:353,27,0:0,0,2,7 chr1 200881392 . C T 581.77 PASS AC=2;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 1/1:0,57:57:99:1742,171,0:0,0,21,36 chr1 200884909 . G GGTGTGTGTGT,GGTGT,GGTGTGTGT,GGT,GGTGTGT 52.73 PASS AC=0,0,0,2,0;AF=0.133,0.2,0.267,0.267,0.133;AN=2;DP=86;FS=0;MQRankSum=0.727;ReadPosRankSum=-0.727;set=variant-variant2-variant3-variant6-variant11-variant12-variant13-variant17-variant21-variant22-variant23-variant27-variant32-variant36-variant43 GT:DP:GQ:SB 4/4:4:14:0,0,2,2 chr1 200884943 . C T 41.09 PASS AC=2;AF=0.938;AN=2;DP=44;FS=0;MQRankSum=0.736;ReadPosRankSum=0.736;set=variant16-variant17-variant22-variant23-variant27-variant28-variant33-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:225,15,0:0,0,2,3 chr1 200884945 . C T 41.09 PASS AC=2;AF=0.875;AN=2;DP=21;FS=0;MQRankSum=0.736;ReadPosRankSum=0.736;set=variant16-variant23-variant28-variant33 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:225,15,0:0,0,2,3 chr1 200884985 . C T 196.77 PASS AC=2;AF=0.786;AN=2;DP=30;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant12-variant23-variant33-variant38-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:139,12,0:0,0,1,3 chr1 200939642 . C T 897.13 PASS AC=2;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 1/1:0,35:35:99:1142,105,0:0,0,13,22 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 1/1:0,93:93:99:2801,278,0:0,0,48,45 chr1 200942385 . G A 1306.31 PASS AC=2;AF=0.583;AN=2;DP=514;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant16-variant23-variant29-variant33 GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2189,212,0:0,0,37,34 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 1/1:0,46:46:99:2062,139,0:0,0,30,16 chr1 200957697 . A G 329.79 PASS AC=2;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 1/1:0,15:15:45:603,45,0:0,0,12,3 chr1 200960307 . G A 368.41 PASS AC=2;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 1/1:0,16:16:48:609,48,0:0,0,3,13 chr1 200965601 . G A 830.74 PASS AC=2;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 1/1:0,57:57:99:1738,171,0:0,0,23,34 chr1 200967490 . A G 117.84 PASS AC=2;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 1/1:0,26:26:78:891,78,0:0,0,18,8 chr1 201008582 . T TG 151.64 PASS AC=2;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 1/1:0,8:8:24:261,24,0:0,0,8,0 chr1 201009182 . A G 685.07 PASS AC=1;AF=0.591;AN=2;DP=1017;MQ=60;set=variant-variant10-variant15-variant17-variant19-variant22-variant23-variant26-variant27-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:35,56:91:99:1464,0,882:12,23,19,37 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 0/1:26,30:56:99:757,0,602:12,14,18,12 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 1/1:0,36:36:99:1250,108,0:0,0,9,27 chr1 201010862 . T C 337.64 PASS AC=2;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 1/1:0,22:22:66:813,66,0:0,0,4,18 chr1 201012247 . C T 377.4 PASS AC=1;AF=0.643;AN=2;DP=149;FractionInformativeReads=1;MQ=60;set=variant15-variant17-variant22-variant23-variant26-variant27-variant38 GT:AD:DP:GQ:PL:SB 0/1:7,12:19:99:379,0,221:6,1,10,2 chr1 201016646 . C T 977.41 PASS AC=1;AF=0.545;AN=2;DP=1021;MQ=60;set=variant-variant10-variant15-variant17-variant19-variant22-variant23-variant26-variant27-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:38,27:65:99:833,0,1007:24,14,20,7 chr1 201017687 . C CT 1008.95 PASS AC=1;AF=0.6;AN=2;DP=1116;MQ=60;set=variant-variant10-variant15-variant17-variant19-variant22-variant23-variant26-variant27-variant38 GT:AD:DP:GQ:PL:SB 0/1:42,54:96:99:1743,0,1278:27,15,26,28 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 0/1:31,42:73:99:1128,0,770:21,10,24,18 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 0/1:5,4:9:99:112,0,160:1,4,1,3 chr1 201021619 . C G 323.43 PASS AC=1;AF=0.563;AN=2;DP=533;MQ=60;set=variant-variant10-variant14-variant15-variant17-variant19-variant22-variant23-variant25-variant26-variant27-variant30-variant31-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:17,13:30:99:388,0,655:16,1,12,1 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 0/1:11,12:23:99:464,0,402:0,11,0,12 chr1 201038687 . A G 1054.56 PASS AC=2;AF=0.633;AN=2;DP=2567;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2459,228,0:0,0,27,49 chr1 201042618 . G A 389.72 PASS AC=1;AF=0.667;AN=2;DP=651;MQ=60;set=variant3-variant5-variant9-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,6:21:99:171,0,437:12,3,6,0 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 0/1:19,8:27:99:142,0,389:8,11,8,0 chr1 201044748 . A G 2400.4 PASS AC=2;AF=0.782;AN=2;DP=7390;set=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-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,160:160:99:4581,480,0:0,0,75,85 chr1 201046025 . G T 1173.68 PASS AC=1;AF=0.5;AN=2;DP=1013;MQ=60;set=variant5-variant14-variant15-variant23-variant25-variant30-variant32 GT:AD:DP:GQ:PL:SB 0/1:70,58:128:99:1222,0,1793:35,35,32,26 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 0/1:33,47:80:99:1135,0,815:20,13,27,20 chr1 201047075 . A G 830.63 PASS AC=2;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 1/1:0,92:92:99:3497,276,0:0,0,55,37 chr1 201047111 . A G 938.57 PASS AC=1;AF=0.583;AN=2;DP=3187;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant27-variant28-variant29-variant33-variant34-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:78,54:132:99:1151,0,1819:45,33,26,28 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 0/1:21,33:54:99:957,0,632:18,3,25,8 chr1 201052310 . A T 4065.59 PASS AC=1;AF=0.583;AN=2;DP=5148;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant27-variant28-variant29-variant33-variant34-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:114,89:203:99:3331,0,5338:65,49,57,32 chr1 201052312 . A C 4059.6 PASS AC=1;AF=0.583;AN=2;DP=5245;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant27-variant28-variant29-variant33-variant34-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:122,91:213:99:3331,0,5338:67,55,57,34 chr1 201052474 . T C 1816.92 PASS AC=1;AF=0.583;AN=2;DP=3828;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant27-variant28-variant29-variant33-variant34-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:68,64:132:99:1687,0,1662:27,41,21,43 chr1 201052562 . G T 496.81 PASS AC=1;AF=0.583;AN=2;DP=749;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant27-variant28-variant29-variant33-variant34-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,19:29:99:619,0,283:2,8,2,17 chr1 201060865 . G A 1312.17 PASS AC=1;AF=0.615;AN=2;DP=3837;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant13-variant15-variant16-variant17-variant18-variant19-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant34-variant36-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,61:100:99:1654,0,967:15,24,28,33 chr1 201079458 . T A 347.27 PASS AC=2;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 1/1:0,72:72:99:2161,214,0:0,0,26,46 chr1 201081283 . AC A,ACC 525.29 PASS AC=2,0;AF=0.5,0.063;AN=2;DP=817;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant11-variant15-variant17-variant18-variant20-variant21-variant23-variant30-variant33-variant39-variant41 GT:DP:GQ:SB 1/1:45:99:0,0,33,12 chr1 201083343 . A G 754.73 PASS AC=2;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 1/1:0,77:77:99:2672,231,0:0,0,35,42 chr1 201083506 . A G 1267.92 PASS AC=2;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 1/1:0,117:117:99:3750,349,0:0,0,59,58 chr1 201083886 . C G 1564.03 PASS AC=2;AF=0.533;AN=2;DP=2636;MQ=60;set=variant-variant4-variant6-variant7-variant11-variant15-variant17-variant18-variant20-variant21-variant23-variant30-variant33-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,169:169:99:4725,507,0:0,0,80,89 chr1 201096383 . A G 565.45 PASS AC=2;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 1/1:0,24:24:72:907,72,0:0,0,10,14 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 0/1:20,7:27:98:98,0,570:9,11,4,3 chr1 201112981 . A G 2086.61 PASS AC=1;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 0/1:48,59:107:99:1432,0,1176:29,19,31,28 chr1 201113118 . A G 1724.33 PASS AC=1;AF=0.932;AN=2;DP=4962;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:78,48:126:99:1077,0,1772:32,46,19,29 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 0/1:102,65:167:99:1399,0,2721:51,51,32,33 chr1 201116018 . C G 1234.79 PASS AC=1;AF=0.932;AN=2;DP=2556;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:26,26:52:99:673,0,693:9,17,10,16 chr1 201122784 . C T 441.42 PASS AC=1;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 0/1:22,27:49:99:712,0,524:12,10,18,9 chr1 201122947 . T G 1564.58 PASS AC=1;AF=0.932;AN=2;DP=4504;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:51,58:109:99:1475,0,1222:26,25,28,30 chr1 201163191 . G T 1454.03 PASS AC=2;AF=0.681;AN=2;DP=2349;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:1998,188,0:0,0,39,24 chr1 201166124 . T C 1026.93 PASS AC=2;AF=0.614;AN=2;DP=1309;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant8-variant14-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant37-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1620,153,0:0,0,36,15 chr1 201166281 . C T 2119.6 PASS AC=2;AF=0.615;AN=2;DP=5459;MQ=60;set=variant4-variant5-variant6-variant8-variant11-variant14-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,146:146:99:4443,393,0:0,0,71,75 chr1 201166383 . G A 3568.04 PASS AC=2;AF=0.681;AN=2;DP=5646;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,131:131:99:4005,392,0:0,0,55,76 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 1/1:0,104:104:99:3208,311,0:0,0,44,60 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 1/1:0,40:40:99:1299,120,0:0,0,28,12 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 1/1:0,87:87:99:2456,260,0:0,0,47,40 chr1 201171007 . T G 503.79 PASS AC=1;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 0/1:12,19:31:99:539,0,286:3,9,7,12 chr1 201173104 . C T 321.22 PASS AC=1;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 0/1:33,15:48:99:304,0,874:11,22,5,10 chr1 201175075 . C G 479.47 PASS AC=1;AF=0.529;AN=2;DP=575;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant9-variant13-variant14-variant15-variant17-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,8:24:99:247,0,502:13,3,7,1 chr1 201175227 . C A 3948.19 PASS AC=1;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 0/1:81,86:167:99:1984,0,1880:42,39,48,38 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 0/1:101,86:187:99:2027,0,2271:49,52,45,41 chr1 201175715 . G T 2284.79 PASS AC=1;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 0/1:32,57:89:99:1449,0,755:16,16,31,26 chr1 201176018 . A G 947.96 PASS AC=1;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 0/1:23,23:46:99:599,0,640:12,11,12,11 chr1 201176108 . G A 944.65 PASS AC=1;AF=0.55;AN=2;DP=1276;MQ=60;set=variant3-variant4-variant6-variant9-variant13-variant14-variant15-variant17-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant33-variant34-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,28:53:99:726,0,669:10,15,14,14 chr1 201176711 . G T 2606.89 PASS AC=1;AF=0.563;AN=2;DP=570;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant21-variant23-variant26-variant28-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:48,44:92:99:1074,0,1288:23,25,23,21 chr1 201176968 . A G 1782.73 PASS AC=1;AF=0.55;AN=2;DP=1894;MQ=60;set=variant3-variant4-variant6-variant9-variant13-variant14-variant15-variant17-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant33-variant34-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,26:62:99:643,0,929:17,19,14,12 chr1 201177246 . T C 1909.09 PASS AC=1;AF=0.55;AN=2;DP=2523;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant9-variant13-variant14-variant15-variant17-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant33-variant34-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:64,49:113:99:1246,0,1581:30,34,24,25 chr1 201177278 . C T 1853.34 PASS AC=1;AF=0.55;AN=2;DP=2558;MQ=60;set=variant3-variant4-variant6-variant9-variant13-variant14-variant15-variant17-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant33-variant34-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:59,45:104:99:1094,0,1416:28,31,23,22 chr1 201177538 . G T 1416.02 PASS AC=1;AF=0.55;AN=2;DP=1960;MQ=60;set=variant3-variant4-variant6-variant9-variant13-variant14-variant15-variant17-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant33-variant34-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,39:85:99:861,0,1185:23,23,19,20 chr1 201178470 . G A 5638.48 PASS AC=1;AF=0.55;AN=2;DP=5211;set=variant3-variant4-variant6-variant9-variant13-variant14-variant15-variant17-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant33-variant34-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:135,127:262:99:3199,0,3852:81,54,77,50 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 0/1:368,113:481:99:3225,0,17953:168,200,35,78 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 0/1:361,92:453:99:2814,0,17736:162,199,24,68 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 0/1:347,71:418:99:1995,0,17569:150,197,18,53 chr1 201179599 . G C 882.38 PASS AC=1;AF=0.543;AN=2;DP=594;FractionInformativeReads=1;set=variant5-variant8-variant10-variant11-variant12-variant14-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,10:13:85:360,0,85:3,0,5,5 chr1 201180084 . G T 5267.04 PASS AC=1;AF=0.55;AN=2;DP=6291;set=variant3-variant4-variant6-variant9-variant13-variant14-variant15-variant17-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant33-variant34-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:138,107:245:99:2544,0,3682:51,87,42,65 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 0/1:130,69:199:99:2365,0,5544:78,52,28,41 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 0/1:142,60:202:99:2228,0,5881:87,55,24,36 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 0/1:155,51:206:99:1817,0,6468:91,64,21,30 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 0/1:176,39:215:99:1197,0,6910:100,76,15,24 chr1 201180269 . G A 11868.1 PASS AC=1;AF=0.563;AN=2;DP=3356;set=variant5-variant8-variant21-variant23-variant26-variant28-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:208,200:408:99:4810,0,4968:103,105,109,91 chr1 201180501 . T C 6641.65 PASS AC=1;AF=0.548;AN=2;DP=10278;set=variant3-variant4-variant6-variant9-variant13-variant14-variant15-variant17-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant33-variant34-variant37-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:229,206:435:99:5077,0,5951:109,120,111,95 chr1 201181217 . A G 3714.61 PASS AC=1;AF=0.55;AN=2;DP=4390;MQ=60;set=variant3-variant4-variant6-variant9-variant13-variant14-variant15-variant17-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant33-variant34-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:81,108:189:99:2635,0,1866:40,41,58,50 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 1/1:0,194:194:99:7519,583,0:0,0,100,94 chr1 201181920 . G T 1804.9 PASS AC=1;AF=0.55;AN=2;DP=2227;FractionInformativeReads=1;set=variant3-variant4-variant6-variant9-variant13-variant14-variant15-variant17-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant33-variant34-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:57,36:93:99:786,0,1434:28,29,20,16 chr1 201182779 . A G 1014.02 PASS AC=1;AF=0.55;AN=2;DP=1585;MQ=60;set=variant3-variant4-variant6-variant9-variant13-variant14-variant15-variant17-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant33-variant34-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,14:46:99:330,0,756:15,17,3,11 chr1 201183363 . C T 2012.84 PASS AC=1;AF=0.55;AN=2;DP=3290;MQ=60;set=variant3-variant4-variant6-variant9-variant13-variant14-variant15-variant17-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant33-variant34-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:89,58:147:99:1299,0,2210:50,39,35,23 chr1 201183402 . T C 2953.29 PASS AC=1;AF=0.55;AN=2;DP=4080;MQ=60;set=variant3-variant4-variant6-variant9-variant13-variant14-variant15-variant17-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant33-variant34-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:102,69:171:99:1583,0,2506:53,49,35,34 chr1 201184097 . G A 2642.55 PASS AC=1;AF=0.523;AN=2;DP=2013;MQ=60;set=variant5-variant8-variant10-variant11-variant12-variant14-variant16-variant17-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,37:65:99:983,0,665:11,17,19,18 chr1 201184275 . C T 743.17 PASS AC=1;AF=0.55;AN=2;DP=790;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant9-variant13-variant14-variant15-variant17-variant19-variant20-variant23-variant27-variant29-variant30-variant31-variant33-variant34-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,13:34:99:341,0,549:8,13,7,6 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 1/1:1,140:141:99:4148,413,0:1,0,62,78 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 1/1:0,96:96:99:3042,288,0:0,0,35,61 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 1/1:0,18:18:54:618,54,0:0,0,4,14 chr1 201190732 . G A 2039.56 PASS AC=1;AF=0.5;AN=2;DP=3096;MQ=60;set=variant5-variant8-variant10-variant11-variant12-variant14-variant17-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,63:111:99:1558,0,1206:26,22,32,31 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 1/1:0,95:95:99:3104,285,0:0,0,54,41 chr1 201193830 . C G 2266.8 PASS AC=1;AF=0.5;AN=2;DP=180;FS=3.418;FractionInformativeReads=1;MQ=60;MQRankSum=0.66;QD=12.59;ReadPosRankSum=2.052;SOR=0.495;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:83,97:180:99:2295,0,2013:33,50,44,53 chr1 201195119 . C T 1994.67 PASS AC=2;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 1/1:1,169:170:99:5088,483,0:1,0,96,73 chr1 201196066 . C T 5137.96 PASS AC=1;AF=0.5;AN=2;DP=365;FS=0.799;FractionInformativeReads=1;MQ=60;MQRankSum=1.564;QD=14.08;ReadPosRankSum=2.731;SOR=0.652;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:152,213:365:99:5166,0,3657:78,74,106,107 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 0/1:8,7:15:99:189,0,258:7,1,5,2 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 0/1:12,23:35:99:597,0,232:7,5,15,8 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 0/1:46,65:111:99:1639,0,933:27,19,35,30 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 0/1:36,27:63:99:646,0,936:17,19,13,14 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 0/1:23,35:58:99:902,0,518:13,10,17,18 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 1/1:0,4:4:12:173,12,0:0,0,0,4 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 1/1:0,83:83:99:2645,249,0:0,0,36,47 chr1 201282167 . C G 241.77 PASS AC=2;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 1/1:0,22:22:66:850,66,0:0,0,19,3 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 1/1:0,39:39:99:1215,117,0:0,0,23,16 chr1 201285909 . A G 322.85 PASS AC=2;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 1/1:0,12:12:36:417,36,0:0,0,2,10 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 1/1:0,33:33:99:1555,105,0:0,0,21,12 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 1/1:0,39:39:99:1666,117,0:0,0,24,15 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 1/1:0,23:23:69:684,69,0:0,0,13,10 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 1/1:0,39:39:99:1256,116,0:0,0,25,14 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 1/1:0,39:39:99:1263,117,0:0,0,29,10 chr1 201291066 . C T 3618.84 PASS AC=2;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 1/1:0,136:136:99:4143,407,0:0,0,80,56 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 1/1:0,69:69:99:2147,207,0:0,0,38,31 chr1 201293512 . TG T 2618.6 PASS AC=2;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 1/1:0,81:81:99:2889,244,0:0,0,43,38 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 1/1:0,14:14:42:519,42,0:0,0,10,4 chr1 201293985 . G A 415.31 PASS AC=2;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 1/1:0,19:19:57:702,57,0:0,0,14,5 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 1/1:0,10:10:30:328,30,0:0,0,6,4 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 1/1:0,17:17:51:498,51,0:0,0,10,7 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 1/1:0,32:32:96:1014,96,0:0,0,19,13 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 1/1:0,60:60:99:2031,179,0:0,0,22,38 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 1/1:0,61:61:99:2100,183,0:0,0,27,34 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 1/1:0,85:85:99:2636,255,0:0,0,45,40 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 1/1:0,107:107:99:3139,321,0:0,0,55,52 chr1 201300317 . C T 969.17 PASS AC=1;AF=0.5;AN=2;DP=65;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.301;QD=14.91;ReadPosRankSum=1.145;SOR=0.697;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:26,39:65:99:997,0,619:14,12,21,18 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 1/1:0,86:86:99:2817,258,0:0,0,30,56 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 1/1:0,87:87:99:2917,260,0:0,0,32,55 chr1 201301696 . G A 556.26 PASS AC=1;AF=0.588;AN=2;DP=811;MQ=60;set=variant2-variant7-variant9-variant13-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant31-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,10:35:99:335,0,772:11,14,2,8 chr1 201301711 . G A 470.05 PASS AC=1;AF=0.5;AN=2;DP=327;MQ=60;set=variant2-variant7-variant20-variant22-variant23-variant25-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,9:34:99:253,0,726:13,12,3,6 chr1 201301737 . G GCCCCCACCCTGA 415.45 PASS AC=1;AF=0.559;AN=2;DP=695;MQ=60;set=variant2-variant7-variant9-variant13-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant31-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,8:29:99:338,0,1320:11,10,5,3 chr1 201301873 . A G 1760.62 PASS AC=2;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 1/1:0,66:66:99:2168,198,0:0,0,35,31 chr1 201301906 . C G 2392.59 PASS AC=2;AF=0.852;AN=2;DP=4417;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2309,210,0:0,0,38,32 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 1/1:0,124:124:99:3404,370,0:0,0,67,57 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 1/1:0,84:84:99:2476,252,0:0,0,35,49 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 1/1:0,132:132:99:3978,396,0:0,0,59,73 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 1/1:0,37:37:99:1243,111,0:0,0,23,14 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 0/1:39,33:72:99:711,0,982:16,23,13,20 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 1/1:0,29:29:87:889,87,0:0,0,18,11 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 1/1:0,36:36:99:1433,108,0:0,0,5,31 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 1/1:0,30:30:90:1199,90,0:0,0,3,27 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 1/1:0,70:70:99:2043,208,0:0,0,37,33 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 1/1:0,37:37:99:1188,111,0:0,0,14,23 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 1/1:0,104:104:99:4673,313,0:0,0,62,42 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 1/1:0,74:74:99:2395,222,0:0,0,27,47 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 0/1:11,6:17:99:138,0,349:9,2,4,2 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 0/1:35,46:81:99:1168,0,806:21,14,25,21 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 0/1:61,44:105:99:1054,0,1537:28,33,18,26 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 0/1:91,58:149:99:1262,0,2247:43,48,24,34 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 0/1:17,21:38:99:563,0,436:7,10,6,15 chr1 201368463 . G GT 2463.31 PASS AC=1;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 0/1:61,59:120:99:1946,0,2054:40,21,39,20 chr1 201376007 . G C 894.03 PASS AC=2;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 1/1:0,75:75:99:2308,224,0:0,0,36,39 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 1/1:0,42:42:99:1353,126,0:0,0,24,18 chr1 201377885 . G A 1490.81 PASS AC=2;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 1/1:0,36:36:99:1559,108,0:0,0,16,20 chr1 201377891 . C A 787.33 PASS AC=2;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 1/1:0,34:34:99:1530,102,0:0,0,14,20 chr1 201377894 . A T 1524.62 PASS AC=2;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 1/1:0,34:34:99:1530,102,0:0,0,14,20 chr1 201379091 . G A 297.36 PASS AC=1;AF=0.5;AN=2;DP=81;FractionInformativeReads=1;MQ=60;set=variant23-variant33-variant34 GT:AD:DP:GQ:PL:SB 0/1:7,15:22:99:326,0,155:3,4,8,7 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 1/1:0,21:21:62:714,62,0:0,0,14,7 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 1/1:0,32:32:96:1184,96,0:0,0,23,9 chr1 201386916 . C T 714.78 PASS AC=1;AF=0.5;AN=2;DP=106;MQ=60;set=variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:21,29:50:99:743,0,592:14,7,16,13 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 0/1:6,5:11:99:135,0,115:3,3,2,3 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 0/1:30,19:49:99:420,0,796:18,12,11,8 chr1 201434740 . G A 1412.29 PASS AC=1;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 0/1:40,24:64:99:680,0,1112:22,18,18,6 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 0/1:76,63:139:99:1584,0,1889:48,28,35,28 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 0/1:20,28:48:99:1124,0,788:10,10,16,12 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 0/1:12,9:21:99:188,0,315:4,8,3,6 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 1/1:0,23:23:69:873,69,0:0,0,10,13 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 1/1:0,8:8:24:286,24,0:0,0,7,1 chr1 201465839 . T C 103.54 PASS AC=2;AF=0.967;AN=2;DP=151;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant14-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:169,12,0:0,0,1,3 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 1/1:0,123:123:99:3738,368,0:0,0,75,48 chr1 201489286 . C G 443.83 PASS AC=2;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 1/1:0,56:56:99:1759,168,0:0,0,32,24 chr1 201687406 . G A 408 PASS AC=2;AF=0.54;AN=2;DP=1162;MQ=60;set=variant-variant3-variant4-variant5-variant9-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant32-variant34-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1232,105,0:0,0,26,9 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 1/1:0,77:77:99:2321,230,0:0,0,48,29 chr1 201688515 . T A 294.99 PASS AC=2;AF=0.54;AN=2;DP=698;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant9-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant32-variant34-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:550,54,0:0,0,13,5 chr1 201688832 . T C 87.21 PASS AC=2;AF=0.56;AN=2;DP=700;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant9-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant32-variant34-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:656,72,0:0,0,11,13 chr1 201749520 . G C 1252.01 PASS AC=2;AF=0.611;AN=2;DP=2796;MQ=60;set=variant-variant3-variant4-variant5-variant9-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant34-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2547,234,0:0,0,53,25 chr1 201752429 . A C 280.59 PASS AC=2;AF=0.673;AN=2;DP=584;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant9-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:962,78,0:0,0,23,3 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 0/1:28:99:8,7,10,3 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 0/1:7,20:27:99:528,0,161:1,6,6,14 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 1/1:0,70:70:99:2337,210,0:0,0,24,46 chr1 201773707 . TAA TA,T 376.62 PASS AC=0,1;AF=0.435,0.087;AN=2;DP=1641;set=variant2-variant4-filterInvariant6-variant7-variant8-variant10-variant11-filterInvariant12-variant15-variant18-variant19-variant20-variant22-filterInvariant23-variant26-variant29-variant30-variant31-variant32-variant34-variant37-variant38-variant41 GT:DP:GQ:SB 0/2:24:99:9,8,3,4 chr1 201773731 . T A 161.1 PASS AC=1;AF=0.5;AN=2;DP=39;FS=1.348;FractionInformativeReads=0.949;MQ=60;MQRankSum=0.141;QD=4.13;ReadPosRankSum=-0.642;SOR=0.368;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:23,14:37:99:189,0,586:9,14,7,7 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 0/1:39,27:66:99:632,0,1078:15,24,13,14 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 0/1:37,25:62:99:577,0,924:16,21,11,14 chr1 201790633 . GACACACACACACACACACAC GAC,GACACACACACACACACACACAC,GACACACACACACACACAC,GACACACACACACACAC,G,GACACACACACACACACACACACAC,GACACAC 241.33 PASS AC=0,0,1,0,0,0,0;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 0/3:8:69:2,2,2,2 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 0/1:20,14:34:99:322,0,536:7,13,7,7 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 0/1:17:99:5,2,5,5 chr1 201793222 . G A 450.83 PASS AC=1;AF=0.583;AN=2;DP=250;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant23-variant25-variant30-variant31 GT:AD:DP:GQ:PL:SB 0/1:25,13:38:99:335,0,601:13,12,6,7 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 1/1:0,17:17:51:527,51,0:0,0,5,12 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 0/1:51:99:18,20,5,8 chr1 201823593 . A G 594.78 PASS AC=1;AF=0.556;AN=2;DP=307;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant14-variant18-variant23-variant25-variant30-variant31-variant33 GT:AD:DP:GQ:PL:SB 0/1:10,20:30:99:601,0,256:8,2,14,6 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 0/1:34,30:64:99:708,0,771:14,20,14,16 chr1 201827919 . C G 563.89 PASS AC=1;AF=0.556;AN=2;DP=312;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant14-variant18-variant23-variant25-variant30-variant31-variant33 GT:AD:DP:GQ:PL:SB 0/1:29,15:44:99:326,0,706:18,11,10,5 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 1/1:0,15:15:45:544,45,0:0,0,12,3 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 1/1:0,86:86:99:2938,259,0:0,0,46,40 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 1/1:0,42:42:99:1786,127,0:0,0,13,29 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 1/1:0,74:74:99:2433,222,0:0,0,26,48 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 1/1:0,44:44:99:1509,132,0:0,0,23,21 chr1 201845432 . C T 1113.87 PASS AC=1;AF=0.556;AN=2;DP=716;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant14-variant18-variant23-variant25-variant30-variant31-variant33 GT:AD:DP:GQ:PL:SB 0/1:44,22:66:99:500,0,1084:17,27,11,11 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 0/1:55:9:3,4,20,28 chr1 201846615 . TCACACACACACA T,TCACACACACACACA,TCACACACACACACACA,TCACACACACA 2734.61 PASS AC=1,0,1,0;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 1/3:27:99:0,0,18,9 chr1 201846684 . G T 633.69 PASS AC=1;AF=0.556;AN=2;DP=566;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant14-variant18-variant23-variant25-variant30-variant31-variant33 GT:AD:DP:GQ:PL:SB 0/1:24,36:60:99:844,0,435:12,12,22,14 chr1 201847265 . G T 782.81 PASS AC=1;AF=0.556;AN=2;DP=563;MQ=60;set=variant4-variant5-variant14-variant18-variant23-variant25-variant30-variant31-variant33 GT:AD:DP:GQ:PL:SB 0/1:31,29:60:99:585,0,799:19,12,15,14 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 0/1:8,14:22:99:509,0,206:5,3,5,9 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 1/1:0,38:38:99:1746,117,0:0,0,23,15 chr1 201851571 . AAAAC A 100.68 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=52;FS=5.842;FractionInformativeReads=0.327;MQ=60;MQRankSum=-1.634;QD=1.94;ReadPosRankSum=1.845;SOR=2.494;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:12,5:17:99:138,0,327:8,4,5,0 chr1 201851574 . AC A 118.93 PASS AC=1;AF=0.5;AN=2;DP=424;set=filterInvariant3-variant4-filterInvariant6-variant11-filterInvariant13-variant16-variant17-variant23-filterInvariant27 GT:AD:DP:GQ:PL:SB 0/1:5,12:17:99:266,0,138:5,0,8,4 chr1 201852299 . TC TCCC,TCC,T 1327.23 PASS AC=0,2,0;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 2/2:51:73:0,3,13,35 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 0/1:30,19:49:99:361,0,763:15,15,9,10 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 1/1:0,58:58:99:1686,174,0:0,0,24,34 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 0/1:78,87:165:99:2396,0,1883:35,43,33,54 chr1 201861180 . G T 858.03 PASS AC=1;AF=0.5;AN=2;DP=294;MQ=60;set=variant4-variant23-variant25-variant31 GT:AD:DP:GQ:PL:SB 0/1:26,28:54:99:694,0,756:15,11,13,15 chr1 201861215 . G C 1062.64 PASS AC=1;AF=0.5;AN=2;DP=303;FractionInformativeReads=1;MQ=60;set=variant4-variant23-variant25-variant31 GT:AD:DP:GQ:PL:SB 0/1:32,33:65:99:811,0,992:19,13,19,14 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 1/1:0,111:111:99:3470,333,0:0,0,51,60 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 1/1:0,49:49:99:1578,147,0:0,0,18,31 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 1/1:0,25:25:75:826,75,0:0,0,8,17 chr1 201926403 . T G 2628.11 PASS AC=1;AF=0.583;AN=2;DP=1071;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant15-variant18-variant19-variant23-variant28-variant29-variant30-variant32-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:69,40:109:99:815,0,1635:39,30,23,17 chr1 201932615 . TTG T 1264.51 PASS AC=1;AF=0.591;AN=2;DP=193;MQ=60;set=variant2-variant6-variant15-variant18-variant19-variant23-variant28-variant29-variant30-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,5:15:99:177,0,398:6,4,4,1 chr1 201934578 . G A 1285.51 PASS AC=1;AF=0.583;AN=2;DP=700;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant15-variant18-variant19-variant23-variant28-variant29-variant30-variant32-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,27:47:99:741,0,606:15,5,16,11 chr1 201938482 . C T 79.91 PASS AC=1;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 0/1:1,6:7:25:205,0,25:1,0,5,1 chr1 201938995 . C T 6504.36 PASS AC=1;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 0/1:198,206:404:99:5128,0,4965:104,94,110,96 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 0/1:83,71:154:99:1628,0,1942:35,48,27,44 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 0/1:46,46:92:99:1157,0,1211:16,30,16,30 chr1 201952294 . C G 679.27 PASS AC=1;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 0/1:11,8:19:99:283,0,717:1,10,2,6 chr1 201952310 . T G 559.49 PASS AC=1;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 0/1:11,8:19:99:300,0,685:3,8,2,6 chr1 201952440 . C CCTT 727.34 PASS AC=1;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 0/1:18,24:42:99:984,0,793:11,7,14,10 chr1 201952574 . T C 1917.18 PASS AC=1;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 0/1:50,58:108:99:1409,0,1118:26,24,28,30 chr1 201952755 . T A 697.79 PASS AC=1;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 0/1:22,20:42:99:518,0,578:9,13,6,14 chr1 201966894 . G GTTT,GTTTT,GTT,GT,GTTTTT 48.39 PASS AC=0,2,0,0,0;AF=0.258,0.403,0.177,0.032,0.032;AN=2;DP=424;set=variant3-variant4-variant6-variant7-variant8-variant10-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 2/2:9:27:0,0,3,6 chr1 201969082 . G A 659.53 PASS AC=2;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 1/1:0,64:64:99:2141,192,0:0,0,41,23 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 1/1:0,257:257:99:7573,769,0:0,0,120,137 chr1 201970748 . G A 848.72 PASS AC=2;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 1/1:1,73:74:99:2253,180,0:0,1,34,39 chr1 201977600 . C A 110.05 PASS AC=1;AF=0.609;AN=2;DP=556;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant10-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:102,0,195:5,3,4,3 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 0/1:9,16:25:99:347,0,175:4,5,8,8 chr1 201977860 . GT G 279.49 PASS AC=1;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 0/1:5,4:9:79:79,0,105:2,3,0,4 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 0/1:16,16:32:99:395,0,319:9,7,11,5 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 0/1:59,42:101:99:1395,0,2058:33,26,23,19 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 0/1:64,58:122:99:1493,0,1644:37,27,31,27 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 0/1:17:74:10,0,5,2 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 0/1:60,58:118:99:1465,0,1551:27,33,22,36 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 0/1:17,16:33:99:654,0,1302:9,8,9,7 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 0/1:17,17:34:99:654,0,1302:9,8,10,7 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 0/1:27,26:53:99:694,0,706:9,18,11,15 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 0/1:13,14:27:99:378,0,422:3,10,4,10 chr1 201985648 . GAA GA,G,GAAA 3965.58 PASS AC=1,0,0;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 0/1:231:99:43,51,80,57 chr1 201985731 . G A 2872.3 PASS AC=1;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 0/1:144,132:276:99:3130,0,3396:62,82,60,72 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 1/1:0,63:63:99:2044,189,0:0,0,42,21 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 1/1:1,122:123:99:3693,355,0:0,1,66,56 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 1/1:0,157:157:99:4805,470,0:0,0,82,75 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 1/1:0,182:182:99:5577,546,0:0,0,86,96 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 1/1:0,106:106:99:3102,317,0:0,0,62,44 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 1/1:0,44:44:99:1475,131,0:0,0,18,26 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 1/1:0,26:26:77:954,77,0:0,0,3,23 chr1 202107422 . AACACACAC AAC,AACAC,AACACACACAC,AACACAC,A,AACACACACACACAC 961.24 PASS AC=2,0,0,0,0,0;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 1/1:20:60:0,0,12,8 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 1/1:0,56:56:99:2189,168,0:0,0,9,47 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 1/1:0,84:84:99:2626,251,0:0,0,45,39 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 1/1:0,77:77:99:2355,230,0:0,0,38,39 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 1/1:0,4:4:12:180,12,0:0,0,4,0 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 1/1:0,14:14:42:582,42,0:0,0,13,1 chr1 202129205 . G A 282.54 PASS AC=1;AF=0.5;AN=2;DP=11;FS=3.09;FractionInformativeReads=1;MQ=60;MQRankSum=0.566;QD=25.69;ReadPosRankSum=1.377;SOR=1.773;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:3,8:11:48:311,0,48:2,1,2,6 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 0/1:47,30:77:99:721,0,1262:27,20,14,16 chr1 202129895 . G A 966.64 PASS AC=1;AF=0.526;AN=2;DP=2667;MQ=60;set=variant-variant2-variant3-variant6-variant12-variant15-variant16-variant20-variant23-variant25-variant27-variant29-variant30-variant33-variant34-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,46:119:99:1088,0,1918:37,36,24,22 chr1 202129930 . G A 738.95 PASS AC=1;AF=0.5;AN=2;DP=281;MQ=60;SOR=0.773;set=variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:89,40:129:99:767,0,2186:44,45,21,19 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 0/1:22,20:42:99:484,0,535:12,10,11,9 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 0/1:33,25:58:99:554,0,771:14,19,11,14 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 1/1:0,170:170:99:5126,510,0:0,0,82,88 chr1 202156135 . C CCCTCGCTCCTCGCTCCTCGCTCCTCGCT,CCCTCGCT,CCCTCGCTCCTCGCTCCTCGCT,CCCTCGCTCCTCGCT,CCCTCGCTCCTCGCTCCTCGCTCCTCGCTCCTCGCT 785.79 PASS AC=1,1,0,0,0;AF=0.159,0.511,0.125,0.057,0.023;AN=2;DP=2824;set=Intersection GT:DP:GQ:SB 2/1:41:99:0,0,17,24 chr1 202156482 . G A 2307.92 PASS AC=2;AF=0.886;AN=2;DP=4825;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,94:96:99:2685,238,0:1,1,58,36 chr1 202156628 . A C 2701.97 PASS AC=2;AF=0.898;AN=2;DP=4743;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:3054,296,0:0,0,41,58 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 1/1:0,83:83:99:2436,248,0:0,0,37,46 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 1/1:0,19:19:57:635,57,0:0,0,8,11 chr1 202163516 . C A 4017.32 PASS AC=2;AF=0.886;AN=2;DP=5241;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2791,277,0:0,0,61,32 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 0/1:94,94:188:99:2238,0,2145:49,45,41,53 chr1 202194441 . G C 271.37 PASS AC=2;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 1/1:0,17:17:51:680,51,0:0,0,15,2 chr1 202194508 . AG A 1902.47 PASS AC=1;AF=0.5;AN=2;DP=623;MQ=60;set=variant15-variant16-variant23-variant33-variant34-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,35:79:99:1177,0,1533:26,18,20,15 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 1/1:0,59:59:99:1868,177,0:0,0,40,19 chr1 202249783 . A T 327.71 PASS AC=1;AF=0.5;AN=2;DP=43;FS=4.714;FractionInformativeReads=1;MQ=60;MQRankSum=-0.344;QD=7.62;ReadPosRankSum=-1.644;SOR=0.471;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:28,15:43:99:356,0,752:18,10,7,8 chr1 202266547 . C T 3287.08 PASS AC=2;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 1/1:0,118:118:99:3673,353,0:0,0,65,53 chr1 202266607 . C T 4279.39 PASS AC=2;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 1/1:0,145:145:99:4262,433,0:0,0,73,72 chr1 202274936 . T C 4854.85 PASS AC=2;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 1/1:0,151:151:99:4493,452,0:0,0,73,78 chr1 202276494 . C T 947.45 PASS AC=2;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 1/1:0,67:67:99:2153,201,0:0,0,21,46 chr1 202283667 . A G 984.11 PASS AC=2;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 1/1:0,27:27:81:879,81,0:0,0,19,8 chr1 202287206 . T C 4106.87 PASS AC=2;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 1/1:0,207:207:99:6421,619,0:0,0,100,107 chr1 202287537 . G A 5534.84 PASS AC=2;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 1/1:1,159:160:99:5037,466,0:0,1,101,58 chr1 202287813 . T C 7469.02 PASS AC=2;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 1/1:0,246:246:99:7636,736,0:0,0,120,126 chr1 202288462 . C A 2219.92 PASS AC=2;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 1/1:0,82:82:99:2668,246,0:0,0,34,48 chr1 202318316 . A C 1008.46 PASS AC=2;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 1/1:0,108:108:99:3564,324,0:0,0,37,71 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 1/1:0,60:60:99:1873,180,0:0,0,21,39 chr1 202457784 . T A 466.49 PASS AC=2;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 1/1:0,47:47:99:1370,141,0:0,0,18,29 chr1 202464280 . G A 407.15 PASS AC=2;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 1/1:0,11:11:31:342,31,0:0,0,11,0 chr1 202531741 . C T 239.91 PASS AC=2;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 1/1:0,18:18:54:526,54,0:0,0,12,6 chr1 202536848 . C T 1117.12 PASS AC=2;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 1/1:0,66:66:99:2035,198,0:0,0,36,30 chr1 202550272 . G A 754.51 PASS AC=2;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 1/1:0,60:60:99:1928,179,0:0,0,30,30 chr1 202550547 . G A 465.78 PASS AC=2;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 1/1:0,44:44:99:1318,132,0:0,0,20,24 chr1 202551071 . A G 1337.61 PASS AC=2;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 1/1:0,90:90:99:3000,270,0:0,0,36,54 chr1 202552100 . G A 2624.05 PASS AC=2;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 1/1:0,162:162:99:5095,486,0:0,0,110,52 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 1/1:0,234:234:99:7513,700,0:0,0,87,147 chr1 202552839 . T C 674.71 PASS AC=2;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 1/1:0,43:43:99:1280,129,0:0,0,19,24 chr1 202556304 . C G 1341.5 PASS AC=1;AF=0.5;AN=2;DP=97;FS=3.978;FractionInformativeReads=1;MQ=60;MQRankSum=-2.066;QD=13.83;ReadPosRankSum=1.267;SOR=0.397;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:43,54:97:99:1370,0,1185:13,30,21,33 chr1 202556632 . C CTGTT 628.22 PASS AC=2;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 1/1:0,34:34:99:1559,108,0:0,0,20,14 chr1 202557017 . C T 667.91 PASS AC=2;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 1/1:0,83:83:99:2348,246,0:0,0,41,42 chr1 202557159 . A ATGTT 1004.5 PASS AC=1;AF=0.5;AN=2;DP=109;MQ=60;set=variant12-variant23 GT:AD:DP:GQ:PL:SB 0/1:27,26:53:99:1052,0,1516:14,13,12,14 chr1 202560412 . T C 1233.11 PASS AC=2;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 1/1:0,87:87:99:2790,261,0:0,0,35,52 chr1 202560658 . A G 1422.49 PASS AC=2;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 1/1:0,125:125:99:3915,374,0:0,0,71,54 chr1 202560681 . T G 1611.18 PASS AC=2;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 1/1:0,144:144:99:4569,432,0:0,0,81,63 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 0/1:56,43:99:99:902,0,1517:28,28,22,21 chr1 202563829 . TAC TACAC,TACACACACACACACACAC,TACACACACACACAC,TACACACACACACACACACACAC,T,TACACACACACACACACACAC,TACACACACAC,TACACACACACACACACACACACACACAC,TACACACACACACACAC,TACACACACACAC,TACACACACACACACACACACACAC,TACACACAC 498.81 PASS AC=0,1,0,0,0,0,0,0,1,0,0,0;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 9/2:15:99:0,0,10,5 chr1 202563966 . C T 190.6 PASS AC=1;AF=0.6;AN=2;DP=99;FractionInformativeReads=1;MQ=60;set=variant12-variant15-variant16-variant23-variant41 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:241,0,235:5,5,2,6 chr1 202564040 . C A 109.62 PASS AC=1;AF=0.6;AN=2;DP=103;MQ=60;set=variant12-variant15-variant16-variant23-variant41 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:265,0,225:5,5,6,4 chr1 202564311 . C G 434.8 PASS AC=1;AF=0.5;AN=2;DP=173;FractionInformativeReads=1;MQ=60;set=variant12-variant15-variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:9,12:21:99:342,0,298:4,5,7,5 chr1 202564330 . A T 253.35 PASS AC=2;AF=0.705;AN=2;DP=2027;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:89:961,89,0:0,0,19,11 chr1 202565426 . C T 69.6 PASS AC=1;AF=0.625;AN=2;DP=79;set=variant12-variant15-variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:8,9:17:99:228,0,181:6,2,8,1 chr1 202565428 . CACACACAT C 241.78 PASS AC=1;AF=0.667;AN=2;DP=111;set=variant3-variant12-variant15-variant16-variant23-variant32 GT:AD:DP:GQ:PL:SB 0/1:10,9:19:99:222,0,224:7,3,8,1 chr1 202565436 . T C,TACACACACAC 489.76 PASS AC=1,0;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 0/1:23:99:11,4,5,3 chr1 202565747 . AAAAC A 925.89 PASS AC=1;AF=0.6;AN=2;DP=259;MQ=60;set=variant12-variant15-variant16-variant23-variant41 GT:AD:DP:GQ:PL:SB 0/1:24,27:51:99:1062,0,1273:12,12,17,10 chr1 202569831 . G A 410.06 PASS AC=1;AF=0.5;AN=2;DP=123;FractionInformativeReads=1;MQ=60;set=variant12-variant15-variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:10,13:23:99:390,0,361:0,10,3,10 chr1 202572105 . GCC G 250.95 PASS AC=1;AF=0.692;AN=2;DP=2567;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,25:49:99:848,0,820:9,15,8,17 chr1 202703053 . G A 1764.81 PASS AC=2;AF=0.83;AN=2;DP=3060;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2129,225,0:0,0,31,44 chr1 202705455 . G C 2324.42 PASS AC=2;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 1/1:0,71:71:99:2097,213,0:0,0,34,37 chr1 202715244 . G GA 1197.03 PASS AC=2;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 1/1:0,29:29:87:841,87,0:0,0,16,13 chr1 202715284 . G A 1665.83 PASS AC=2;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 1/1:0,48:48:99:1470,143,0:0,0,27,21 chr1 202718028 . A G 1038.73 PASS AC=2;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 1/1:0,13:13:39:547,39,0:0,0,13,0 chr1 202718202 . G A 4302.04 PASS AC=2;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 1/1:0,139:139:99:3938,416,0:0,0,70,69 chr1 202722277 . G A 922.32 PASS AC=2;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 1/1:0,42:42:99:1237,125,0:0,0,16,26 chr1 202722348 . A G 201.22 PASS AC=2;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 1/1:0,14:14:42:580,42,0:0,0,1,13 chr1 202731986 . C CCTCAA 491.94 PASS AC=2;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 1/1:0,9:9:27:405,27,0:0,0,2,7 chr1 202733238 . C T 2893.82 PASS AC=2;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 1/1:0,93:93:99:2748,279,0:0,0,42,51 chr1 202735751 . T C 6914.51 PASS AC=2;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 1/1:0,211:211:99:6242,632,0:0,0,115,96 chr1 202743634 . G T 70.69 PASS AC=1;AF=0.529;AN=2;DP=146;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant12-variant13-variant14-variant17-variant23-variant26-variant32-variant34-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:73:162,0,73:1,1,3,1 chr1 202743892 . T C 606.14 PASS AC=1;AF=0.533;AN=2;DP=591;FractionInformativeReads=1;MQ=60;set=variant3-variant11-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant27-variant29-variant33-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:18,22:40:99:563,0,489:8,10,8,14 chr1 202778261 . G A 1866.25 PASS AC=2;AF=0.852;AN=2;DP=2474;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1159,108,0:0,0,17,19 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 0/1:77,84:161:99:2098,0,1842:43,34,50,34 chr1 202795154 . C T 2041 PASS AC=1;AF=0.5;AN=2;DP=175;FS=0;FractionInformativeReads=0.994;MQ=60;MQRankSum=0.91;QD=11.66;ReadPosRankSum=-3.208;SOR=0.659;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:94,80:174:99:2069,0,2340:45,49,39,41 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 0/1:13,16:29:99:403,0,340:7,6,8,8 chr1 202848683 . T C 635.31 PASS AC=1;AF=0.5;AN=2;DP=203;FractionInformativeReads=1;MQ=60;set=variant12-variant15-variant23-variant33 GT:AD:DP:GQ:PL:SB 0/1:23,14:37:99:376,0,570:11,12,7,7 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 1/1:0,148:148:99:4348,442,0:0,0,70,78 chr1 202850535 . C CT,CA 132.05 PASS AC=1,0;AF=0.591,0.045;AN=2;DP=186;set=variant-variant19-variant20-variant23-variant24-variant25-variant27-variant28-variant29-variant38-variant39 GT:DP:GQ:SB 0/1:15:71:0,4,1,10 chr1 202861211 . G GAA,GA 547.4 PASS AC=0,2;AF=0.727,0.159;AN=2;DP=1235;set=Intersection GT:DP:GQ:SB 2/2:17:50:0,0,6,11 chr1 202888947 . T C 1830.73 PASS AC=1;AF=0.633;AN=2;DP=778;FractionInformativeReads=1;MQ=60;set=variant-variant11-variant16-variant17-variant23-variant24-variant25-variant27-variant29-variant30-variant33-variant34-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:31,26:57:99:579,0,844:18,13,14,12 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 1/1:0,9:9:27:390,27,0:0,0,0,9 chr1 202896414 . T TC 1008.3 PASS AC=1;AF=0.618;AN=2;DP=611;MQ=60;set=variant-variant11-variant16-variant17-variant23-variant24-variant25-variant27-variant29-variant30-variant33-variant34-variant36-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:17,15:32:99:369,0,433:6,11,4,11 chr1 202917697 . T A 483.89 PASS AC=1;AF=0.5;AN=2;DP=64;FractionInformativeReads=1;MQ=60;set=variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:17,18:35:99:512,0,368:7,10,4,14 chr1 202919851 . G A 194.38 PASS AC=1;AF=0.6;AN=2;DP=411;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant14-variant23-variant24-variant25-variant26-variant27-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:30,13:43:99:286,0,693:17,13,9,4 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 0/1:19,19:38:99:713,0,1152:6,13,6,13 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 0/1:18,18:36:99:715,0,1152:5,13,5,13 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 1/1:0,16:16:48:587,48,0:0,0,6,10 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 0/1:9,6:15:99:124,0,230:4,5,2,4 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 0/1:56,61:117:99:1559,0,1490:25,31,26,35 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 0/1:37,25:62:99:718,0,986:17,20,14,11 chr1 202932154 . G A 1873.94 PASS AC=1;AF=0.5;AN=2;DP=317;FractionInformativeReads=1;MQ=60;set=variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:70,81:151:99:1902,0,1688:37,33,42,39 chr1 202933552 . T TA 99.84 PASS AC=1;AF=0.5;AN=2;DP=69;MQ=60;set=variant5-variant20-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:152,0,188:5,2,4,2 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 0/1:20,18:38:99:440,0,500:8,12,7,11 chr1 202934044 . A G 402.6 PASS AC=1;AF=0.5;AN=2;DP=65;FractionInformativeReads=1;MQ=60;set=variant5-variant20-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:268,0,273:2,7,1,7 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 0/1:10,11:21:99:179,0,221:5,5,5,6 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 0/1:11,10:21:99:221,0,179:5,6,5,5 chr1 202935819 . C A 1299.62 PASS AC=1;AF=0.5;AN=2;DP=220;FractionInformativeReads=1;MQ=60;set=variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:48,50:98:99:1328,0,1287:26,22,22,28 chr1 202935911 . T C 1752.14 PASS AC=1;AF=0.5;AN=2;DP=363;FractionInformativeReads=1;MQ=60;set=variant5-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:61,47:108:99:1117,0,1413:27,34,19,28 chr1 202956340 . T G 2858.66 PASS AC=2;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 1/1:0,57:57:99:1819,171,0:0,0,22,35 chr1 202990110 . CTTTT CTTT,CT,CTTTTT,C,CTT 51.61 PASS AC=1,0,0,0,0;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 0/1:47:99:8,20,7,12 chr1 203003641 . C T 2580.9 PASS AC=1;AF=0.531;AN=2;DP=3408;MQ=60;set=variant-variant6-variant9-variant12-variant16-variant19-variant22-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:101,76:177:99:1829,0,2702:66,35,48,28 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 0/1:59,65:124:99:1734,0,1675:29,30,31,34 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 1/1:0,59:59:99:1894,183,0:0,0,28,31 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 1/1:0,8:8:24:300,24,0:0,0,2,6 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 1/1:0,178:178:99:5310,532,0:0,0,90,88 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 1/1:0,119:119:99:3370,356,0:0,0,54,65 chr1 203008286 . C G 270.6 PASS AC=2;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 1/1:0,55:55:99:1780,165,0:0,0,20,35 chr1 203012705 . C G 748.7 PASS AC=2;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 1/1:0,78:78:99:2501,234,0:0,0,23,55 chr1 203012906 . G A 498.49 PASS AC=2;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 1/1:0,63:63:99:1887,188,0:0,0,38,25 chr1 203014196 . T C 259.59 PASS AC=2;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 1/1:0,8:8:24:279,24,0:0,0,3,5 chr1 203019091 . G A 191.04 PASS AC=2;AF=0.625;AN=2;DP=52;FractionInformativeReads=1;MQ=60;set=variant23-variant27-variant29-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:219,21,0:0,0,1,6 chr1 203020454 . A G 537.56 PASS AC=1;AF=0.5;AN=2;DP=113;FractionInformativeReads=1;MQ=60;set=variant23-variant29-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,20:35:99:566,0,404:9,6,11,9 chr1 203023122 . A C 3358.27 PASS AC=1;AF=0.6;AN=2;DP=3969;MQ=60;set=variant3-variant4-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant23-variant26-variant28-variant30-variant32-variant33-variant34-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:74,82:156:99:2011,0,1885:31,43,40,42 chr1 203023240 . G GGC 1589.4 PASS AC=1;AF=0.6;AN=2;DP=1726;MQ=60;set=variant3-variant4-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant23-variant26-variant28-variant30-variant32-variant33-variant34-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:24,39:63:99:1565,0,1021:7,17,12,27 chr1 203025096 . CTTT C,CTT 1082.82 PASS AC=0,1;AF=0.5,0.1;AN=2;DP=463;MQ=60;set=variant2-variant5-variant11-filterInvariant22-variant23-variant30-variant31-variant34-variant36-variant37 GT:DP:GQ:SB 0/2:30:99:11,11,4,4 chr1 203025209 . G C 1174.62 PASS AC=1;AF=0.55;AN=2;DP=1556;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant8-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant23-variant26-variant28-variant30-variant32-variant33-variant34-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:28,34:62:99:935,0,709:14,14,16,18 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 0/1:12,10:22:99:309,0,363:10,2,9,1 chr1 203030207 . G A 1045.43 PASS AC=1;AF=0.5;AN=2;DP=492;FractionInformativeReads=1;MQ=60;set=variant23-variant27-variant29-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,47:105:99:1074,0,1404:25,33,18,29 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 0/1:21,30:51:99:752,0,459:11,10,16,14 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 0/1:37,39:76:99:894,0,854:21,16,21,18 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 0/1:34,30:64:99:753,0,847:22,12,19,11 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 1/1:0,21:21:63:823,63,0:0,0,17,4 chr1 203040740 . T C 615.58 PASS AC=2;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 1/1:0,62:62:99:1872,186,0:0,0,37,25 chr1 203040816 . G C 1110.68 PASS AC=2;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 1/1:0,141:141:99:4138,421,0:0,0,73,68 chr1 203045901 . G A,T 709.99 PASS AC=2,0;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 1/1:65:99:0,0,35,30 chr1 203046195 . A G 323.89 PASS AC=2;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 1/1:0,41:41:99:1355,123,0:0,0,18,23 chr1 203046466 . C T 884.61 PASS AC=1;AF=0.533;AN=2;DP=775;MQ=60;set=variant3-variant4-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant23-variant26-variant30-variant34-variant40 GT:AD:DP:GQ:PL:SB 0/1:23,26:49:99:635,0,522:13,10,14,12 chr1 203046534 . A G 496.23 PASS AC=1;AF=0.533;AN=2;DP=675;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant23-variant26-variant30-variant34-variant40 GT:AD:DP:GQ:PL:SB 0/1:18,19:37:99:377,0,338:8,10,9,10 chr1 203046675 . G C 311.82 PASS AC=1;AF=0.533;AN=2;DP=729;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant23-variant26-variant30-variant34-variant40 GT:AD:DP:GQ:PL:SB 0/1:36,12:48:99:304,0,858:19,17,6,6 chr1 203046779 . C T 469.51 PASS AC=1;AF=0.536;AN=2;DP=542;MQ=60;set=variant3-variant4-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant23-variant26-variant30-variant40 GT:AD:DP:GQ:PL:SB 0/1:18,8:26:99:201,0,531:8,10,5,3 chr1 203047621 . C A 531.66 PASS AC=2;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 1/1:0,37:37:99:1105,111,0:0,0,18,19 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 1/1:0,12:12:36:460,36,0:0,0,10,2 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 1/1:0,85:85:99:2533,255,0:0,0,43,42 chr1 203055101 . A G 2847.53 PASS AC=1;AF=0.727;AN=2;DP=5283;MQ=60;set=variant-variant2-variant3-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,70:163:99:1757,0,2526:37,56,24,46 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 0/1:28,26:54:99:586,0,560:16,12,15,11 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 0/1:88,81:169:99:1967,0,2198:33,55,29,52 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 0/1:11,6:17:99:146,0,269:4,7,1,5 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 0/1:24,18:42:99:681,0,1582:6,18,7,11 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 1/1:0,82:82:99:2553,246,0:0,0,40,42 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 0/1:40,37:77:99:1008,0,1004:21,19,24,13 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 1/1:0,71:71:99:2598,214,0:0,0,39,32 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 1/1:0,54:54:99:1810,165,0:0,0,35,19 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 0/1:35,33:68:99:1279,0,1387:22,13,20,13 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 0/1:25,25:50:99:734,0,700:12,13,6,19 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 0/1:10,13:23:99:392,0,297:3,7,3,10 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 0/1:5,12:17:99:364,0,152:0,5,3,9 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 0/1:74,68:142:99:1579,0,1900:43,31,35,33 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 1/1:0,110:110:99:3510,330,0:0,0,46,64 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 0/1:6,13:19:99:325,0,133:2,4,6,7 chr1 203150208 . G A 847.61 PASS AC=1;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 0/1:12,16:28:99:417,0,364:10,2,13,3 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 0/1:8,29:37:99:900,0,242:6,2,20,9 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 1/1:0,86:86:99:2660,258,0:0,0,31,55 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 0/1:23,9:32:99:252,0,710:17,6,8,1 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 0/1:48,34:82:99:872,0,1174:29,19,23,11 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 0/1:31,16:47:99:490,0,895:7,24,4,12 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 0/1:18,18:36:99:768,0,1003:7,11,6,12 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 0/1:95,105:200:99:4060,0,6465:41,54,40,65 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 0/1:28,29:57:99:685,0,752:17,11,18,11 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 0/1:11,22:33:99:725,0,345:9,2,18,4 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 0/1:15,11:26:99:301,0,425:7,8,2,9 chr1 203276437 . C T 1333.12 PASS AC=1;AF=0.5;AN=2;DP=311;FractionInformativeReads=1;MQ=60;set=variant23-variant40 GT:AD:DP:GQ:PL:SB 0/1:84,62:146:99:1361,0,2023:39,45,28,34 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 1/1:0,29:29:87:884,87,0:0,0,12,17 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 0/1:5,3:8:67:67,0,112:3,2,2,1 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 0/1:2,22:24:20:588,0,20:1,1,12,10 chr1 203309966 . G C 798.26 PASS AC=1;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 0/1:10,20:30:99:550,0,195:4,6,7,13 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 0/1:27,28:55:99:751,0,771:13,14,15,13 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 1/1:0,127:127:99:3961,379,0:0,0,70,57 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 1/1:0,57:57:99:1769,171,0:0,0,34,23 chr1 203444849 . T G 63 PASS AC=2;AF=0.8;AN=2;DP=130;MQ=60;set=variant2-variant4-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant31-variant33-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:106,9,0:0,0,1,2 chr1 203452226 . T C 674.14 PASS AC=1;AF=0.583;AN=2;DP=935;FractionInformativeReads=1;MQ=60;set=variant4-variant10-variant18-variant20-variant23-variant26-variant30-variant31-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,17:51:99:379,0,1007:20,14,7,10 chr1 203456098 . T C 923.52 PASS AC=1;AF=0.583;AN=2;DP=870;FractionInformativeReads=1;MQ=60;set=variant4-variant10-variant18-variant20-variant23-variant26-variant30-variant31-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,47:80:99:1269,0,896:14,19,26,21 chr1 203456221 . C A 1274.24 PASS AC=1;AF=0.583;AN=2;DP=1234;FractionInformativeReads=1;MQ=60;set=variant4-variant10-variant18-variant20-variant23-variant26-variant30-variant31-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,54:107:99:1386,0,1268:29,24,27,27 chr1 203456890 . G GGCA 1318.78 PASS AC=1;AF=0.694;AN=2;DP=3021;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,34:84:99:1291,0,2324:24,26,16,18 chr1 203457961 . T C 1276.41 PASS AC=1;AF=0.571;AN=2;DP=1473;MQ=60;set=variant4-variant7-variant10-variant18-variant20-variant23-variant26-variant30-variant31-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,38:94:99:872,0,1182:25,31,15,23 chr1 203458037 . A T 535.53 PASS AC=1;AF=0.577;AN=2;DP=691;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant10-variant18-variant20-variant23-variant26-variant30-variant31-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,16:39:99:369,0,763:8,15,5,11 chr1 203459566 . C T 211.2 PASS AC=1;AF=0.591;AN=2;DP=310;FractionInformativeReads=1;MQ=60;set=variant4-variant10-variant18-variant20-variant23-variant26-variant31-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,9:24:99:220,0,446:8,7,6,3 chr1 203465396 . T C 4299.44 PASS AC=1;AF=0.63;AN=2;DP=3131;MQ=60;set=variant3-variant4-variant5-variant7-variant10-variant12-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,60:101:99:1445,0,1008:18,23,24,36 chr1 203465570 . C G 198.14 PASS AC=1;AF=0.691;AN=2;DP=592;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:186,0,228:2,6,3,4 chr1 203468165 . C A 356.83 PASS AC=1;AF=0.583;AN=2;DP=351;FractionInformativeReads=1;MQ=60;set=variant4-variant10-variant18-variant20-variant23-variant26-variant30-variant31-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,12:29:99:315,0,477:5,12,3,9 chr1 203473044 . T C 468.79 PASS AC=1;AF=0.681;AN=2;DP=1025;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,16:26:99:568,0,275:5,5,2,14 chr1 203596280 . C T 709.77 PASS AC=1;AF=0.5;AN=2;DP=175;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant23-variant39 GT:AD:DP:GQ:PL:SB 0/1:14,19:33:99:488,0,282:6,8,6,13 chr1 203596318 . A G 991.72 PASS AC=2;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 1/1:0,32:32:96:986,96,0:0,0,15,17 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 1/1:0,14:14:42:497,42,0:0,0,9,5 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 1/1:0,59:59:99:1637,176,0:0,0,30,29 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 1/1:0,49:49:99:1502,146,0:0,0,26,23 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 1/1:0,40:40:99:1800,120,0:0,0,17,23 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 1/1:0,40:40:99:1800,120,0:0,0,17,23 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 1/1:0,126:126:99:3833,378,0:0,0,67,59 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 1/1:0,163:163:99:5068,489,0:0,0,87,76 chr1 203667536 . A G 1421.92 PASS AC=1;AF=0.553;AN=2;DP=2079;MQ=60;set=variant4-variant10-variant11-variant12-variant13-variant16-variant18-variant22-variant23-variant24-variant25-variant28-variant31-variant32-variant36-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:40,58:98:99:1548,0,859:14,26,21,37 chr1 203698672 . CAA CA,CAAA,C 226.51 PASS AC=1,0,0;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 0/1:34:99:14,7,10,3 chr1 203709034 . A G 353.12 PASS AC=1;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 0/1:28,28:56:99:647,0,717:14,14,14,14 chr1 203709068 . T C 450.79 PASS AC=1;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 0/1:30,27:57:99:627,0,772:16,14,15,12 chr1 203709569 . CTTT CT,CTT,CTTTT,C 863.68 PASS AC=1,0,0,0;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 0/1:68:99:18,12,19,19 chr1 203740615 . T C 3000.35 PASS AC=2;AF=0.743;AN=2;DP=3627;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2518,228,0:0,0,30,46 chr1 203741110 . C T 862.4 PASS AC=1;AF=0.542;AN=2;DP=710;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant10-variant15-variant18-variant23-variant26-variant29-variant33-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,34:49:99:727,0,318:10,5,19,15 chr1 203741368 . C A 878.6 PASS AC=2;AF=0.743;AN=2;DP=1064;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:706,66,0:0,0,8,14 chr1 203744258 . T C 205.68 PASS AC=2;AF=0.766;AN=2;DP=307;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:317,27,0:0,0,3,6 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 1/1:2,188:190:99:6095,550,0:2,0,104,84 chr1 203766395 . T C 3564.59 PASS AC=2;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 1/1:0,93:93:99:3098,278,0:0,0,32,61 chr1 203766827 . T C 2864.06 PASS AC=2;AF=0.712;AN=2;DP=3777;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3635,346,0:0,0,55,61 chr1 203770945 . ATT AT,A,ATTT 940.64 PASS AC=2,0,0;AF=0.58,0.307,0.011;AN=2;DP=2312;MQ=60;set=Intersection GT:DP:GQ:SB 1/1:47:99:0,1,24,22 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 1/1:2,27:29:26:636,26,0:1,1,8,19 chr1 203771842 . C CT 331.78 PASS AC=2;AF=0.691;AN=2;DP=712;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant36-filterInvariant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:229,24,0:0,0,0,8 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 1/1:0,37:37:99:1233,111,0:0,0,26,11 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 1/1:0,93:93:99:2816,279,0:0,0,36,57 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 1/1:0,66:66:99:2014,197,0:0,0,42,24 chr1 203839273 . C T 780.9 PASS AC=2;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 1/1:0,23:23:69:704,69,0:0,0,15,8 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 1/1:0,192:192:99:5713,575,0:0,0,107,85 chr1 204006095 . A G 1444.8 PASS AC=1;AF=0.615;AN=2;DP=2903;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant12-variant14-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,52:94:99:1375,0,1010:28,14,35,17 chr1 204006451 . G A 308.14 PASS AC=1;AF=0.62;AN=2;DP=462;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant10-variant12-variant14-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant30-variant31-variant33-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,8:15:99:274,0,251:6,1,4,4 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 1/1:0,41:41:99:1416,123,0:0,0,31,10 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 1/1:0,91:91:99:2747,270,0:0,0,55,36 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 1/1:0,19:19:57:747,57,0:0,0,3,16 chr1 204081655 . A T,ACACACACACT,ACACACT,ACACACACT,ACACACACACACACT 960.61 PASS AC=1,1,0,0,0;AF=0.433,0.233,0.233,0.033,0.033;AN=2;DP=729;MQRankSum=-0.603;ReadPosRankSum=0.733;set=variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant19-variant23-variant17-variant25-variant27-variant29-variant33-variant34 GT:DP:GQ:SB 1/2:20:99:0,0,13,7 chr1 204082002 . C T 1309.73 PASS AC=1;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 0/1:41,48:89:99:1418,0,1194:23,18,25,23 chr1 204082323 . C T 332.79 PASS AC=1;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 0/1:11,14:25:99:426,0,336:2,9,4,10 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 1/1:0,34:34:99:969,102,0:0,0,16,18 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 1/1:0,35:35:99:1010,105,0:0,0,21,14 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 1/1:0,198:198:99:5821,593,0:0,0,110,88 chr1 204115934 . C T 984.93 PASS AC=1;AF=0.636;AN=2;DP=3006;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant17-variant18-variant19-variant21-variant23-variant25-variant27-variant28-variant29-variant30-variant34-variant36-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:84,72:156:99:1778,0,1969:40,44,32,40 chr1 204116624 . G T 2611.13 PASS AC=1;AF=0.583;AN=2;DP=1472;MQ=60;set=variant7-variant19-variant23-variant28-variant29-variant30 GT:AD:DP:GQ:PL:SB 0/1:118,135:253:99:3362,0,2823:53,65,58,77 chr1 204124865 . C T 1527.96 PASS AC=1;AF=0.62;AN=2;DP=2623;MQ=60;set=variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:54,41:95:99:1037,0,1338:29,25,24,17 chr1 204125272 . C A 1448.67 PASS AC=1;AF=0.548;AN=2;DP=2363;MQ=60;set=variant7-variant9-variant13-variant16-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:73,43:116:99:1044,0,1951:48,25,29,14 chr1 204125987 . T C 634.65 PASS AC=1;AF=0.542;AN=2;DP=384;FractionInformativeReads=1;MQ=60;set=variant7-variant13-variant19-variant21-variant23-variant28-variant29-variant30-variant34-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:11,6:17:99:108,0,285:3,8,1,5 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 0/1:30,20:50:99:504,0,687:18,12,13,7 chr1 204159922 . T C 2624.64 PASS AC=1;AF=0.55;AN=2;DP=1574;MQ=60;set=variant3-variant7-variant19-variant21-variant23-variant28-variant29-variant30-variant34-variant39 GT:AD:DP:GQ:PL:SB 0/1:76,58:134:99:1237,0,1816:42,34,32,26 chr1 204167467 . T C 742.79 PASS AC=1;AF=0.5;AN=2;DP=554;FractionInformativeReads=1;MQ=60;set=variant5-variant11-variant20-variant23-variant25-variant33-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,38:73:99:1029,0,888:20,15,23,15 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 0/1:20,15:35:99:364,0,592:15,5,10,5 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 0/1:30,23:53:99:551,0,815:15,15,13,10 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 0/1:43,24:67:99:624,0,1143:22,21,12,12 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 0/1:56,38:94:99:846,0,1442:27,29,19,19 chr1 204191148 . ATCTC ATC,ATCTCTCTCTCTCTC,ATCTCTC,ATCTCTCTCTCTCTCTCTC,ATCTCTCTCTCTCTCTCTCTCTC,A,ATCTCTCTCTCTCTCTCTCTC,ATCTCTCTC,ATCTCTCTCTCTCTCTC 369.01 PASS AC=1,0,0,1,0,0,0,0,0;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 1/4:23:99:0,0,9,14 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 0/1:42,30:72:99:710,0,1090:21,21,16,14 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 0/1:5,9:14:99:238,0,137:4,1,6,3 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 0/1:8,11:19:99:235,0,243:6,2,5,6 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 0/1:24,23:47:99:604,0,629:7,17,7,16 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 0/1:52,61:113:99:1341,0,1378:32,20,36,25 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 0/1:11,16:27:99:513,0,298:4,7,10,6 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 0/1:22,15:37:99:358,0,703:12,10,8,7 chr1 204214975 . TACACACAC TAC,TACACAC,T,TACAC 1010.66 PASS AC=1,0,0,0;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 0/1:27:99:1,6,6,14 chr1 204216410 . C T 5956.25 PASS AC=1;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 0/1:102,68:170:99:1545,0,2330:54,48,37,31 chr1 204216468 . C T 5271.6 PASS AC=1;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 0/1:82,50:132:99:1034,0,2039:36,46,23,27 chr1 204216601 . G A 1528.13 PASS AC=1;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 0/1:30,28:58:99:706,0,878:12,18,12,16 chr1 204216762 . C T 403.45 PASS AC=1;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 0/1:17,15:32:99:410,0,362:7,10,8,7 chr1 204218633 . G C 800.96 PASS AC=1;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 0/1:24,9:33:99:254,0,591:10,14,3,6 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 1/1:0,9:9:27:302,27,0:0,0,3,6 chr1 204219850 . G A 1527.06 PASS AC=1;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 0/1:32,30:62:99:700,0,816:10,22,13,17 chr1 204230581 . G A 1323.58 PASS AC=1;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 0/1:30,49:79:99:1220,0,728:10,20,21,28 chr1 204234196 . GGT G,GGTGT,GGTGTGT 2004.54 PASS AC=0,1,0;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 0/2:64:99:13,21,12,18 chr1 204234222 . T C 2812.67 PASS AC=1;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 0/1:36,27:63:99:1015,0,1784:15,21,14,13 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 0/1:36,27:63:99:1015,0,1784:15,21,14,13 chr1 204237113 . TC T 1023.55 PASS AC=1;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 0/1:14,12:26:99:406,0,487:9,5,7,5 chr1 204237416 . C T 2816.02 PASS AC=1;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 0/1:62,60:122:99:1338,0,1517:30,32,31,29 chr1 204379617 . T C 4944.53 PASS AC=2;AF=0.989;AN=2;DP=7006;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:4216,420,0:0,0,69,71 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 1/1:0,47:47:99:1470,140,0:0,0,34,13 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 1/1:0,102:102:99:4464,307,0:0,0,45,57 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 1/1:0,99:99:99:4464,307,0:0,0,43,56 chr1 204416380 . G C 191.18 PASS AC=1;AF=0.5;AN=2;DP=13;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.493;QD=14.71;ReadPosRankSum=0.811;SOR=0.551;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:219,0,240:6,1,5,1 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 1/1:0,36:36:99:1110,108,0:0,0,19,17 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 1/1:0,23:23:69:742,69,0:0,0,17,6 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 1/1:0,48:48:99:1475,143,0:0,0,29,19 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 1/1:1,6:7:10:151,10,0:1,0,5,1 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 1/1:0,60:60:99:2690,181,0:0,0,20,40 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 1/1:0,59:59:99:2690,181,0:0,0,20,39 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 1/1:0,58:58:99:2655,178,0:0,0,20,38 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 1/1:0,57:57:99:2655,178,0:0,0,19,38 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 1/1:0,12:12:36:519,36,0:0,0,1,11 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 1/1:2,154:156:99:4652,418,0:1,1,67,87 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 1/1:0,54:54:99:1803,162,0:0,0,39,15 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 1/1:0,33:33:99:1254,102,0:0,0,20,13 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 1/1:0,18:18:54:722,54,0:0,0,14,4 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 1/1:0,4:4:12:139,12,0:0,0,1,3 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 1/1:0,144:144:99:4387,429,0:0,0,64,80 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 1/1:1,78:79:99:2417,199,0:0,1,39,39 chr1 204494436 . C T 955.99 PASS AC=1;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 0/1:27,38:65:99:1049,0,691:19,8,24,14 chr1 204495595 . GTT GTTT,GTTTT,G 514.13 PASS AC=1,0,0;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 0/1:26:99:4,9,4,9 chr1 204505976 . GA G 335.63 PASS AC=1;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 0/1:9,5:14:99:114,0,238:6,3,3,2 chr1 204506107 . C T 1194.34 PASS AC=1;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 0/1:24,16:40:99:289,0,554:12,12,7,9 chr1 204512100 . T C 625.1 PASS AC=1;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 0/1:8,12:20:99:277,0,211:2,6,5,7 chr1 204515863 . C T 444.37 PASS AC=1;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 0/1:13,6:19:99:132,0,400:10,3,4,2 chr1 204516025 . A G 2592.95 PASS AC=1;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 0/1:57,44:101:99:876,0,1234:29,28,23,21 chr1 204518842 . C A 5770.27 PASS AC=1;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 0/1:91,66:157:99:1683,0,2394:54,37,37,29 chr1 204519187 . C G 6734.33 PASS AC=1;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 0/1:104,107:211:99:2620,0,2496:50,54,47,60 chr1 204519258 . G GT 2002.13 PASS AC=1;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 0/1:42,39:81:99:621,0,786:12,30,13,26 chr1 204519692 . GT G 279.59 PASS AC=1;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 0/1:6,6:12:99:119,0,109:2,4,3,3 chr1 204520209 . C T 2994.87 PASS AC=1;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 0/1:9,29:38:99:895,0,184:2,7,6,23 chr1 204520589 . CTTTTTTTTTTT CTT,CT,CTTTTTT,CTTTTTTTTTT,CTTTTT,CTTTT,C,CTTT,CTTTTTTTT 242.23 PASS AC=0,0,0,0,1,0,0,0,0;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 0/5:9:99:3,3,0,3 chr1 204522457 . T C 1764.91 PASS AC=1;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 0/1:29,45:74:99:1288,0,914:16,13,24,21 chr1 204522489 . C T 1733.74 PASS AC=1;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 0/1:26,33:59:99:1096,0,779:17,9,20,13 chr1 204524474 . G T 496.69 PASS AC=1;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 0/1:6,7:13:99:257,0,154:5,1,7,0 chr1 204525054 . GT G 8077.97 PASS AC=1;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 0/1:112,128:240:99:2884,0,2358:59,53,65,63 chr1 204525568 . G T 157.45 PASS AC=1;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 0/1:8,3:11:99:102,0,237:3,5,0,3 chr1 204526721 . G A 1060.73 PASS AC=1;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 0/1:14,8:22:99:263,0,523:13,1,8,0 chr1 204527057 . TAAC T 3174.27 PASS AC=1;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 0/1:40,53:93:99:1995,0,1524:16,24,23,30 chr1 204586805 . G A 1917.24 PASS AC=1;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 0/1:37,37:74:99:1029,0,1007:15,22,19,18 chr1 204587240 . G A 3282 PASS AC=1;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 0/1:44,52:96:99:1248,0,1082:22,22,24,28 chr1 204587364 . C T 1680.27 PASS AC=1;AF=0.5;AN=2;DP=131;FS=0.675;FractionInformativeReads=0.992;MQ=60;MQRankSum=-1.196;QD=12.83;ReadPosRankSum=-0.258;SOR=0.585;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:57,73:130:99:1708,0,1475:36,21,44,29 chr1 204589066 . C T 1184.97 PASS AC=1;AF=0.5;AN=2;DP=1792;MQ=60;set=variant2-variant7-variant12-variant14-variant17-variant19-variant23-variant24-variant25-variant26-variant28-variant30-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:56,57:113:99:1361,0,1431:28,28,26,31 chr1 204590044 . G A 1264.54 PASS AC=1;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 0/1:4,18:22:99:541,0,117:3,1,10,8 chr1 204591237 . A G 620.32 PASS AC=1;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 0/1:28,34:62:99:814,0,806:9,19,16,18 chr1 204889555 . CTTT C,CTT,CT 179.15 PASS AC=0,0,1;AF=0.206,0.088,0.206;AN=2;DP=156;set=variant-variant3-variant5-variant9-variant10-variant12-variant19-variant20-variant21-variant23-variant24-variant28-variant30-variant31-variant32-variant39-variant44 GT:DP:GQ:SB 0/3:11:16:2,0,7,2 chr1 204889575 . T C 71.38 PASS AC=1;AF=0.563;AN=2;DP=93;FractionInformativeReads=1;set=variant-variant7-variant12-variant23-variant26-variant34-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:15,4:19:70:70,0,500:13,2,3,1 chr1 204913271 . C G 544.1 PASS AC=1;AF=0.538;AN=2;DP=1602;MQ=60;set=variant-variant2-variant3-variant8-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant36-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,24:58:99:601,0,835:21,13,15,9 chr1 204913652 . A G 91.72 PASS AC=2;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 1/1:0,10:10:30:348,30,0:0,0,2,8 chr1 204915393 . A G 1140.01 PASS AC=2;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 1/1:0,92:92:99:2854,276,0:0,0,43,49 chr1 204917680 . C T 650.15 PASS AC=1;AF=0.54;AN=2;DP=1356;MQ=60;set=variant-variant2-variant3-variant8-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant36-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,27:46:99:794,0,540:13,6,20,7 chr1 204921258 . A G 1214.46 PASS AC=1;AF=0.567;AN=2;DP=3676;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant29-variant31-variant32-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,66:121:99:1600,0,1373:26,29,28,38 chr1 204926980 . C T 597.86 PASS AC=1;AF=0.5;AN=2;DP=1560;set=variant-variant2-variant3-variant8-variant11-variant12-variant14-variant16-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:31,21:52:99:559,0,748:12,19,5,16 chr1 204931077 . G A 390.03 PASS AC=1;AF=0.5;AN=2;DP=563;MQ=60;set=variant-variant2-variant3-variant8-variant11-variant12-variant14-variant16-variant20-variant21-variant23-variant24-variant25-variant28-variant30-variant31-variant33-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:365,0,467:11,2,10,3 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 1/1:0,113:113:99:3388,337,0:0,0,66,47 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 1/1:0,103:103:99:3481,309,0:0,0,40,63 chr1 204945338 . CTA C 2374.58 PASS AC=1;AF=0.523;AN=2;DP=2873;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant11-variant12-variant14-variant15-variant20-variant21-variant23-variant24-variant25-variant28-variant30-variant31-variant33-variant36-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:60,49:109:99:1868,0,2385:26,34,19,30 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 0/1:45,51:96:99:1237,0,1043:23,22,24,27 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 0/1:23,37:60:99:955,0,544:8,15,16,21 chr1 204953459 . A ATG 238.79 PASS AC=2;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 1/1:0,10:10:30:371,30,0:0,0,1,9 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 0/1:6,14:20:99:420,0,163:5,1,11,3 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 0/1:11,20:31:99:770,0,687:3,8,4,16 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 0/1:10,17:27:99:710,0,693:2,8,3,14 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 0/1:6,4:10:99:147,0,213:5,1,4,0 chr1 204966428 . C G 867.28 PASS AC=2;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 1/1:0,104:104:99:3215,310,0:0,0,53,51 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 1/1:0,92:92:99:2923,274,0:0,0,32,60 chr1 204966749 . A G 597.28 PASS AC=1;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 0/1:27,30:57:99:838,0,637:8,19,8,22 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 0/1:7,3:10:73:73,0,205:5,2,3,0 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 0/1:47,32:79:99:769,0,1206:29,18,22,10 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 0/1:74,49:123:99:1069,0,1720:39,35,27,22 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 0/1:10,9:19:99:229,0,275:4,6,3,6 chr1 204978533 . A G 4174.58 PASS AC=2;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 1/1:0,98:98:99:3106,293,0:0,0,48,50 chr1 204978643 . C A 2424.86 PASS AC=2;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 1/1:0,121:121:99:3549,361,0:0,0,60,61 chr1 204978704 . G A 502.74 PASS AC=1;AF=0.5;AN=2;DP=1654;MQ=60;set=variant-variant2-variant4-variant8-variant11-variant12-variant15-variant21-variant23-variant24-variant28-variant30-variant36 GT:AD:DP:GQ:PL:SB 0/1:64,54:118:99:1387,0,1613:32,32,23,31 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 1/1:0,43:43:99:1584,129,0:0,0,20,23 chr1 204988183 . C A 1363.89 PASS AC=1;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 0/1:33,41:74:99:1054,0,868:20,13,21,20 chr1 204988535 . T C 715.17 PASS AC=1;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 0/1:28,22:50:99:543,0,728:12,16,10,12 chr1 204988603 . C CCATTCATT,CCATTCATTCATT,CCATTCATTCATTCATT,CCATT 727.14 PASS AC=1,1,0,0;AF=0.625,0.273,0.011,0.034;AN=2;DP=2091;set=Intersection GT:DP:GQ:SB 1/2:30:99:0,0,14,16 chr1 204989163 . T G 2241.75 PASS AC=1;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 0/1:38,43:81:99:988,0,1127:17,21,21,22 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 1/1:0,66:66:99:2178,197,0:0,0,30,36 chr1 204991517 . A C 84.91 PASS AC=1;AF=0.5;AN=2;DP=2175;set=filterInvariant-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant15-filterInvariant16-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant26-filterInvariant27-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-variant36-filterInvariant38-filterInvariant40-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:52,20:72:99:220,0,1041:8,44,20,0 chr1 204991596 . C G 1515.74 PASS AC=1;AF=0.583;AN=2;DP=2059;MQ=60;set=variant3-variant4-variant6-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant20-variant23-variant25-variant26-variant27-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,31:65:99:819,0,1091:12,22,17,14 chr1 204991770 . C T 785.67 PASS AC=1;AF=0.548;AN=2;DP=1303;MQ=60;set=variant3-variant4-variant6-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant20-variant23-variant25-variant26-variant27-variant34-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,29:60:99:870,0,884:12,19,9,20 chr1 205022207 . C G 381.37 PASS AC=1;AF=0.5;AN=2;DP=242;MQ=60;set=variant5-variant13-variant14-variant23-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:18,24:42:99:660,0,469:12,6,16,8 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 0/1:7,4:11:99:147,0,283:3,4,0,4 chr1 205031116 . C T 2270.17 PASS AC=1;AF=0.569;AN=2;DP=7194;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant27-variant28-variant30-variant31-variant32-variant34-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:112,153:265:99:3480,0,2607:56,56,79,74 chr1 205033283 . G A 408.53 PASS AC=1;AF=0.586;AN=2;DP=463;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant27-variant28-variant30-variant31-variant32-variant34-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,14:18:99:512,0,129:4,0,10,4 chr1 205033374 . T C 1477.73 PASS AC=1;AF=0.569;AN=2;DP=3130;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant27-variant28-variant30-variant31-variant32-variant34-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,54:90:99:1396,0,825:25,11,34,20 chr1 205033518 . C G 2232.94 PASS AC=1;AF=0.5;AN=2;DP=675;FractionInformativeReads=1;MQ=60;set=variant5-variant13-variant14-variant23 GT:AD:DP:GQ:PL:SB 0/1:75,97:172:99:2544,0,1656:36,39,46,51 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 0/1:37,17:54:99:591,0,8387:21,16,17,0 chr1 205038731 . C T 2522.09 PASS AC=2;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 1/1:0,64:64:99:1955,191,0:0,0,21,43 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 0/1:31,26:57:99:643,0,1204:10,21,9,17 chr1 205039295 . A C 922.36 PASS AC=1;AF=0.5;AN=2;DP=1227;MQ=60;set=variant2-variant4-variant7-variant10-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant31-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,29:53:99:776,0,921:8,16,9,20 chr1 205040835 . A G 156.22 PASS AC=2;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 1/1:0,11:11:33:333,33,0:0,0,7,4 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 0/1:14,12:26:99:285,0,389:8,6,7,5 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 0/1:31,34:65:99:878,0,697:17,14,22,12 chr1 205041542 . T C 206.62 PASS AC=1;AF=0.529;AN=2;DP=384;MQ=60;set=variant2-variant4-variant7-variant10-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant29-variant31-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:232,0,144:4,2,7,1 chr1 205042583 . C T 190.95 PASS AC=1;AF=0.5;AN=2;DP=300;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant10-variant15-variant17-variant18-variant19-variant22-variant23-variant31-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:121,0,201:5,3,4,1 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 0/1:18,18:36:99:488,0,393:9,9,10,8 chr1 205044339 . A G 2449.37 PASS AC=1;AF=0.597;AN=2;DP=1849;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant10-variant12-variant13-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,22:45:99:479,0,580:11,12,11,11 chr1 205044354 . G A 1548.25 PASS AC=2;AF=0.886;AN=2;DP=2819;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1488,117,0:0,0,18,19 chr1 205044416 . C A 1344.87 PASS AC=2;AF=0.909;AN=2;DP=3003;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:1783,165,0:0,0,30,25 chr1 205044842 . T C 234.01 PASS AC=1;AF=0.5;AN=2;DP=358;MQ=60;set=variant2-variant4-variant7-variant10-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant31-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:240,0,354:2,9,2,5 chr1 205044866 . G C 863.29 PASS AC=2;AF=0.886;AN=2;DP=1146;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:934,75,0:0,0,8,17 chr1 205045087 . G A 1208.93 PASS AC=1;AF=0.609;AN=2;DP=1719;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant10-variant12-variant13-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,28:57:99:693,0,727:14,15,11,17 chr1 205046894 . T C 838.14 PASS AC=1;AF=0.5;AN=2;DP=990;MQ=60;set=variant2-variant4-variant7-variant10-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant31-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,18:46:99:390,0,806:16,12,10,8 chr1 205052939 . G A 2932.65 PASS AC=2;AF=0.875;AN=2;DP=4143;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2775,243,0:0,0,34,47 chr1 205053219 . C T 2401.77 PASS AC=2;AF=0.886;AN=2;DP=5392;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,114:114:99:3555,340,0:0,0,62,52 chr1 205053759 . A ACT 1168.21 PASS AC=2;AF=0.898;AN=2;DP=965;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:870,60,0:0,0,0,20 chr1 205055949 . G A 2296.37 PASS AC=2;AF=0.886;AN=2;DP=2960;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1831,173,0:0,0,33,25 chr1 205056326 . ATT A,AT,ATTT 253.97 PASS AC=0,0,1;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 0/3:9:53:0,5,1,3 chr1 205056844 . T TTA 2262.45 PASS AC=2;AF=0.886;AN=2;DP=2903;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:2111,150,0:0,0,22,28 chr1 205063949 . C T 168.24 PASS AC=1;AF=0.609;AN=2;DP=788;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant29-variant30-variant32-variant33-variant34-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:252,0,359:9,2,7,2 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 0/1:38,33:71:99:831,0,1039:25,13,18,15 chr1 205067972 . CAA CA,C,CAAAA 67.31 PASS AC=0,2,0;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 2/2:5:5:0,1,4,0 chr1 205070573 . G A 440.7 PASS AC=1;AF=0.63;AN=2;DP=256;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant10-variant12-variant15-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:99:198,0,106:3,0,6,0 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 0/1:12,8:20:99:178,0,317:7,5,5,3 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 0/1:10,17:27:99:443,0,278:1,9,7,10 chr1 205085358 . T C 211.85 PASS AC=1;AF=0.531;AN=2;DP=457;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant10-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant31-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,13:27:99:376,0,349:6,8,4,9 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 0/1:37,48:85:99:1023,0,907:22,15,27,21 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 0/1:23,33:56:99:875,0,582:12,11,15,18 chr1 205112911 . T C 885.09 PASS AC=1;AF=0.5;AN=2;DP=985;MQ=60;set=variant2-variant4-variant7-variant8-variant10-variant13-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant31-variant34-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,21:40:99:510,0,483:10,9,11,10 chr1 205113833 . A G 720.3 PASS AC=1;AF=0.5;AN=2;DP=1503;MQ=60;set=variant2-variant4-variant7-variant8-variant10-variant13-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant31-variant34-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,28:68:99:850,0,1221:11,29,6,22 chr1 205114653 . G GT,GTT 602.7 PASS AC=1,0;AF=0.533,0.033;AN=2;DP=3303;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-filterInvariant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-filterInvariant27-filterInvariant30-variant31-variant34-variant37-variant38-filterInvariant40-variant41-filterInvariant42-variant43-variant44 GT:DP:GQ:SB 0/1:84:99:15,33,12,24 chr1 205114659 . T TG 255.01 PASS AC=1;AF=0.5;AN=2;DP=89;FS=5.535;FractionInformativeReads=0.787;MQ=59.81;MQRankSum=-0.386;QD=2.87;ReadPosRankSum=3.46;SOR=1.477;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:48,22:70:99:292,0,1723:18,30,5,17 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 0/1:40,40:80:99:1542,0,1502:14,26,14,26 chr1 205114873 . C G 913.09 PASS AC=1;AF=0.594;AN=2;DP=964;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant10-variant12-variant13-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:184,0,267:5,5,5,3 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 0/1:23,17:40:99:413,0,592:12,11,8,9 chr1 205115150 . C A 807.09 PASS AC=1;AF=0.5;AN=2;DP=1203;MQ=60;set=variant2-variant4-variant7-variant8-variant10-variant13-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant31-variant34-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,23:47:99:632,0,683:14,10,13,10 chr1 205129319 . G A 771.37 PASS AC=1;AF=0.5;AN=2;DP=1279;MQ=60;set=variant2-variant4-variant7-variant8-variant10-variant13-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant31-variant34-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,37:57:99:840,0,484:10,10,15,22 chr1 205130413 . A G 2290.47 PASS AC=2;AF=0.955;AN=2;DP=3669;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1713,177,0:0,0,29,30 chr1 205131059 . G GAC 1018.58 PASS AC=2;AF=0.886;AN=2;DP=1545;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,18:18:57:720,57,0:0,0,11,7 chr1 205157100 . T C 111.61 PASS AC=2;AF=0.757;AN=2;DP=296;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:212,15,0:0,0,2,3 chr1 205157108 . A G 361.63 PASS AC=2;AF=0.905;AN=2;DP=313;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-variant36-variant37-variant38-variant39-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 205225457 . G A 3543.38 PASS AC=1;AF=0.589;AN=2;DP=3638;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,55:107:99:1422,0,1342:28,24,29,26 chr1 205238275 . A G 3690.14 PASS AC=1;AF=0.614;AN=2;DP=4362;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant16-variant17-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:92,95:187:99:2288,0,2253:51,41,53,42 chr1 205238530 . C T 7002 PASS AC=1;AF=0.614;AN=2;DP=5408;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant16-variant17-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:154,114:268:99:2630,0,3831:77,77,55,59 chr1 205239031 . C G 151.77 PASS AC=1;AF=0.614;AN=2;DP=622;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant16-variant17-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:7,12:19:99:350,0,162:2,5,3,9 chr1 205240141 . G T 1785.66 PASS AC=1;AF=0.66;AN=2;DP=1233;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant16-variant17-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,33:51:99:1345,0,902:10,8,19,14 chr1 205240145 . A G 1714.76 PASS AC=1;AF=0.652;AN=2;DP=1125;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant16-variant17-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:17,34:51:99:1348,0,881:9,8,20,14 chr1 205240251 . C T 1813.96 PASS AC=1;AF=0.614;AN=2;DP=1590;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant16-variant17-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant33-variant34-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,41:61:99:1145,0,502:12,8,22,19 chr1 205240913 . A G 765.82 PASS AC=2;AF=0.955;AN=2;DP=1735;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:1029,90,0:0,0,20,10 chr1 205241659 . T C 1478.75 PASS AC=2;AF=0.955;AN=2;DP=2692;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1493,141,0:0,0,26,21 chr1 205272926 . C T 1347.81 PASS AC=1;AF=0.567;AN=2;DP=1664;MQ=60;set=variant2-variant4-variant12-variant19-variant21-variant23-variant24-variant28-variant32-variant34-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:53,36:89:99:964,0,1497:29,24,19,17 chr1 205272983 . C G 1495.38 PASS AC=1;AF=0.571;AN=2;DP=1759;MQ=60;set=variant2-variant4-variant12-variant19-variant21-variant23-variant24-variant28-variant32-variant34-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:58,48:106:99:1181,0,1570:34,24,28,20 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 0/1:6,16:22:99:516,0,152:5,1,13,3 chr1 205275061 . C T 368.2 PASS AC=2;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 1/1:0,8:8:24:352,24,0:0,0,8,0 chr1 205275206 . A T 6847.12 PASS AC=2;AF=0.989;AN=2;DP=6006;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:5683,388,0:0,0,79,50 chr1 205275207 . G T 6847.12 PASS AC=2;AF=0.989;AN=2;DP=6043;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:5683,388,0:0,0,79,50 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 1/1:0,91:91:99:2988,273,0:0,0,33,58 chr1 205312280 . C G 224.78 PASS AC=2;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 1/1:0,41:41:99:1588,123,0:0,0,35,6 chr1 205312848 . G A 692.17 PASS AC=1;AF=0.593;AN=2;DP=1727;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant9-variant12-variant13-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant33-variant36-variant37-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,36:63:99:992,0,668:10,17,14,22 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 1/1:0,38:38:99:1073,113,0:0,0,15,23 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 0/1:18,9:27:99:154,0,483:12,6,5,4 chr1 205317676 . T C 327.23 PASS AC=2;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 1/1:0,27:27:81:1184,81,0:0,0,9,18 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 1/1:0,25:25:75:1114,75,0:0,0,8,17 chr1 205325458 . G A 66.19 PASS AC=1;AF=0.542;AN=2;DP=264;MQ=60;set=variant-variant6-variant18-variant23-variant24-variant27-variant31-variant36-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,7:20:99:195,0,327:9,4,6,1 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 0/1:48,39:87:99:873,0,1213:26,22,21,18 chr1 205389592 . G A 1575.1 PASS AC=1;AF=0.5;AN=2;DP=472;FractionInformativeReads=1;MQ=60;set=variant2-variant23-variant25-variant38 GT:AD:DP:GQ:PL:SB 0/1:58,25:83:99:523,0,1349:30,28,13,12 chr1 205473728 . T TTCC 204.75 PASS AC=1;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 0/1:25,6:31:99:203,0,982:12,13,4,2 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 0/1:31,17:48:99:448,0,708:14,17,11,6 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 1/1:0,80:80:99:2513,240,0:0,0,40,40 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 1/1:0,116:116:99:3717,348,0:0,0,55,61 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 1/1:0,189:189:99:5700,564,0:0,0,88,101 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 1/1:1,120:121:99:3447,323,0:1,0,61,59 chr1 205501181 . T C 3068.84 PASS AC=2;AF=0.662;AN=2;DP=6184;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,158:158:99:5039,474,0:0,0,66,92 chr1 205553346 . ATTT ATT,ATTTT,ATTTTT,ATTTTTT,A 115.16 PASS AC=0,0,0,1,0;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 0/4:14:99:0,7,1,6 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 0/1:26,41:67:99:1677,0,1497:8,18,19,22 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 0/1:23,40:63:99:1607,0,1430:7,16,20,20 chr1 205555145 . G A 91.5 PASS AC=1;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 0/1:6,7:13:99:177,0,137:4,2,4,3 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 0/1:40,45:85:99:1065,0,971:14,26,17,28 chr1 205561496 . C T 305.47 PASS AC=1;AF=0.75;AN=2;DP=37;FS=0;set=variant6-variant13-variant18-variant23 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:98:98,0,135:0,4,1,3 chr1 205568442 . G A 600.88 PASS AC=1;AF=0.643;AN=2;DP=1050;MQ=60;set=variant2-variant4-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant28-variant29-variant31-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:32,18:50:99:382,0,793:11,21,6,12 chr1 205580687 . G A 3318.5 PASS AC=1;AF=0.5;AN=2;DP=239;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.411;QD=13.88;ReadPosRankSum=4.378;SOR=0.669;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:103,136:239:99:3347,0,2571:41,62,55,81 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 1/1:1,6:7:11:176,11,0:0,1,4,2 chr1 205601199 . G A 1856.74 PASS AC=2;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 1/1:0,54:54:99:1538,161,0:0,0,25,29 chr1 205615791 . A G 3736.5 PASS AC=2;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 1/1:0,105:105:99:2953,314,0:0,0,60,45 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 1/1:0,19:19:57:573,57,0:0,0,3,16 chr1 205630893 . A G 678.83 PASS AC=1;AF=0.5;AN=2;DP=966;FractionInformativeReads=1;MQ=60;set=variant5-variant9-variant11-variant12-variant13-variant14-variant15-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,19:39:99:454,0,532:14,6,11,8 chr1 205632932 . A G 798.79 PASS AC=1;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 0/1:5,8:13:99:167,0,156:0,5,3,5 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 1/1:0,7:7:21:205,21,0:0,0,4,3 chr1 205682405 . A G 583.72 PASS AC=1;AF=0.5;AN=2;DP=30;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.215;QD=19.46;ReadPosRankSum=1.635;SOR=0.653;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:11,19:30:99:612,0,270:2,9,4,15 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 1/1:0,338:338:99:10064,1013,0:0,0,159,179 chr1 205684067 . T C 1168.37 PASS AC=1;AF=0.5;AN=2;DP=866;FractionInformativeReads=1;MQ=60;set=variant6-variant9-variant12-variant13-variant17-variant23-variant24-variant26-variant28-variant32-variant37-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,27:57:99:865,0,845:19,11,20,7 chr1 205685352 . T C 9775.68 PASS AC=1;AF=0.575;AN=2;DP=6737;MQ=60;set=variant2-variant6-variant7-variant9-variant12-variant13-variant14-variant16-variant17-variant23-variant24-variant26-variant27-variant28-variant32-variant33-variant37-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:141,152:293:99:3601,0,3604:84,57,87,65 chr1 205686004 . C G 623.35 PASS AC=1;AF=0.5;AN=2;DP=65;FS=3.702;FractionInformativeReads=1;MQ=60;MQRankSum=-0.694;QD=9.59;ReadPosRankSum=-1.18;SOR=1.283;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:40,25:65:99:652,0,1093:16,24,7,18 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 0/1:87:99:23,17,21,26 chr1 205687213 . TA T,TAA 911.53 PASS AC=1,0;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 0/1:223:99:75,74,43,31 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 0/1:104,124:228:99:2789,0,4630:41,63,55,69 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 0/1:22,27:49:99:822,0,600:5,17,8,19 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 1/1:0,5:5:15:222,15,0:0,0,5,0 chr1 205737450 . T C 908.22 PASS AC=2;AF=0.955;AN=2;DP=2592;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1597,141,0:0,0,12,35 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 1/1:12:9:0,1,3,8 chr1 205737956 . G C 464.01 PASS AC=2;AF=0.955;AN=2;DP=1420;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:702,63,0:0,0,15,6 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 1/1:0,182:182:99:5413,544,0:0,0,85,97 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 1/1:1,139:140:99:4032,409,0:0,1,66,73 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 0/1:55,36:91:99:895,0,1380:24,31,15,21 chr1 205738327 . GGTT G 2020.7 PASS AC=1;AF=0.5;AN=2;DP=1209;MQ=60;set=variant6-variant9-variant12-variant13-variant17-variant23-variant24-variant26-variant28-variant32-variant37-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,30:58:99:798,0,1030:13,15,13,17 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 1/1:0,39:39:99:1274,117,0:0,0,25,14 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 1/1:0,91:91:99:2819,273,0:0,0,40,51 chr1 205739266 . C T 1200.02 PASS AC=1;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 0/1:26,21:47:99:544,0,704:10,16,9,12 chr1 205739382 . G A 722.49 PASS AC=1;AF=0.5;AN=2;DP=53;FS=0;FractionInformativeReads=0.981;MQ=60;MQRankSum=-0.287;QD=13.63;ReadPosRankSum=-0.676;SOR=0.652;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:22,30:52:99:751,0,591:12,10,16,14 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 1/1:0,58:58:99:1919,174,0:0,0,35,23 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 1/1:0,7:7:21:223,21,0:0,0,4,3 chr1 205740437 . AAAAG A 352.37 PASS AC=1;AF=0.5;AN=2;DP=149;MQ=60;set=variant7-variant9-variant23-variant24-variant27-variant28-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:9,3:12:99:99,0,346:8,1,2,1 chr1 205744138 . G T 1462.29 PASS AC=1;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 0/1:101,123:224:99:2835,0,2412:52,49,60,63 chr1 205744218 . C T 1247.58 PASS AC=1;AF=0.5;AN=2;DP=1042;MQ=60;set=variant9-variant13-variant23-variant24-variant28-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:90,72:162:99:1778,0,2335:36,54,28,44 chr1 205744546 . C A 551.67 PASS AC=1;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 0/1:47,34:81:99:654,0,1091:24,23,19,15 chr1 205759195 . G A 282.92 PASS AC=1;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 0/1:28,28:56:99:602,0,786:11,17,14,14 chr1 205759876 . T C 674.71 PASS AC=1;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 0/1:36,27:63:99:698,0,1022:17,19,15,12 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 1/1:0,113:113:99:3351,338,0:0,0,53,60 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 1/1:0,7:7:21:268,21,0:0,0,7,0 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 1/1:0,113:113:99:4034,340,0:0,0,52,61 chr1 205767885 . G A 934.23 PASS AC=1;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 0/1:48,55:103:99:1325,0,1254:24,24,28,27 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 1/1:0,41:41:99:1274,123,0:0,0,24,17 chr1 205801872 . A G 1237.15 PASS AC=1;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 0/1:67,61:128:99:1375,0,1330:31,36,28,33 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 1/1:0,74:74:99:2310,222,0:0,0,26,48 chr1 205812614 . C T 226.57 PASS AC=1;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 0/1:3,4:7:99:110,0,116:2,1,3,1 chr1 205813672 . T C 414.07 PASS AC=1;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 0/1:3,5:8:81:157,0,81:2,1,3,2 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 1/1:0,11:11:33:442,33,0:0,0,7,4 chr1 205814188 . G A 301.29 PASS AC=1;AF=0.5;AN=2;DP=92;FractionInformativeReads=1;MQ=60;set=variant11-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:6,17:23:99:470,0,159:1,5,6,11 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 1/1:1,96:97:99:2736,255,0:0,1,50,46 chr1 205814735 . A G 654.44 PASS AC=1;AF=0.5;AN=2;DP=138;FractionInformativeReads=1;MQ=60;set=variant11-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:25,26:51:99:741,0,640:8,17,8,18 chr1 205884646 . CTGTGTG CTG,CTGTGTGTG,C,CTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTG 339.76 PASS AC=1,0,0,0,0;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 0/1:7:99:1,3,0,3 chr1 205886381 . C T 434.12 PASS AC=1;AF=0.5;AN=2;DP=948;MQ=60;set=variant-variant2-variant5-variant9-variant12-variant17-variant23-variant24-variant27-variant28-variant33-variant37 GT:AD:DP:GQ:PL:SB 0/1:27,26:53:99:680,0,689:17,10,14,12 chr1 205888143 . G C 1055.71 PASS AC=1;AF=0.5;AN=2;DP=1327;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant9-variant12-variant17-variant23-variant24-variant27-variant28-variant33-variant37 GT:AD:DP:GQ:PL:SB 0/1:55,30:85:99:761,0,1624:20,35,12,18 chr1 205890679 . T C 3228.27 PASS AC=2;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 1/1:0,157:157:99:4734,471,0:0,0,94,63 chr1 205892411 . T C 1586.87 PASS AC=1;AF=0.5;AN=2;DP=991;MQ=60;set=variant-variant2-variant5-variant9-variant12-variant17-variant23-variant24-variant27-variant33-variant37 GT:AD:DP:GQ:PL:SB 0/1:38,43:81:99:1682,0,2007:20,18,21,22 chr1 205892415 . C T 1619.53 PASS AC=1;AF=0.5;AN=2;DP=974;MQ=60;set=variant-variant2-variant5-variant9-variant12-variant17-variant23-variant24-variant27-variant33-variant37 GT:AD:DP:GQ:PL:SB 0/1:38,42:80:99:1649,0,2010:20,18,21,21 chr1 205893699 . T C 637.27 PASS AC=1;AF=0.5;AN=2;DP=674;MQ=60;set=variant-variant2-variant5-variant9-variant12-variant17-variant23-variant24-variant27-variant33-variant37 GT:AD:DP:GQ:PL:SB 0/1:32,32:64:99:658,0,759:11,21,14,18 chr1 205893753 . AT A 160.39 PASS AC=1;AF=0.559;AN=2;DP=534;MQ=60;set=variant-variant2-variant4-variant5-variant9-variant12-variant20-variant23-variant24-variant26-variant27-variant31-variant33-variant34-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:313,0,280:3,8,4,8 chr1 205896235 . G A 1553.48 PASS AC=1;AF=0.559;AN=2;DP=2190;MQ=60;set=variant-variant2-variant4-variant5-variant9-variant12-variant17-variant20-variant23-variant24-variant26-variant27-variant31-variant33-variant34-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:63,44:107:99:1134,0,1634:32,31,25,19 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 1/1:0,66:66:99:2324,198,0:0,0,38,28 chr1 205896948 . A G 293.1 PASS AC=1;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 0/1:4,17:21:45:598,0,45:3,1,14,3 chr1 205897876 . C T 821.44 PASS AC=1;AF=0.5;AN=2;DP=1049;MQ=60;set=variant-variant5-variant9-variant12-variant17-variant23-variant24-variant27-variant33-variant37 GT:AD:DP:GQ:PL:SB 0/1:44,34:78:99:796,0,1218:25,19,21,13 chr1 205898638 . C T 289.99 PASS AC=1;AF=0.5;AN=2;DP=480;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant9-variant10-variant12-variant17-variant22-variant23-variant24-variant25-variant27-variant33-variant37 GT:AD:DP:GQ:PL:SB 0/1:15,17:32:99:524,0,417:4,11,6,11 chr1 205899311 . T A 42.2 PASS AC=1;AF=0.5;AN=2;DP=190;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant9-variant12-variant17-variant20-variant22-variant23-variant24-variant27-variant33-variant37 GT:AD:DP:GQ:PL:SB 0/1:7,12:19:99:402,0,202:1,6,2,10 chr1 205901287 . T A 153.12 PASS AC=1;AF=0.5;AN=2;DP=408;MQ=60;set=variant-variant5-variant9-variant10-variant12-variant17-variant20-variant22-variant23-variant24-variant25-variant27-variant33-variant37 GT:AD:DP:GQ:PL:SB 0/1:20,15:35:99:512,0,611:4,16,1,14 chr1 205901788 . G T 252.99 PASS AC=1;AF=0.583;AN=2;DP=443;MQ=60;set=variant-variant2-variant5-variant9-variant10-variant12-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:150,0,194:5,0,4,0 chr1 206231295 . C T 826.83 PASS AC=1;AF=0.5;AN=2;DP=70;FS=0.889;FractionInformativeReads=1;MQ=60;MQRankSum=-0.306;QD=11.81;ReadPosRankSum=1.388;SOR=0.58;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:33,37:70:99:855,0,849:15,18,18,19 chr1 206239403 . C T 1170.71 PASS AC=1;AF=0.5;AN=2;DP=612;MQ=60;set=variant15-variant20-variant23-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,38:117:99:851,0,2017:43,36,22,16 chr1 206239415 . C T 1149.86 PASS AC=1;AF=0.5;AN=2;DP=625;MQ=60;set=variant15-variant20-variant23-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,42:127:99:905,0,2108:46,39,24,18 chr1 206239574 . T C 630.04 PASS AC=1;AF=0.5;AN=2;DP=255;FractionInformativeReads=1;MQ=60;set=variant15-variant20-variant23-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,12:34:99:391,0,606:7,15,2,10 chr1 206239956 . A G 374.07 PASS AC=1;AF=0.583;AN=2;DP=53;FractionInformativeReads=1;MQ=60;set=variant15-variant20-variant23-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:99:102,0,203:3,2,2,1 chr1 206239993 . C A 561.99 PASS AC=1;AF=0.5;AN=2;DP=89;FS=0;FractionInformativeReads=1;MQ=60;set=variant15-variant20-variant23-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:148,0,240:6,1,4,1 chr1 206240271 . G A 939.57 PASS AC=1;AF=0.5;AN=2;DP=412;FractionInformativeReads=1;MQ=60;set=variant15-variant20-variant23-variant34-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,29:60:99:684,0,850:14,17,10,19 chr1 206332163 . C T 117.4 PASS AC=1;AF=0.5;AN=2;DP=13;FS=0;FractionInformativeReads=1;MQ=60;set=variant15-variant23 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:31:121,0,31:0,1,1,3 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 0/1:6,7:13:99:182,0,160:6,0,7,0 chr1 206516261 . C T 1383.04 PASS AC=1;AF=0.5;AN=2;DP=7344;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:66,71:137:99:1739,0,1524:46,20,54,17 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 0/1:138:99:66,41,26,5 chr1 206566904 . T C 4778.55 PASS AC=1;AF=0.5;AN=2;DP=13435;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:155,86:241:99:1781,0,4050:90,65,57,29 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 0/1:162,90:252:99:1966,0,4350:49,113,32,58 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 0/1:69,15:84:99:323,0,2377:8,61,2,13 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 0/1:11,6:17:98:98,0,206:6,5,3,3 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 0/1:73,47:120:99:1107,0,1719:38,35,22,25 chr1 206623685 . G T 4103.51 PASS AC=2;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 1/1:0,167:167:99:4857,499,0:0,0,92,75 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 0/1:20,27:47:99:780,0,516:6,14,6,21 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 0/1:64,68:132:99:1936,0,1659:21,43,27,41 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 1/1:0,36:36:99:1118,108,0:0,0,13,23 chr1 206626828 . C G 200.76 PASS AC=1;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 0/1:10,4:14:99:127,0,347:1,9,1,3 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 1/1:0,9:9:27:366,27,0:0,0,9,0 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 0/1:3,8:11:81:231,0,81:3,0,6,2 chr1 206634429 . A G 1309.53 PASS AC=1;AF=0.591;AN=2;DP=1992;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant9-variant13-variant14-variant15-variant20-variant21-variant23-variant27-variant28-variant31-variant32-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,35:82:99:838,0,1289:23,24,20,15 chr1 206634997 . C T 920.57 PASS AC=1;AF=0.591;AN=2;DP=1227;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant9-variant13-variant14-variant15-variant20-variant21-variant23-variant27-variant28-variant31-variant32-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,15:51:99:334,0,1042:17,19,8,7 chr1 206635245 . TAC TACACAC,T,TACAC,TACACACAC 277.64 PASS AC=0,2,0,0;AF=0.44,0.393,0.071,0.036;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-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 2/2:6:18:0,0,2,4 chr1 206635295 . T G 391.81 PASS AC=1;AF=0.591;AN=2;DP=413;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant9-variant13-variant14-variant15-variant20-variant21-variant23-variant27-variant28-variant31-variant32-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:178,0,314:6,4,5,1 chr1 206636228 . A G 1155.97 PASS AC=1;AF=0.5;AN=2;DP=87;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.981;QD=13.29;ReadPosRankSum=-2.136;SOR=0.779;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:45,42:87:99:1184,0,1216:28,17,27,15 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 0/1:24,22:46:99:443,0,482:9,15,2,20 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 0/1:43,41:84:99:1089,0,1009:20,23,24,17 chr1 206637133 . C T 1424.21 PASS AC=1;AF=0.591;AN=2;DP=1315;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant9-variant13-variant14-variant15-variant20-variant21-variant23-variant27-variant28-variant31-variant32-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,23:51:99:599,0,799:15,13,9,14 chr1 206637395 . C T 544.51 PASS AC=1;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 0/1:26,31:57:99:884,0,665:14,12,17,14 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 0/1:46,40:86:99:1020,0,1289:12,34,13,27 chr1 206643772 . C G 416.33 PASS AC=1;AF=0.643;AN=2;DP=181;FractionInformativeReads=1;MQ=60;set=variant9-variant19-variant23-variant27-variant29-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,16:26:99:422,0,240:5,5,11,5 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 0/1:10,6:16:99:137,0,225:6,4,2,4 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 0/1:13,20:33:99:572,0,400:11,2,14,6 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 1/1:0,174:174:99:5057,521,0:0,0,99,75 chr1 206647787 . T C 3973.81 PASS AC=2;AF=0.841;AN=2;DP=8262;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,189:189:99:5619,567,0:0,0,90,99 chr1 206648037 . C G 430.99 PASS AC=1;AF=0.559;AN=2;DP=2121;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,24:42:99:618,0,459:10,8,14,10 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 0/1:11,9:20:99:208,0,311:2,9,3,6 chr1 206651107 . G A 957.61 PASS AC=1;AF=0.58;AN=2;DP=2374;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant11-variant14-variant15-variant18-variant19-variant20-variant23-variant25-variant26-variant27-variant30-variant31-variant33-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,30:61:99:706,0,771:17,14,17,13 chr1 206651350 . C T 255.77 PASS AC=1;AF=0.58;AN=2;DP=1065;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant11-variant14-variant15-variant18-variant19-variant20-variant23-variant25-variant26-variant27-variant30-variant31-variant33-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,25:40:99:714,0,430:4,11,7,18 chr1 206664396 . A T 997.06 PASS AC=2;AF=0.841;AN=2;DP=1378;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:89:938,89,0:0,0,15,15 chr1 206664407 . T G 403.02 PASS AC=2;AF=0.818;AN=2;DP=1488;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:925,96,0:0,0,16,16 chr1 206665896 . C G 2006.69 PASS AC=2;AF=0.818;AN=2;DP=6417;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,141:141:99:4629,422,0:0,0,66,75 chr1 206666734 . T G 390.62 PASS AC=1;AF=0.571;AN=2;DP=1569;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant14-variant15-variant18-variant19-variant20-variant23-variant25-variant26-variant27-variant30-variant31-variant33-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,23:41:99:622,0,441:8,10,12,11 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 0/2:60:99:9,20,11,20 chr1 206669465 . C T 1345.1 PASS AC=1;AF=0.553;AN=2;DP=3132;MQ=60;set=variant2-variant3-variant4-variant5-variant11-variant15-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,76:149:99:1741,0,1893:43,30,41,35 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 0/1:32,47:79:99:1045,0,718:16,16,20,27 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 0/1:14,20:34:99:486,0,310:7,7,9,11 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 0/1:3,10:13:99:411,0,158:1,2,4,6 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 0/1:62,48:110:99:1113,0,1682:36,26,28,20 chr1 206680983 . A C 648 PASS AC=2;AF=0.795;AN=2;DP=3864;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2091,213,0:0,0,34,37 chr1 206730641 . C A 1749.63 PASS AC=1;AF=0.6;AN=2;DP=1137;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant12-variant14-variant16-variant17-variant19-variant21-variant23-variant25-variant26-variant33-variant34-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,34:69:99:760,0,879:14,21,16,18 chr1 206730691 . G C 1515.11 PASS AC=1;AF=0.6;AN=2;DP=913;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant12-variant14-variant16-variant17-variant19-variant21-variant23-variant25-variant26-variant33-variant34-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,27:56:99:573,0,770:10,19,12,15 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 1/1:0,89:89:99:2627,266,0:0,0,33,56 chr1 206760474 . T C 2081 PASS AC=2;AF=0.898;AN=2;DP=3933;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,71:71:99:2800,213,0:0,0,45,26 chr1 206760476 . G A 1323.15 PASS AC=1;AF=0.619;AN=2;DP=1960;MQ=60;set=variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant15-variant17-variant18-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant33-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:40,32:72:99:770,0,1160:26,14,19,13 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 0/1:40,24:64:99:867,0,2264:15,25,11,13 chr1 206760694 . T C 1156.91 PASS AC=1;AF=0.625;AN=2;DP=1914;MQ=60;set=variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant15-variant17-variant18-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:42,24:66:99:861,0,2308:15,27,10,14 chr1 206761938 . T C 2022.02 PASS AC=1;AF=0.64;AN=2;DP=1820;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant11-variant12-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant33-variant34-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,33:53:99:865,0,465:11,9,19,14 chr1 206766819 . AGAGC A 614.93 PASS AC=1;AF=0.726;AN=2;DP=600;set=variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,16:18:36:618,0,36:2,0,12,4 chr1 206766843 . AGAGTGTGTGTGTGC A 37.05 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=28;FS=5.348;FractionInformativeReads=0.786;MQ=59.76;MQRankSum=1.49;QD=1.32;ReadPosRankSum=0.298;SOR=0.105;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:18,4:22:74:74,0,620:14,4,2,2 chr1 206766845 . AGTGTGTGTGTGCGT AGT,AGTGTGTGTGTGTGTGTGT,AGTGCGT,AGTGTGTGTGTGTGTGCGT,AGTGTGTGTGTGTGTGT,AGTGTGTGTGTGTGTGTGTGTGTGCGT,AGTGTGTGTGTGTGTGTGTGTGT,A,AGTGTGTGTGTGTGTGTGTGTGTGT 137.73 PASS AC=1,0,0,0,0,0,0,0,0;AF=0.389,0.056,0.093,0.037,0.019,0.019,0.019,0.019,0.019;AN=2;DP=869;set=variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant13-variant15-variant17-variant18-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant36-variant37-variant39-variant42-variant43 GT:DP:GQ:SB 0/1:22:99:8,4,8,2 chr1 206766857 . C CGTGTGTGT,CGTGTGTGTGT,CGTGTGTGTGTGTGT 654.2 PASS AC=1,0,0;AF=0.318,0.182,0.136;AN=2;DP=382;set=variant6-variant7-variant8-variant12-variant14-variant3-variant23-variant24-variant4-variant26-variant44 GT:DP:GQ:SB 0/1:28:99:14,6,6,2 chr1 206769047 . T C 1803.88 PASS AC=1;AF=0.63;AN=2;DP=1230;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant12-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant33-variant34-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,20:32:99:586,0,323:9,3,13,7 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 0/1:9,9:18:99:226,0,218:5,4,7,2 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 0/1:8,7:15:99:253,0,319:6,2,7,0 chr1 206772753 . A G 1142.34 PASS AC=2;AF=0.898;AN=2;DP=1460;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:955,81,0:0,0,19,8 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 1/1:1,80:81:99:2325,204,0:1,0,37,43 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 0/1:7,9:16:99:195,0,234:7,0,4,5 chr1 206776200 . C T 2086.86 PASS AC=2;AF=0.898;AN=2;DP=2432;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,31:31:99:1418,99,0:0,0,20,11 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 1/1:0,35:35:99:1484,105,0:0,0,22,13 chr1 206778642 . A C 360.85 PASS AC=1;AF=0.63;AN=2;DP=280;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant12-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant33-variant34-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:68:121,0,68:2,1,3,3 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 0/1:8,4:12:89:89,0,278:2,6,1,3 chr1 206810946 . C T 1950.92 PASS AC=1;AF=0.64;AN=2;DP=1001;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant19-variant21-variant22-variant23-variant27-variant28-variant30-variant32-variant34-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,16:29:99:545,0,420:11,2,14,2 chr1 206904464 . C T 2702.02 PASS AC=1;AF=0.611;AN=2;DP=4732;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant31-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,67:145:99:1459,0,1991:39,39,32,35 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 0/2:49:99:6,10,15,18 chr1 206907482 . C T 524.78 PASS AC=1;AF=0.5;AN=2;DP=280;FractionInformativeReads=1;MQ=60;set=variant2-variant15-variant17-variant23-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,24:55:99:608,0,880:14,17,11,13 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 0/1:13,26:39:99:677,0,321:10,3,16,10 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 0/1:73,70:143:99:1631,0,1634:38,35,39,31 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 1/1:0,36:36:99:1144,108,0:0,0,12,24 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 1/1:0,109:109:99:3521,327,0:0,0,55,54 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 1/1:0,33:33:99:1211,99,0:0,0,25,8 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 1/1:0,74:74:99:2139,222,0:0,0,28,46 chr1 206972072 . C T 302.52 PASS AC=2;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 1/1:0,24:24:72:775,72,0:0,0,13,11 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 0/1:16:85:0,7,3,6 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 1/1:0,24:24:72:735,72,0:0,0,14,10 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 1/1:0,15:15:45:584,45,0:0,0,14,1 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 1/1:0,86:86:99:2722,258,0:0,0,37,49 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 1/1:0,15:15:45:539,45,0:0,0,4,11 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 1/1:0,90:90:99:2679,270,0:0,0,43,47 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 1/1:0,32:32:95:877,95,0:0,0,15,17 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 1/1:0,14:14:42:573,42,0:0,0,13,1 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 1/1:0,61:61:99:1947,182,0:0,0,42,19 chr1 207072959 . C T 1191.83 PASS AC=2;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 1/1:0,48:48:99:1683,144,0:0,0,13,35 chr1 207074905 . T C 5731.19 PASS AC=2;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 1/1:0,157:157:99:4701,470,0:0,0,85,72 chr1 207075171 . T C 863.28 PASS AC=2;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 1/1:0,16:16:48:658,48,0:0,0,9,7 chr1 207077645 . T C 528.73 PASS AC=2;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 1/1:0,11:11:33:457,33,0:0,0,11,0 chr1 207086969 . A G 2125.93 PASS AC=2;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 1/1:0,59:59:99:2086,177,0:0,0,45,14 chr1 207087435 . C T 3535.7 PASS AC=2;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 1/1:0,107:107:99:3468,320,0:0,0,35,72 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 0/1:17,10:27:99:131,0,324:8,9,5,5 chr1 207102293 . A T 434.81 PASS AC=2;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 1/1:0,10:10:30:281,30,0:0,0,5,5 chr1 207108191 . CAT C 685.74 PASS AC=2;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 1/1:0,40:40:99:1469,121,0:0,0,13,27 chr1 207109116 . C T 2486.17 PASS AC=2;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 1/1:2,106:108:99:3114,302,0:1,1,47,59 chr1 207109167 . G A 1747.03 PASS AC=2;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 1/1:2,63:65:99:1940,145,0:1,1,21,42 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 0/1:9,15:24:99:441,0,248:7,2,11,4 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 0/1:65,65:130:99:1841,0,1577:32,33,34,31 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 0/1:32,49:81:99:1239,0,660:16,16,26,23 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 0/1:15,19:34:99:486,0,450:10,5,11,8 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 0/1:19,27:46:99:699,0,534:13,6,15,12 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 0/1:42,34:76:99:908,0,994:17,25,13,21 chr1 207135828 . G A 684.09 PASS AC=1;AF=0.5;AN=2;DP=136;FractionInformativeReads=1;MQ=60;set=variant23-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,26:57:99:712,0,781:15,16,10,16 chr1 207139046 . A G 248.04 PASS AC=1;AF=0.5;AN=2;DP=104;MQ=60;set=variant8-variant16-variant18-variant23-variant31-variant32-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:149,0,221:7,0,4,1 chr1 207139362 . C G 558.53 PASS AC=1;AF=0.5;AN=2;DP=188;FractionInformativeReads=1;set=variant8-variant16-variant18-variant23-variant31-variant32-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,16:31:99:479,0,454:3,12,4,12 chr1 207140440 . C T 1139.74 PASS AC=1;AF=0.5;AN=2;DP=747;FractionInformativeReads=1;MQ=60;set=variant8-variant16-variant18-variant23-variant31-variant32-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,58:99:99:1315,0,977:24,17,31,27 chr1 207142507 . T C 109.47 PASS AC=1;AF=0.5;AN=2;DP=96;MQ=60;set=variant8-variant16-variant18-variant23-variant31-variant32-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,11:12:10:410,0,10:1,0,9,2 chr1 207143296 . C T 51.2 PASS AC=1;AF=0.5;AN=2;DP=48;FS=0;FractionInformativeReads=1;MQ=60;set=variant8-variant16-variant18-variant23-variant31-variant32-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:68:240,0,68:2,1,5,1 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 0/1:24,26:50:99:713,0,603:15,9,18,8 chr1 207143550 . C T 904.15 PASS AC=1;AF=0.5;AN=2;DP=635;FractionInformativeReads=1;MQ=60;set=variant8-variant16-variant18-variant23-variant31-variant32-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,63:86:99:1679,0,519:9,14,29,34 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 1/1:0,91:91:99:3018,273,0:0,0,47,44 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 0/1:290:99:121,98,34,37 chr1 207221409 . T C 11015.5 PASS AC=2;AF=0.989;AN=2;DP=14304;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,336:336:99:9691,1006,0:0,0,166,170 chr1 207235659 . A G 116.82 PASS AC=1;AF=0.5;AN=2;DP=38;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant15-variant23-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,7:8:22:239,0,22:1,0,5,2 chr1 207237233 . GGT GGGGTGTGTGTGTGTGT,GGGGTGTGTGTGTGTGTGT,GGGGTGTGTGTGTGTGTGTGT,G,GGTGTGTGTGTGTGTGT,GGGGTGTGTGTGTGTGTGTGTGTGT,GGTGT,GGTGTGT,GGGGGGTGTGTGTGTGT 2834.86 PASS AC=0,0,0,0,0,0,1,0,0;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 0/7:48:99:6,23,4,15 chr1 207243851 . A G 383.6 PASS AC=2;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 1/1:2,27:29:52:849,52,0:1,1,14,13 chr1 207245045 . T C 778.2 PASS AC=2;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 1/1:0,53:53:99:1704,159,0:0,0,15,38 chr1 207245080 . A AT 237.4 PASS AC=2;AF=0.604;AN=2;DP=517;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant15-variant16-variant18-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant34-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:450,48,0:0,0,2,14 chr1 207246004 . A G 412.7 PASS AC=2;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 1/1:0,28:28:84:899,84,0:0,0,15,13 chr1 207247476 . TTC T 613.95 PASS AC=2;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 1/1:0,26:26:78:1159,78,0:0,0,11,15 chr1 207249855 . G A 1388.04 PASS AC=2;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 1/1:0,82:82:99:2907,245,0:0,0,35,47 chr1 207249974 . A ACTGACTGACAGACAGACTTTAGTGTCTGTGTG 784.89 PASS AC=2;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 1/1:2,64:66:99:3059,109,0:1,1,33,31 chr1 207250300 . G A 4848.65 PASS AC=2;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 1/1:0,304:304:99:9030,909,0:0,0,132,172 chr1 207250456 . C T 1481.43 PASS AC=2;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 1/1:0,69:69:99:2373,207,0:0,0,25,44 chr1 207250570 . A G 1408.97 PASS AC=2;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 1/1:0,65:65:99:2255,195,0:0,0,38,27 chr1 207250631 . A G 2765.03 PASS AC=2;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 1/1:0,172:172:99:5463,514,0:0,0,114,58 chr1 207253031 . C T 1387.12 PASS AC=2;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 1/1:0,59:59:99:1858,177,0:0,0,26,33 chr1 207253165 . A G 1656.89 PASS AC=2;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 1/1:0,32:32:96:1014,96,0:0,0,13,19 chr1 207253487 . A G 1924.07 PASS AC=1;AF=0.533;AN=2;DP=2560;MQ=60;set=variant5-variant8-variant14-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant32-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,55:134:99:1259,0,2019:41,38,32,23 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 1/1:1,137:138:99:4214,384,0:1,0,61,76 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 0/1:48,42:90:99:959,0,1294:17,31,19,23 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 0/1:30,35:65:99:809,0,795:12,18,18,17 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 0/1:27,32:59:99:996,0,892:3,24,6,26 chr1 207273399 . ATGTGTGTG A,ATGTGTG,ATGTG,ATG 96.34 PASS AC=0,1,1,0;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 3/2:20:78:0,6,1,13 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 1/1:0,28:28:84:895,84,0:0,0,10,18 chr1 207297680 . T C 2071.17 PASS AC=2;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 1/1:0,64:64:99:1891,191,0:0,0,27,37 chr1 207300259 . A G 842.55 PASS AC=1;AF=0.611;AN=2;DP=2638;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant23-variant25-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,53:95:99:1495,0,1048:18,24,15,38 chr1 207300381 . T A 39.19 PASS AC=1;AF=0.591;AN=2;DP=236;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant9-variant12-variant14-variant17-variant18-variant23-variant25-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,3:11:95:95,0,321:0,8,0,3 chr1 207304900 . T C 330.64 PASS AC=1;AF=0.593;AN=2;DP=1243;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant12-variant13-variant17-variant18-variant19-variant20-variant23-variant25-variant28-variant29-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,21:46:99:541,0,662:15,10,15,6 chr1 207314388 . C T 1721.86 PASS AC=1;AF=0.647;AN=2;DP=758;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant15-variant16-variant19-variant21-variant22-variant23-variant24-variant27-variant28-variant30-variant31-variant40 GT:AD:DP:GQ:PL:SB 0/1:13,22:35:99:601,0,280:6,7,14,8 chr1 207500293 . C T 335.87 PASS AC=1;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 0/1:6,17:23:99:504,0,150:1,5,4,13 chr1 207504669 . G A 263.04 PASS AC=1;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 0/1:14,21:35:99:541,0,368:4,10,8,13 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 1/1:0,59:59:99:2043,177,0:0,0,14,45 chr1 207510548 . A G 240.08 PASS AC=1;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 0/1:10,14:24:99:493,0,365:9,1,13,1 chr1 207510596 . G A 554.66 PASS AC=1;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 0/1:27,33:60:99:962,0,799:21,6,24,9 chr1 207512577 . T TTAA 97.61 PASS AC=2;AF=1;AN=2;DP=182;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,4,0 chr1 207520788 . G A 442.16 PASS AC=1;AF=0.652;AN=2;DP=355;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant12-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant30-variant31-variant33-variant34-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:145,0,238:6,1,4,1 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 0/1:35,47:82:99:1332,0,832:21,14,27,20 chr1 207627918 . G A 1220.36 PASS AC=1;AF=0.5;AN=2;DP=1003;MQ=60;set=variant7-variant8-variant22-variant23-variant24-variant26-variant27-variant29 GT:AD:DP:GQ:PL:SB 0/1:56,52:108:99:1313,0,1487:19,37,19,33 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 0/1:6,15:21:99:528,0,179:6,0,14,1 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 0/1:10,12:22:99:393,0,345:3,7,7,5 chr1 207646322 . G A 1253 PASS AC=2;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 1/1:0,79:79:99:2327,235,0:0,0,36,43 chr1 207646462 . G A 571.52 PASS AC=2;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 1/1:0,46:46:99:1415,138,0:0,0,18,28 chr1 207646898 . T C 1068.4 PASS AC=2;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 1/1:0,87:87:99:2763,260,0:0,0,49,38 chr1 207646923 . G A 1311.11 PASS AC=2;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 1/1:0,92:92:99:2970,275,0:0,0,46,46 chr1 207648173 . T C 547.31 PASS AC=1;AF=0.5;AN=2;DP=442;FractionInformativeReads=1;MQ=60;set=variant7-variant8-variant22-variant23-variant24-variant26-variant27-variant29 GT:AD:DP:GQ:PL:SB 0/1:25,21:46:99:578,0,597:16,9,15,6 chr1 207653178 . C G 1114.45 PASS AC=2;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 1/1:0,32:32:96:951,96,0:0,0,21,11 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 1/1:0,62:62:99:2058,186,0:0,0,25,37 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 0/1:23,24:47:99:639,0,647:9,14,9,15 chr1 207662912 . T C 11102.8 PASS AC=2;AF=0.909;AN=2;DP=12807;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,290:290:99:8962,868,0:0,0,148,142 chr1 207663256 . G GT,GTT 971.36 PASS AC=2,0;AF=0.886,0.011;AN=2;DP=1813;MQ=60;set=Intersection GT:DP:GQ:SB 1/1:39:88:1,0,7,31 chr1 207669343 . G A 312.36 PASS AC=1;AF=0.5;AN=2;DP=165;FractionInformativeReads=1;set=variant4-variant5-variant7-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant33-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:76:76,0,115:3,0,2,1 chr1 207679307 . A G 5772.17 PASS AC=2;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 1/1:0,157:157:99:4738,469,0:0,0,92,65 chr1 207753345 . C T 487.83 PASS AC=2;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 1/1:0,24:24:72:912,72,0:0,0,20,4 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 1/1:0,110:110:99:3203,329,0:0,0,50,60 chr1 207784968 . A G 4058.84 PASS AC=2;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 1/1:0,107:107:99:3355,321,0:0,0,53,54 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 1/1:0,66:66:99:2007,198,0:0,0,35,31 chr1 207813726 . T C 40.97 PASS AC=2;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 1/1:0,6:6:18:205,18,0:0,0,3,3 chr1 207818719 . G A 2619.11 PASS AC=2;AF=0.6;AN=2;DP=5461;MQ=60;set=variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant32-variant34-variant36-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:3,191:194:99:5338,539,0:1,2,83,108 chr1 207850560 . A G 286.77 PASS AC=2;AF=0.808;AN=2;DP=63;FS=0;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant11-variant12-variant18-variant21-variant23-variant24-variant26-variant28-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:225,15,0:0,0,5,0 chr1 207850589 . A C 235.3 PASS AC=2;AF=0.75;AN=2;DP=77;FS=0;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant11-variant12-variant13-variant18-variant21-variant23-variant24-variant26-variant28-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:270,18,0:0,0,6,0 chr1 207850652 . CAAAAAAA CAA,C,CA,CAAA 118.44 PASS AC=0,0,1,0;AF=0.071,0.179,0.25,0.036;AN=2;DP=204;set=variant5-variant6-variant7-variant8-variant10-variant12-variant16-variant18-variant23-variant24-variant34-variant36-variant41-variant42 GT:DP:GQ:SB 0/3:17:88:1,4,12,0 chr1 207850879 . C T 3392.24 PASS AC=2;AF=0.607;AN=2;DP=3277;set=variant5-variant6-variant7-variant10-variant11-variant12-variant16-variant21-variant23-variant26-variant28-variant34-variant38-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,218:218:99:6534,652,0:0,0,110,108 chr1 207851611 . A G 1860.34 PASS AC=2;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 1/1:2,161:163:99:4570,438,0:1,1,76,85 chr1 207851760 . G A 397.91 PASS AC=2;AF=0.596;AN=2;DP=838;MQ=60;set=variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant32-variant34-variant36-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:683,57,0:0,0,4,15 chr1 207857158 . T C 1485.58 PASS AC=2;AF=0.6;AN=2;DP=2470;set=variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant26-variant27-variant28-variant32-variant34-variant36-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:2756,258,0:0,0,58,28 chr1 207872595 . A G 2787.6 PASS AC=2;AF=0.607;AN=2;DP=3619;set=variant5-variant6-variant7-variant10-variant11-variant12-variant16-variant21-variant23-variant26-variant28-variant34-variant38-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,256:256:99:7540,767,0:0,0,147,109 chr1 207872657 . C T 3608.84 PASS AC=2;AF=0.607;AN=2;DP=5072;set=variant5-variant6-variant7-variant10-variant11-variant12-variant16-variant21-variant23-variant26-variant28-variant34-variant38-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,345:345:99:9853,1033,0:0,0,180,165 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 1/1:2,132:134:99:5850,313,0:1,1,64,68 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 1/1:2,132:134:99:5850,313,0:1,1,64,68 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 1/1:2,130:132:99:5850,313,0:1,1,62,68 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 1/1:0,99:99:99:2911,296,0:0,0,41,58 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 1/1:0,75:75:99:2327,225,0:0,0,32,43 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 1/1:0,16:16:48:549,48,0:0,0,3,13 chr1 207959122 . CTTTT C,CT,CTTT 763.59 PASS AC=0,2,0;AF=0.511,0.375,0.114;AN=2;DP=1566;FS=0;MQ=60;set=Intersection GT:DP:GQ:SB 2/2:23:69:0,0,4,19 chr1 207959136 . T TAAA,TAA 763.34 PASS AC=0,2;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 2/2:24:72:0,0,4,20 chr1 208060806 . G A 1247.78 PASS AC=2;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 1/1:0,51:51:99:2259,153,0:0,0,26,25 chr1 208060807 . A G 1247.78 PASS AC=2;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 1/1:0,50:50:99:2259,153,0:0,0,26,24 chr1 208062260 . T C 906.75 PASS AC=2;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 1/1:0,48:48:99:1545,144,0:0,0,16,32 chr1 208062973 . A T 389.7 PASS AC=2;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 1/1:0,70:70:99:2125,209,0:0,0,35,35 chr1 208063067 . G A 1144.4 PASS AC=2;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 1/1:0,58:58:99:1887,174,0:0,0,28,30 chr1 208063626 . T A 315.08 PASS AC=1;AF=0.5;AN=2;DP=25;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.333;QD=12.6;ReadPosRankSum=2.584;SOR=0.859;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:13,12:25:99:343,0,348:6,7,5,7 chr1 208063808 . G A 173.01 PASS AC=2;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 1/1:0,38:38:99:1122,114,0:0,0,17,21 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 1/1:0,5:5:15:214,15,0:0,0,4,1 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 1/1:0,40:40:99:1113,118,0:0,0,20,20 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 1/1:0,30:30:90:930,90,0:0,0,12,18 chr1 208197147 . A C 707.9 PASS AC=1;AF=0.5;AN=2;DP=52;FS=1.052;FractionInformativeReads=1;MQ=60;MQRankSum=0.174;QD=13.61;ReadPosRankSum=1.221;SOR=0.532;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:24,28:52:99:736,0,616:14,10,15,13 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 1/1:0,80:80:99:2508,240,0:0,0,43,37 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 1/1:0,62:62:99:1963,186,0:0,0,31,31 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 1/1:0,53:53:99:1788,159,0:0,0,28,25 chr1 208199993 . T TTC 57.28 PASS AC=1;AF=0.5;AN=2;DP=825;set=filterInvariant2-variant11-filterInvariant16-filterInvariant19-variant20-variant23-filterInvariant24-variant26-filterInvariant32-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,11:37:99:128,0,716:14,12,8,3 chr1 208199998 . T TC,TCTC 1400.58 PASS AC=1,0;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 0/1:42:99:8,6,15,13 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 0/1:29,14:43:99:156,0,710:16,13,8,6 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 1/1:0,108:108:99:3181,324,0:0,0,47,61 chr1 208206946 . C G 266.86 PASS AC=1;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 0/1:17,10:27:99:200,0,470:6,11,4,6 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 1/1:0,4:4:12:139,12,0:0,0,1,3 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 1/1:0,54:54:99:1730,162,0:0,0,32,22 chr1 208208034 . G C 624.35 PASS AC=1;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 0/1:20,16:36:99:443,0,555:6,14,4,12 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 1/1:0,4:4:12:177,12,0:0,0,0,4 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 1/1:0,21:21:63:717,63,0:0,0,9,12 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 1/1:0,111:111:99:3337,332,0:0,0,51,60 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 1/1:0,44:44:99:1618,132,0:0,0,36,8 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 1/1:0,8:8:24:360,24,0:0,0,1,7 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 1/1:0,8:8:24:360,24,0:0,0,1,7 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 1/1:0,106:106:99:3116,317,0:0,0,59,47 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 1/1:0,104:104:99:3146,312,0:0,0,38,66 chr1 208270244 . A C 386.43 PASS AC=1;AF=0.688;AN=2;DP=1467;set=variant-variant4-variant5-variant7-variant8-variant9-variant13-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant34-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,22:55:99:520,0,871:15,18,8,14 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 1/1:0,88:88:99:4041,274,0:0,0,58,30 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 1/1:0,14:14:44:583,44,0:0,0,5,9 chr1 209603996 . A G 377.92 PASS AC=2;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 1/1:0,47:47:99:1547,141,0:0,0,16,31 chr1 209605636 . TAGCAGCAGCAGCAGCAGC TAGCAGC,T 1080.09 PASS AC=2,0;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 1/1:52:99:0,0,17,35 chr1 209778737 . G A 1777.02 PASS AC=1;AF=0.536;AN=2;DP=515;MQ=60;set=variant-variant5-variant8-variant17-variant18-variant20-variant22-variant23-variant25-variant27-variant28-variant33-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,9:28:99:261,0,552:13,6,8,1 chr1 209778771 . G C 2596.92 PASS AC=1;AF=0.536;AN=2;DP=898;MQ=60;set=variant-variant5-variant8-variant17-variant18-variant20-variant22-variant23-variant25-variant27-variant28-variant33-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,20:53:99:451,0,814:22,11,13,7 chr1 209779652 . T G 3777.59 PASS AC=1;AF=0.536;AN=2;DP=1877;MQ=60;set=variant-variant5-variant8-variant17-variant18-variant20-variant22-variant23-variant25-variant27-variant28-variant33-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:60,63:123:99:1481,0,1383:33,27,31,32 chr1 209781125 . T C 2399.27 PASS AC=1;AF=0.567;AN=2;DP=2023;MQ=60;set=variant-variant5-variant8-variant17-variant18-variant20-variant22-variant23-variant25-variant27-variant28-variant30-variant33-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:78,49:127:99:1156,0,2097:42,36,31,18 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 0/1:14:99:2,5,0,7 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 0/1:34,32:66:99:823,0,842:22,12,20,12 chr1 209782545 . A G 279.14 PASS AC=1;AF=0.632;AN=2;DP=615;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant7-variant10-variant11-variant12-variant17-variant19-variant23-variant24-variant27-variant28-variant31-variant32-variant34-variant36-variant37-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,11:26:99:279,0,492:4,11,3,8 chr1 209784663 . A C 46.72 PASS AC=2;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 1/1:0,16:16:48:643,48,0:0,0,13,3 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 0/1:43,42:85:99:985,0,1029:17,26,16,26 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 0/1:14,12:26:99:413,0,359:6,8,4,8 chr1 209785206 . G A 1994.4 PASS AC=1;AF=0.55;AN=2;DP=1450;set=variant5-variant9-variant12-variant19-variant23-variant24-variant28-variant36-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:65,56:121:99:1485,0,1582:38,27,36,20 chr1 209785957 . T G 406.24 PASS AC=2;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 1/1:0,32:32:95:1116,95,0:0,0,20,12 chr1 209786078 . G A 1315.01 PASS AC=2;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 1/1:0,112:112:99:3187,335,0:0,0,59,53 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 0/1:18,9:27:99:226,0,536:8,10,2,7 chr1 209787037 . A T 428.15 PASS AC=1;AF=0.5;AN=2;DP=77;FractionInformativeReads=1;MQ=60;set=variant23-variant28 GT:AD:DP:GQ:PL:SB 0/1:24,19:43:99:456,0,628:12,12,13,6 chr1 209788213 . T C 242.87 PASS AC=2;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 1/1:0,9:9:27:288,27,0:0,0,6,3 chr1 209788514 . G A 3037.72 PASS AC=1;AF=0.559;AN=2;DP=1519;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant8-variant9-variant14-variant15-variant23-variant26-variant28-variant29-variant33-variant34-variant36-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,49:90:99:1389,0,1074:19,22,24,25 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 0/1:36,21:57:99:495,0,940:15,21,7,14 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 1/1:0,131:131:99:4920,397,0:0,0,54,77 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 0/1:15,10:25:99:277,0,350:9,6,8,2 chr1 209799253 . A G 4514.61 PASS AC=1;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 0/1:57,72:129:99:1778,0,1353:27,30,34,38 chr1 209801707 . T C 1065.48 PASS AC=1;AF=0.556;AN=2;DP=250;FractionInformativeReads=1;MQ=60;set=variant3-variant9-variant13-variant14-variant23-variant26-variant28-variant33-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,8:25:99:164,0,382:8,9,3,5 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 1/1:0,48:48:99:1724,144,0:0,0,11,37 chr1 209807972 . G A 854.45 PASS AC=2;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 1/1:0,109:109:99:3389,325,0:0,0,37,72 chr1 209811886 . T G 1415.23 PASS AC=2;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 1/1:0,112:112:99:3566,335,0:0,0,61,51 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 1/1:0,48:48:99:1648,144,0:0,0,17,31 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 1/1:0,23:23:69:739,69,0:0,0,13,10 chr1 209849002 . T C 1070.58 PASS AC=1;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 0/1:82,91:173:99:2277,0,2081:43,39,49,42 chr1 209849399 . AG A 1022.88 PASS AC=1;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 0/1:47,38:85:99:1274,0,1635:18,29,20,18 chr1 209849406 . T G 3029.64 PASS AC=2;AF=0.977;AN=2;DP=3978;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:3125,255,0:0,0,39,46 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 1/1:0,50:50:99:1558,150,0:0,0,25,25 chr1 209880216 . C CA 5144.26 PASS AC=1;AF=0.577;AN=2;DP=1840;MQ=60;set=variant6-variant8-variant10-variant14-variant19-variant20-variant23-variant24-variant31-variant32-variant33-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:73,59:132:99:1704,0,2206:41,32,33,26 chr1 209880259 . T G 4858.1 PASS AC=1;AF=0.577;AN=2;DP=1833;MQ=60;set=variant6-variant8-variant10-variant14-variant19-variant20-variant23-variant24-variant31-variant32-variant33-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:69,57:126:99:1454,0,1854:41,28,33,24 chr1 209880508 . GA G 1543.15 PASS AC=1;AF=0.559;AN=2;DP=1067;MQ=60;set=variant6-variant8-variant10-variant13-variant14-variant19-variant20-variant23-variant24-variant31-variant32-variant33-variant37-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,23:39:99:527,0,313:5,11,8,15 chr1 209905734 . G C 1700.85 PASS AC=1;AF=0.571;AN=2;DP=798;MQ=60;set=variant6-variant8-variant10-variant14-variant19-variant20-variant23-variant24-variant31-variant32-variant33-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:29,18:47:99:533,0,726:19,10,15,3 chr1 209908100 . G A 1202.81 PASS AC=1;AF=0.577;AN=2;DP=570;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant10-variant14-variant19-variant23-variant24-variant31-variant32-variant33-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,15:30:99:359,0,461:4,11,5,10 chr1 209929299 . G A 61.77 PASS AC=1;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 0/1:3,3:6:68:68,0,77:2,1,2,1 chr1 209929579 . C A 2550.36 PASS AC=1;AF=0.567;AN=2;DP=1032;MQ=60;set=variant6-variant8-variant10-variant14-variant19-variant20-variant23-variant24-variant25-variant31-variant32-variant33-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:39,44:83:99:982,0,911:19,20,21,23 chr1 209931799 . C T 193.6 PASS AC=1;AF=0.614;AN=2;DP=226;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant8-variant10-variant13-variant14-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant31-variant33-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:63:63,0,120:3,1,2,1 chr1 209932297 . T A 112.92 PASS AC=1;AF=0.591;AN=2;DP=308;MQ=60;set=variant3-variant6-variant8-variant10-variant13-variant14-variant17-variant19-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:34:117,0,34:1,1,3,0 chr1 209933331 . A G 1280.78 PASS AC=1;AF=0.587;AN=2;DP=1839;MQ=60;set=variant3-variant6-variant8-variant10-variant13-variant14-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,51:97:99:1216,0,1060:27,19,27,24 chr1 209933540 . A G 2217.85 PASS AC=1;AF=0.587;AN=2;DP=3058;MQ=60;set=variant3-variant6-variant8-variant10-variant13-variant14-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,58:134:99:1396,0,1749:40,36,28,30 chr1 209933757 . G C 791.38 PASS AC=1;AF=0.587;AN=2;DP=1571;MQ=60;set=variant3-variant6-variant8-variant10-variant13-variant14-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,32:65:99:816,0,886:16,17,13,19 chr1 209935778 . A G 1676.39 PASS AC=1;AF=0.587;AN=2;DP=2731;MQ=60;set=variant3-variant6-variant8-variant10-variant13-variant14-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,42:87:99:1028,0,1145:25,20,21,21 chr1 209936060 . A G 246.5 PASS AC=1;AF=0.5;AN=2;DP=348;set=variant3-variant8-variant13-variant14-variant20-variant23-variant28-variant32-variant33-variant38-variant39-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:359,0,3803:6,6,2,8 chr1 209936064 . T C 256.61 PASS AC=1;AF=0.5;AN=2;DP=310;set=variant3-variant13-variant14-variant20-variant23-variant28-variant32-variant33-variant38-variant39-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:12,8:20:99:338,0,3806:6,6,1,7 chr1 209936075 . T TTAGTAACTAGCTGTTACTAAGAGAAAGGAAGCTTTCCTTTGAATATGGAA,TTAGTAACTAGCTGTTACTAAGA,TTA,TTAGTAACTAGCTGTTACTAAGAGAAA,TTAGTAACTAGCTGTTACTAAGAGAAAGGAA 166.03 PASS AC=0,0,1,0,0;AF=0.083,0.083,0.167,0.083,0.083;AN=2;DP=165;FractionInformativeReads=1;set=variant3-variant13-variant14-variant23-variant33-variant38 GT:DP:GQ:SB 0/3:21:99:8,7,0,6 chr1 209936076 . G GTAACTA 268.98 PASS AC=1;AF=0.5;AN=2;DP=52;FractionInformativeReads=1;MQ=60;set=variant14-variant23 GT:AD:DP:GQ:PL:SB 0/1:14,4:18:99:195,0,4257:8,6,0,4 chr1 209936078 . C CTGTTACTAAGAG,CTGTTACTAAGAGA 193.29 PASS AC=0,1;AF=0.25,0.25;AN=2;DP=56;FractionInformativeReads=1;MQ=60;set=variant14-variant23 GT:DP:GQ:SB 0/2:22:99:8,10,0,4 chr1 209936466 . A G 2025.09 PASS AC=1;AF=0.587;AN=2;DP=2209;MQ=60;set=variant3-variant6-variant8-variant10-variant13-variant14-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,54:108:99:1423,0,1364:24,30,22,32 chr1 209936571 . A G 1425.32 PASS AC=1;AF=0.609;AN=2;DP=1315;MQ=60;set=variant3-variant6-variant8-variant10-variant13-variant14-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,27:64:99:685,0,924:16,21,10,17 chr1 209936631 . G A 633.18 PASS AC=1;AF=0.565;AN=2;DP=633;MQ=60;set=variant3-variant6-variant8-variant10-variant13-variant14-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,13:28:99:341,0,422:5,10,5,8 chr1 209936673 . C G 523.18 PASS AC=1;AF=0.587;AN=2;DP=484;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant8-variant10-variant13-variant14-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:408,0,462:7,6,8,5 chr1 209936914 . C T 1822.47 PASS AC=1;AF=0.587;AN=2;DP=3139;MQ=60;set=variant3-variant6-variant8-variant10-variant13-variant14-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,61:134:99:1410,0,1843:36,37,25,36 chr1 209936964 . T TCA 2092.07 PASS AC=1;AF=0.587;AN=2;DP=2250;MQ=60;set=variant3-variant6-variant8-variant10-variant13-variant14-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,37:93:99:1344,0,2493:24,32,16,21 chr1 209948711 . A C 2272.19 PASS AC=1;AF=0.614;AN=2;DP=3383;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:96,69:165:99:1715,0,2379:47,49,32,37 chr1 209950681 . T C 1061.93 PASS AC=1;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 0/1:26,14:40:99:363,0,678:12,14,6,8 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 1/1:0,69:69:99:2089,207,0:0,0,34,35 chr1 209950848 . G A 991.26 PASS AC=1;AF=0.605;AN=2;DP=1353;MQ=60;set=variant3-variant4-variant7-variant8-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,33:61:99:807,0,697:11,17,16,17 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 0/1:118,115:233:99:2758,0,2743:61,57,56,59 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 0/1:16,26:42:99:706,0,438:9,7,13,13 chr1 209956542 . C A 1479.65 PASS AC=1;AF=0.614;AN=2;DP=2189;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,56:93:99:1359,0,879:20,17,27,29 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 1/1:0,9:9:27:283,27,0:0,0,4,5 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 0/1:12,8:20:99:184,0,480:7,5,4,4 chr1 209960925 . T C 230.41 PASS AC=1;AF=0.619;AN=2;DP=666;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant23-variant26-variant28-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,12:20:99:318,0,289:4,4,7,5 chr1 209961023 . T A 506.47 PASS AC=1;AF=0.614;AN=2;DP=683;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:423,0,377:7,9,8,9 chr1 209961314 . T C 550.29 PASS AC=1;AF=0.611;AN=2;DP=649;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant8-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,12:27:99:312,0,351:10,5,8,4 chr1 209963803 . G A 1682.94 PASS AC=1;AF=0.614;AN=2;DP=1805;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,37:67:99:987,0,836:21,9,23,14 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 0/1:125:99:26,22,43,34 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 0/1:74,58:132:99:1428,0,1860:32,42,25,33 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 0/1:11,9:20:99:261,0,347:3,8,4,5 chr1 209974528 . CAAAA CAA,CAAAAA,CA,CAAA,C,CAAAAAAA 120.24 PASS AC=0,1,0,0,0,0;AF=0.125,0.141,0.016,0.188,0.016,0.016;AN=2;DP=1581;set=variant-variant3-variant4-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant30-variant31-variant32-variant33-filterInvariant34-filterInvariant37-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:21:99:9,3,8,1 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 0/1:26,23:49:99:577,0,663:11,15,10,13 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 1/1:0,10:10:30:363,30,0:0,0,9,1 chr1 210001586 . A G 2547.29 PASS AC=2;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 1/1:0,84:84:99:2658,251,0:0,0,30,54 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 0/1:19,29:48:99:714,0,450:13,6,17,12 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 1/1:0,55:55:99:1618,165,0:0,0,34,21 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 1/1:0,87:87:99:2729,260,0:0,0,51,36 chr1 210004332 . G A 2487.93 PASS AC=1;AF=0.6;AN=2;DP=3305;MQ=60;set=variant3-variant4-variant7-variant8-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant30-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,72:147:99:1610,0,1969:35,40,36,36 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 1/1:0,6:6:18:266,18,0:0,0,5,1 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 1/1:0,6:6:18:266,18,0:0,0,5,1 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 1/1:0,152:152:99:4320,454,0:0,0,90,62 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 1/1:0,50:50:99:1605,150,0:0,0,31,19 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 1/1:0,18:18:54:667,54,0:0,0,3,15 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 1/1:0,55:55:99:1743,165,0:0,0,30,25 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 1/1:0,54:54:99:2388,163,0:0,0,30,24 chr1 210016709 . A T 2749.31 PASS AC=1;AF=0.6;AN=2;DP=3092;MQ=60;set=variant3-variant4-variant7-variant8-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant30-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,48:119:99:1302,0,1935:31,40,16,32 chr1 210017083 . G A 1317.77 PASS AC=1;AF=0.625;AN=2;DP=1408;MQ=60;set=variant3-variant4-variant7-variant8-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant30-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,25:44:99:776,0,523:9,10,7,18 chr1 210017335 . CAAAT C 1105.41 PASS AC=1;AF=0.6;AN=2;DP=1011;MQ=60;set=variant3-variant4-variant7-variant8-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant30-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,25:61:99:921,0,1818:15,21,13,12 chr1 210025751 . G A 4578.83 PASS AC=1;AF=0.625;AN=2;DP=4550;MQ=60;set=variant3-variant4-variant7-variant8-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant30-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:126,113:239:99:2804,0,3157:58,68,44,69 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 0/1:72,71:143:99:1686,0,1669:29,43,26,45 chr1 210027026 . G A 331.77 PASS AC=1;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 0/1:13,8:21:99:167,0,356:8,5,5,3 chr1 210027654 . T C 2397.27 PASS AC=1;AF=0.625;AN=2;DP=3070;MQ=60;set=variant3-variant4-variant7-variant8-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant30-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,77:148:99:1719,0,1782:31,40,33,44 chr1 210027669 . TGA T 2715.31 PASS AC=1;AF=0.6;AN=2;DP=2693;MQ=60;set=variant3-variant4-variant7-variant8-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant30-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,65:122:99:2328,0,1912:26,31,24,41 chr1 210027721 . C T 1875.39 PASS AC=1;AF=0.625;AN=2;DP=1523;MQ=60;set=variant3-variant4-variant7-variant8-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant30-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,37:79:99:1361,0,2066:15,27,12,25 chr1 210027723 . T A 1875.39 PASS AC=1;AF=0.6;AN=2;DP=1497;MQ=60;set=variant3-variant4-variant7-variant8-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant30-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,35:76:99:1361,0,2066:15,26,10,25 chr1 210027936 . T C 652.69 PASS AC=1;AF=0.6;AN=2;DP=808;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant8-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant30-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,17:41:99:399,0,648:12,12,9,8 chr1 210028454 . G T 996.72 PASS AC=1;AF=0.71;AN=2;DP=3658;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,53:134:99:1140,0,2002:42,39,25,28 chr1 210029430 . G C 1205.99 PASS AC=1;AF=0.605;AN=2;DP=1407;MQ=60;set=variant3-variant4-variant7-variant8-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant30-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,52:80:99:1303,0,590:12,16,25,27 chr1 210030197 . C T 276.57 PASS AC=1;AF=0.63;AN=2;DP=675;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant30-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,22:41:99:539,0,484:7,12,10,12 chr1 210030639 . T C 2991.21 PASS AC=1;AF=0.605;AN=2;DP=2886;set=variant3-variant4-variant7-variant8-variant10-variant11-variant12-variant13-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant30-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,85:164:99:2287,0,1897:46,33,56,29 chr1 210030730 . C A 5038.44 PASS AC=1;AF=0.636;AN=2;DP=6426;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant30-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:153,145:298:99:3670,0,3959:86,67,77,68 chr1 210111733 . G A 1263.21 PASS AC=1;AF=0.676;AN=2;DP=3932;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,64:111:99:1824,0,1224:14,33,17,47 chr1 210139069 . G A 149.75 PASS AC=2;AF=0.867;AN=2;DP=49;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant9-variant10-variant13-variant14-variant15-variant17-variant23-variant25-variant27-variant31-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:132,9,0:0,0,3,0 chr1 210267893 . TGAA T 1980.72 PASS AC=1;AF=0.545;AN=2;DP=1371;MQ=60;set=variant9-variant11-variant15-variant19-variant20-variant23-variant24-variant25-variant30-variant34-variant36 GT:AD:DP:GQ:PL:SB 0/1:45,60:105:99:2364,0,1935:19,26,23,37 chr1 210332615 . A G 327.6 PASS AC=1;AF=0.5;AN=2;DP=19;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.362;QD=17.24;ReadPosRankSum=1.197;SOR=1.061;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:8,11:19:99:356,0,259:7,1,10,1 chr1 210334081 . T C 498.45 PASS AC=1;AF=0.55;AN=2;DP=634;MQ=60;set=variant9-variant15-variant19-variant20-variant23-variant24-variant25-variant30-variant34-variant36 GT:AD:DP:GQ:PL:SB 0/1:20,17:37:99:475,0,534:13,7,11,6 chr1 210337043 . A G 3081.29 PASS AC=2;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 1/1:0,237:237:99:7170,709,0:0,0,123,114 chr1 210337726 . G A 396.21 PASS AC=1;AF=0.55;AN=2;DP=166;FractionInformativeReads=1;MQ=60;set=variant9-variant15-variant19-variant20-variant23-variant24-variant25-variant30-variant34-variant36 GT:AD:DP:GQ:PL:SB 0/1:6,13:19:99:507,0,157:1,5,0,13 chr1 210406940 . T C 1489.99 PASS AC=1;AF=0.613;AN=2;DP=1243;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,20:36:99:544,0,497:9,7,14,6 chr1 210407031 . G T 4146.43 PASS AC=1;AF=0.613;AN=2;DP=4123;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,62:117:99:1345,0,1220:33,22,32,30 chr1 210407329 . GTTT GTT,G 1614.26 PASS AC=0,1;AF=0.397,0.172;AN=2;DP=1010;set=variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant18-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant37-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:24:99:6,8,4,6 chr1 210407339 . T TAA,A 454.88 PASS AC=1,0;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 0/1:26:99:5,7,6,8 chr1 210414871 . G GT 49.26 PASS AC=1;AF=0.516;AN=2;DP=1019;set=filterInvariant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant39-variant40-filterInvariant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:239,0,247:7,2,7,3 chr1 210417098 . G A 4202.83 PASS AC=1;AF=0.542;AN=2;DP=1374;MQ=60;set=variant4-variant7-variant8-variant11-variant12-variant13-variant18-variant19-variant20-variant23-variant28-variant38 GT:AD:DP:GQ:PL:SB 0/1:58,53:111:99:1332,0,1659:24,34,24,29 chr1 210417861 . C T 7755.86 PASS AC=1;AF=0.542;AN=2;DP=2492;MQ=60;set=variant4-variant7-variant8-variant11-variant12-variant13-variant18-variant19-variant20-variant23-variant28-variant38 GT:AD:DP:GQ:PL:SB 0/1:90,82:172:99:2242,0,2438:44,46,43,39 chr1 210501504 . T A 193.17 PASS AC=1;AF=0.681;AN=2;DP=463;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,10:21:99:257,0,320:9,2,6,4 chr1 210502184 . G T 139.36 PASS AC=1;AF=0.528;AN=2;DP=424;MQ=60;set=variant-variant3-variant5-variant6-variant8-variant10-variant14-variant20-variant22-variant23-variant26-variant27-variant28-variant30-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,13:30:99:396,0,575:15,2,12,1 chr1 210502580 . A G 3481.62 PASS AC=1;AF=0.571;AN=2;DP=475;MQ=60;set=variant4-variant13-variant18-variant19-variant20-variant23-variant38 GT:AD:DP:GQ:PL:SB 0/1:20,32:52:99:843,0,597:8,12,13,19 chr1 210522080 . CGT CGTGTGTGT,CGTGTGTGTGTGT,CGTGTGT,C,CGTGT,CGTGTGTGTGTGTGT,CGTGTGTGTGT 361.23 PASS AC=2,0,0,0,0,0,0;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 1/1:16:56:0,0,14,2 chr1 210536078 . C G 1437.46 PASS AC=2;AF=0.821;AN=2;DP=3932;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2751,261,0:0,0,57,30 chr1 210536278 . C A 804.58 PASS AC=1;AF=0.529;AN=2;DP=1364;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant14-variant20-variant22-variant23-variant26-variant27-variant28-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,31:92:99:782,0,1628:21,40,8,23 chr1 210536387 . T C 141.14 PASS AC=1;AF=0.529;AN=2;DP=190;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant14-variant20-variant22-variant23-variant26-variant27-variant28-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:153,0,156:0,5,0,4 chr1 210577831 . C T 551.34 PASS AC=1;AF=0.529;AN=2;DP=1118;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant14-variant20-variant22-variant23-variant26-variant27-variant28-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,23:49:99:637,0,576:15,11,14,9 chr1 210577873 . G C 867.29 PASS AC=2;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 1/1:0,58:58:99:2092,174,0:0,0,30,28 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 0/1:31,26:57:99:482,0,1225:17,14,13,13 chr1 210577901 . T C 959.43 PASS AC=1;AF=0.529;AN=2;DP=1609;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant14-variant20-variant22-variant23-variant26-variant27-variant28-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,36:64:99:933,0,1016:13,15,20,16 chr1 210591742 . TG T 1102.63 PASS AC=2;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 1/1:0,79:79:99:2539,238,0:0,0,15,64 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 1/1:0,77:77:99:2290,231,0:0,0,31,46 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 0/1:21,18:39:99:484,0,500:9,12,5,13 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 1/1:0,38:38:99:1339,114,0:0,0,7,31 chr1 210804430 . G A 1152.49 PASS AC=1;AF=0.6;AN=2;DP=754;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant8-variant10-variant13-variant23-variant24-variant28-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,32:66:99:806,0,837:20,14,17,15 chr1 210847514 . A T 945.18 PASS AC=2;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 1/1:0,82:82:99:2414,246,0:0,0,47,35 chr1 210848034 . C T 302.88 PASS AC=1;AF=0.6;AN=2;DP=137;FractionInformativeReads=1;MQ=60;set=variant9-variant23-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,20:34:99:538,0,361:6,8,8,12 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 1/1:0,52:52:99:1459,156,0:0,0,25,27 chr1 210848807 . AT A,ATTT,ATT 2119.3 PASS AC=2,0,0;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 1/1:181:99:6,7,73,95 chr1 210849019 . A T 1109.39 PASS AC=1;AF=0.5;AN=2;DP=602;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant10-variant23-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:49,32:81:99:675,0,1191:21,28,14,18 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 1/1:0,60:60:99:2037,180,0:0,0,35,25 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 1/1:0,48:48:99:1445,144,0:0,0,19,29 chr1 211093590 . C T 44.95 PASS AC=1;AF=0.563;AN=2;DP=330;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant17-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:195,0,179:2,4,2,5 chr1 211192707 . G A 284.73 PASS AC=1;AF=0.556;AN=2;DP=722;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant36-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,11:16:99:350,0,162:0,5,2,9 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 0/1:4,10:14:95:322,0,95:3,1,9,1 chr1 211264140 . A G 599.1 PASS AC=1;AF=0.563;AN=2;DP=321;MQ=60;set=variant2-variant10-variant14-variant17-variant23-variant30-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:17,16:33:99:455,0,477:4,13,4,12 chr1 211280737 . A AC 1576.72 PASS AC=1;AF=0.571;AN=2;DP=659;MQ=60;set=variant2-variant10-variant14-variant23-variant30-variant31-variant35 GT:AD:DP:GQ:PL:SB 0/1:41,41:82:99:894,0,1166:18,23,16,25 chr1 211280783 . G A 685.14 PASS AC=1;AF=0.5;AN=2;DP=281;MQ=60;set=variant4-variant10-variant17-variant22-variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:23,25:48:99:600,0,594:7,16,9,16 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 1/1:0,9:9:27:255,27,0:0,0,9,0 chr1 211447625 . G A 1720.99 PASS AC=2;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 1/1:0,123:123:99:3600,369,0:0,0,64,59 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 1/1:15:35:1,0,12,2 chr1 211452678 . G A 1120.04 PASS AC=2;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 1/1:0,71:71:99:2101,213,0:0,0,32,39 chr1 211452728 . G A 987.98 PASS AC=2;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 1/1:0,42:42:99:1304,126,0:0,0,14,28 chr1 211487347 . GT G 3393.26 PASS AC=2;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 1/1:0,169:169:99:6313,509,0:0,0,74,95 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 1/1:2,306:308:99:9180,840,0:2,0,153,153 chr1 211488538 . C A 22314.8 PASS AC=2;AF=0.977;AN=2;DP=28584;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,621:623:99:18744,1818,0:1,1,339,282 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 1/1:0,204:204:99:6342,612,0:0,0,104,100 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 1/1:0,18:18:54:755,54,0:0,0,17,1 chr1 211529846 . A G 1649.09 PASS AC=1;AF=0.5;AN=2;DP=1042;MQ=60;set=variant12-variant19-variant23-variant33-variant40 GT:AD:DP:GQ:PL:SB 0/1:93,88:181:99:2177,0,2153:47,46,40,48 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 0/2:22:6:2,1,15,4 chr1 211651907 . G A 539.73 PASS AC=1;AF=0.5;AN=2;DP=396;MQ=60;set=variant5-variant12-variant16-variant19-variant20-variant21-variant23-variant25-variant33-variant40 GT:AD:DP:GQ:PL:SB 0/1:21,12:33:99:369,0,666:16,5,10,2 chr1 211665809 . C G 1127.28 PASS AC=1;AF=0.5;AN=2;DP=167;FractionInformativeReads=1;MQ=60;set=variant23-variant33 GT:AD:DP:GQ:PL:SB 0/1:35,45:80:99:1156,0,817:14,21,22,23 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 0/1:40,50:90:99:1091,0,831:21,19,26,24 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 0/1:91,95:186:99:2371,0,2044:55,36,58,37 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 1/1:0,53:53:99:1602,159,0:0,0,24,29 chr1 211918115 . C T 3549.09 PASS AC=1;AF=0.553;AN=2;DP=5067;set=variant4-variant8-variant9-variant10-variant11-variant12-variant16-variant19-variant22-variant23-variant24-variant25-variant26-variant29-variant31-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:138,118:256:99:2617,0,3132:67,71,57,61 chr1 211919937 . T C 2589.37 PASS AC=1;AF=0.543;AN=2;DP=3279;MQ=60;set=variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant19-variant22-variant23-variant24-variant25-variant26-variant29-variant31-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:63,75:138:99:1912,0,1638:33,30,41,34 chr1 211920624 . G A 2492.04 PASS AC=1;AF=0.553;AN=2;DP=3467;MQ=60;set=variant4-variant8-variant9-variant10-variant11-variant12-variant16-variant19-variant22-variant23-variant24-variant25-variant26-variant29-variant31-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:65,88:153:99:2375,0,1604:43,22,58,30 chr1 211921229 . C A 4795.29 PASS AC=1;AF=0.553;AN=2;DP=8393;MQ=60;set=variant4-variant8-variant9-variant10-variant11-variant12-variant16-variant19-variant22-variant23-variant24-variant25-variant26-variant29-variant31-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:206,166:372:99:3986,0,5391:102,104,91,75 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 0/1:25,20:45:99:527,0,690:8,17,5,15 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 0/1:77,71:148:99:1691,0,1784:34,43,31,40 chr1 211922603 . G A 2088.39 PASS AC=1;AF=0.553;AN=2;DP=2587;MQ=60;set=variant4-variant8-variant9-variant10-variant11-variant12-variant16-variant19-variant22-variant23-variant24-variant25-variant26-variant29-variant31-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:54,57:111:99:1352,0,1166:24,30,27,30 chr1 212003211 . C CT 431.83 PASS AC=1;AF=0.563;AN=2;DP=726;MQ=60;set=variant2-variant4-variant6-variant7-variant8-variant9-variant10-filterInvariant11-variant12-variant14-variant16-variant19-variant22-variant23-variant24-variant25-variant26-variant29-variant31-variant36-variant37-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,13:17:62:312,0,62:0,4,8,5 chr1 212004100 . C G 157.42 PASS AC=1;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 0/1:10,13:23:99:299,0,220:4,6,7,6 chr1 212113995 . G A 3747.04 PASS AC=1;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 0/1:67,53:120:99:1064,0,1918:30,37,22,31 chr1 212114662 . A G 3991.23 PASS AC=1;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 0/1:37,33:70:99:1274,0,2874:15,22,14,19 chr1 212114663 . G A 3991.23 PASS AC=1;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 0/1:37,33:70:99:1274,0,2874:15,22,14,19 chr1 212114666 . C G 3841.77 PASS AC=1;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 0/1:36,33:69:99:1274,0,2874:14,22,14,19 chr1 212142054 . GA G 531.24 PASS AC=1;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 0/1:10,15:25:99:283,0,188:1,9,3,12 chr1 212209367 . T TC 489.23 PASS AC=1;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 0/1:11,13:24:99:391,0,320:2,9,1,12 chr1 212217944 . GA G,GAA 105.26 PASS AC=0,1;AF=0.389,0.111;AN=2;DP=189;set=variant3-variant18-variant22-variant23-variant24-filterInvariant25-variant34-variant43-variant44 GT:DP:GQ:SB 0/2:13:99:6,1,4,2 chr1 212217971 . C CTT 1576.82 PASS AC=1;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 0/1:15,18:33:99:710,0,578:11,4,13,5 chr1 212220847 . G A 697.58 PASS AC=1;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 0/1:7,6:13:99:231,0,237:1,6,1,5 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 1/1:0,41:41:99:1289,123,0:0,0,28,13 chr1 212240063 . G A 314.62 PASS AC=1;AF=0.558;AN=2;DP=553;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant36-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:261,0,305:8,3,6,1 chr1 212241714 . TAA TA,TAAAA,TAAA,T 1233.05 PASS AC=1,0,0,0;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 0/1:35:99:7,8,7,13 chr1 212241848 . T C 604.92 PASS AC=1;AF=0.5;AN=2;DP=442;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant12-variant22-variant23-variant26-variant29 GT:AD:DP:GQ:PL:SB 0/1:26,39:65:99:1027,0,699:18,8,25,14 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 1/1:0,13:13:39:463,39,0:0,0,4,9 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 1/1:0,18:18:54:515,54,0:0,0,12,6 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 1/1:0,142:142:99:4136,422,0:0,0,77,65 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 1/1:1,73:74:99:2149,186,0:1,0,27,46 chr1 212277107 . T G 14314.5 PASS AC=1;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 0/1:193,193:386:99:4789,0,4773:82,111,93,100 chr1 212277304 . C G 8681.24 PASS AC=1;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 0/1:119,125:244:99:3145,0,3034:67,52,66,59 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 1/1:178:99:0,0,80,98 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 0/1:23,22:45:99:636,0,638:14,9,16,6 chr1 212475634 . C T 341.13 PASS AC=1;AF=0.559;AN=2;DP=332;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant9-variant14-variant17-variant21-variant23-variant25-variant27-variant28-variant31-variant34-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,8:15:99:271,0,172:2,5,1,7 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 0/1:43,39:82:99:982,0,1074:18,25,14,25 chr1 212521639 . T G 1497.47 PASS AC=2;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 1/1:0,33:33:99:1004,99,0:0,0,22,11 chr1 212526013 . G C 471.87 PASS AC=1;AF=0.526;AN=2;DP=297;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant9-variant14-variant17-variant21-variant23-variant25-variant27-variant28-variant31-variant34-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:210,0,231:6,2,5,1 chr1 212526288 . C T 5527.96 PASS AC=2;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 1/1:0,159:159:99:4997,476,0:0,0,82,77 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 1/1:0,68:68:99:2352,204,0:0,0,23,45 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 0/1:184,206:390:99:4975,0,4556:83,101,96,110 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 0/1:101,155:256:99:3863,0,2435:50,51,71,84 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 0/1:62,69:131:99:2633,0,3704:31,31,38,31 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 0/1:66,68:134:99:2658,0,3766:33,33,36,32 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 0/2:20:63:4,3,2,11 chr1 212551139 . G GCA 36.78 PASS AC=1;AF=0.553;AN=2;DP=373;MQ=60;set=variant-variant4-variant5-variant6-variant9-variant14-variant17-variant21-variant23-variant25-variant27-variant28-variant31-variant34-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:149,0,150:0,4,1,3 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 0/1:15,21:36:99:636,0,467:11,4,17,4 chr1 212560327 . A G 2052.8 PASS AC=2;AF=0.977;AN=2;DP=7215;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,139:139:99:4205,417,0:0,0,65,74 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 0/1:76,61:137:99:1788,0,2128:25,51,19,42 chr1 212615875 . T C 2660.94 PASS AC=1;AF=0.586;AN=2;DP=2554;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant28-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:37,50:87:99:1308,0,823:21,16,29,21 chr1 212616080 . C CATTTT 76.01 PASS AC=1;AF=0.556;AN=2;DP=279;MQ=60;set=variant2-variant5-variant8-variant9-variant12-variant13-variant15-variant16-variant17-variant19-variant21-variant23-variant30-variant31-variant33-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:56:116,0,56:0,1,0,3 chr1 212617829 . C G 531.52 PASS AC=1;AF=0.568;AN=2;DP=2252;set=variant2-variant4-variant5-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant30-variant31-variant33-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:39,35:74:99:945,0,1029:16,23,12,23 chr1 212617860 . CGTGTGTGTGT CGTGT,CGTGTGT,CGTGTGTGTGTGT,CGTGTGTGT,C,CGT 810.5 PASS AC=1,0,0,0,0,0;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 0/1:10:99:0,3,0,7 chr1 212617909 . GTA G 37.79 PASS AC=1;AF=0.5;AN=2;DP=298;set=filterInvariant3-variant5-variant11-variant12-variant16-variant19-variant21-variant23-variant30-variant31-filterInvariant33-variant36 GT:AD:DP:GQ:PL:SB 0/1:10,3:13:94:94,0,351:0,10,0,3 chr1 212619009 . C A 135.11 PASS AC=1;AF=0.55;AN=2;DP=235;set=variant2-variant4-variant5-variant9-variant11-variant12-variant13-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant30-variant31-variant33-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:57:155,0,57:2,0,6,0 chr1 212619339 . T C 3302.63 PASS AC=1;AF=0.586;AN=2;DP=3422;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant28-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:44,56:100:99:1461,0,1077:19,25,22,34 chr1 212738835 . G T 337.55 PASS AC=1;AF=0.5;AN=2;DP=542;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant10-variant11-variant16-variant19-variant23-variant24-variant29-variant32-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,14:29:99:367,0,463:5,10,5,9 chr1 212738909 . T C 143.54 PASS AC=2;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 1/1:0,15:15:45:516,45,0:0,0,6,9 chr1 212799870 . A G 359 PASS AC=2;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 1/1:0,70:70:99:2230,210,0:0,0,39,31 chr1 212799882 . A T 896.17 PASS AC=1;AF=0.5;AN=2;DP=77;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.279;QD=11.64;ReadPosRankSum=-1.268;SOR=0.65;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:39,38:77:99:924,0,974:22,17,21,17 chr1 212799949 . C T 415.48 PASS AC=2;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 1/1:0,97:97:99:2702,289,0:0,0,49,48 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 1/1:0,17:17:51:596,51,0:0,0,11,6 chr1 212870146 . G A 424.61 PASS AC=1;AF=0.5;AN=2;DP=96;FractionInformativeReads=1;MQ=60;set=variant23-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,16:29:99:453,0,336:9,4,11,5 chr1 212870292 . C T 2840.89 PASS AC=1;AF=0.625;AN=2;DP=1139;MQ=60;set=variant7-variant11-variant19-variant22-variant23-variant29-variant32-variant33-variant36-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:52,60:112:99:1492,0,1177:27,25,33,27 chr1 212872852 . T C 835.44 PASS AC=1;AF=0.625;AN=2;DP=423;MQ=60;set=variant7-variant11-variant19-variant22-variant23-variant29-variant32-variant33-variant36-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,15:26:99:394,0,297:6,5,7,8 chr1 212873074 . C T 1382.44 PASS AC=1;AF=0.625;AN=2;DP=425;MQ=60;set=variant7-variant11-variant19-variant22-variant23-variant29-variant32-variant33-variant36-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,10:30:99:288,0,843:8,12,5,5 chr1 212873096 . T C 1256.49 PASS AC=1;AF=0.625;AN=2;DP=379;FractionInformativeReads=1;set=variant7-variant11-variant19-variant22-variant23-variant29-variant32-variant33-variant36-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,6:24:99:187,0,812:7,11,3,3 chr1 212873431 . C T 571.23 PASS AC=1;AF=0.667;AN=2;DP=127;FractionInformativeReads=1;MQ=60;set=variant7-variant11-variant19-variant22-variant23-variant29-variant32-variant33-variant36-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:76:76,0,119:0,3,1,2 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 0/1:17,10:27:99:288,0,431:8,9,2,8 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 0/1:17,7:24:99:242,0,607:11,6,3,4 chr1 212900487 . A G 1492.59 PASS AC=1;AF=0.966;AN=2;DP=1957;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:31,15:46:99:404,0,731:18,13,11,4 chr1 212910577 . C T 4068.67 PASS AC=1;AF=0.5;AN=2;DP=631;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:148,109:257:99:2677,0,4076:75,73,51,58 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 0/1:68,46:114:99:1224,0,1927:27,41,16,30 chr1 212911366 . CTT CT,C 1868.79 PASS AC=0,1;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 0/2:76:99:13,27,14,22 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 0/1:60,79:139:99:2067,0,1534:28,32,33,46 chr1 212912097 . G A 907.31 PASS AC=1;AF=0.5;AN=2;DP=83;FS=0;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:16,19:35:99:750,0,765:3,13,3,16 chr1 212912098 . C G 907.29 PASS AC=1;AF=0.5;AN=2;DP=83;FS=0;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:16,19:35:99:750,0,765:3,13,3,16 chr1 212912108 . ATT A,AT,ATTT 483.4 PASS AC=0,1,0;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 0/2:24:99:1,6,3,14 chr1 212961080 . T TAAAG 358.35 PASS AC=1;AF=0.594;AN=2;DP=302;MQ=60;set=variant-variant4-variant7-variant11-variant16-variant19-variant22-variant23-variant29-variant31-variant32-variant33-variant34-variant36-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:99:201,0,167:0,3,1,4 chr1 212965237 . G C 2505.23 PASS AC=1;AF=0.5;AN=2;DP=303;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:57,66:123:99:1694,0,1466:28,29,37,29 chr1 212965284 . C G 2118.59 PASS AC=1;AF=0.591;AN=2;DP=1870;MQ=60;set=variant-variant4-variant7-variant16-variant19-variant23-variant31-variant32-variant33-variant34-variant36 GT:AD:DP:GQ:PL:SB 0/1:92,75:167:99:1823,0,2343:48,44,42,33 chr1 212965469 . C T 702.89 PASS AC=1;AF=0.594;AN=2;DP=979;MQ=60;set=variant-variant4-variant7-variant11-variant16-variant19-variant22-variant23-variant29-variant31-variant32-variant33-variant34-variant36-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,41:77:99:1069,0,940:10,26,13,28 chr1 212967971 . G C 576.55 PASS AC=1;AF=0.5;AN=2;DP=61;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:8,18:26:99:535,0,284:8,0,14,4 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 0/1:30:99:12,4,9,5 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 1/1:0,36:36:99:1244,108,0:0,0,29,7 chr1 212970439 . G C 807.56 PASS AC=1;AF=0.5;AN=2;DP=177;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:46,45:91:99:1102,0,1021:27,19,26,19 chr1 212970656 . T C 215.8 PASS AC=1;AF=0.5;AN=2;DP=22;FS=0;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:162,0,211:0,7,0,6 chr1 212975906 . T C 525.21 PASS AC=1;AF=0.5;AN=2;DP=68;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:13,12:25:99:372,0,418:8,5,10,2 chr1 212977640 . A G 2332.09 PASS AC=1;AF=0.5;AN=2;DP=338;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:74,90:164:99:2060,0,1728:47,27,56,34 chr1 212981214 . T C 770.42 PASS AC=1;AF=0.5;AN=2;DP=85;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:16,12:28:99:253,0,413:5,11,4,8 chr1 212985553 . C T 374.44 PASS AC=1;AF=0.5;AN=2;DP=78;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:18,27:45:99:553,0,424:9,9,14,13 chr1 212985592 . G A 256.84 PASS AC=1;AF=0.5;AN=2;DP=60;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:12,20:32:99:509,0,321:6,6,8,12 chr1 212988241 . T A 238.67 PASS AC=1;AF=0.5;AN=2;DP=32;FS=0;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:99:137,0,242:6,2,3,1 chr1 212988540 . G C 915.13 PASS AC=1;AF=0.5;AN=2;DP=150;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:47,36:83:99:977,0,1286:28,19,20,16 chr1 212988804 . G A 921.02 PASS AC=1;AF=0.5;AN=2;DP=132;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:30,30:60:99:782,0,764:12,18,9,21 chr1 212988870 . CT C 200.14 PASS AC=1;AF=0.5;AN=2;DP=112;MQ=60;set=variant4-filterInvariant22-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:9,13:22:99:226,0,164:3,6,4,9 chr1 212989356 . G A 1970.11 PASS AC=1;AF=0.5;AN=2;DP=527;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:146,103:249:99:2178,0,3290:75,71,55,48 chr1 212989382 . G A 3740.11 PASS AC=1;AF=0.5;AN=2;DP=547;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:157,107:264:99:3994,0,6864:77,80,52,55 chr1 212989384 . A G 3740.11 PASS AC=1;AF=0.5;AN=2;DP=549;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:157,107:264:99:3994,0,6864:76,81,52,55 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 0/1:17:99:6,4,4,3 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 0/1:60,40:100:99:872,0,1634:39,21,26,14 chr1 213021027 . A G 2439.36 PASS AC=1;AF=0.5;AN=2;DP=371;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:80,91:171:99:2020,0,1888:30,50,39,52 chr1 213021117 . A ATATAAATTCC 626.44 PASS AC=1;AF=0.5;AN=2;DP=83;FS=0;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:13,13:26:99:502,0,508:0,13,0,13 chr1 213021136 . CTTTTTTTTTT C,CTTTTTTTTTTTT,CT,CTTTTTTTTTTTTT,CTTTTTTTT,CTTTTTTTTTTT,CTTTTTTTTTTTTTTT,CTTTTT,CTTTTTT 292.11 PASS AC=0,0,0,0,2,0,0,0,0;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 5/5:3:10:0,0,0,3 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 0/1:77,59:136:99:1330,0,2013:47,30,32,27 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 0/1:101,51:152:99:1048,0,2742:47,54,24,27 chr1 213031408 . T C 1827.7 PASS AC=1;AF=0.5;AN=2;DP=307;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:94,54:148:99:1081,0,2243:42,52,24,30 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 0/1:49,28:77:99:666,0,1217:21,28,14,14 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 0/1:26,24:50:99:689,0,763:16,10,15,9 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 0/1:47,78:125:99:2038,0,994:24,23,42,36 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 1/1:0,114:114:99:3194,340,0:0,0,56,58 chr1 213056966 . C G 435.86 PASS AC=1;AF=0.5;AN=2;DP=45;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:6,10:16:99:342,0,184:2,4,1,9 chr1 213058518 . C T 260.38 PASS AC=1;AF=0.5;AN=2;DP=29;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:99:183,0,104:3,0,5,0 chr1 213058852 . T A 564.11 PASS AC=2;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 1/1:0,7:7:21:307,21,0:0,0,0,7 chr1 213062017 . T TTTG 1574.34 PASS AC=1;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 0/1:17,13:30:99:494,0,672:3,14,2,11 chr1 213068192 . T C 1594.38 PASS AC=1;AF=0.943;AN=2;DP=1357;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:23,20:43:99:587,0,635:16,7,17,3 chr1 213068233 . C T 1173 PASS AC=1;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 0/1:46,40:86:99:1029,0,1126:28,18,27,13 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 0/1:21,23:44:99:500,0,559:12,9,12,11 chr1 213068971 . T G 2243.98 PASS AC=1;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 0/1:64,62:126:99:1706,0,1787:43,21,38,24 chr1 213069474 . CT C 1293.05 PASS AC=1;AF=0.5;AN=2;DP=297;MQ=60;set=variant4-variant23-filterInvariant36-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:30,25:55:99:759,0,574:14,16,14,11 chr1 213069487 . T C 1519.04 PASS AC=1;AF=0.5;AN=2;DP=152;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:43,29:72:99:760,0,1751:21,22,17,12 chr1 213069523 . A G 1774.25 PASS AC=1;AF=0.5;AN=2;DP=226;FractionInformativeReads=1;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:47,50:97:99:1343,0,1251:24,23,31,19 chr1 213069783 . A G 1704.56 PASS AC=1;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 0/1:39,53:92:99:1519,0,1144:23,16,30,23 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 0/1:17,10:27:99:213,0,468:10,7,6,4 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 0/1:123,110:233:99:2917,0,3201:65,58,50,60 chr1 213072716 . CTT C 1184.44 PASS AC=1;AF=0.5;AN=2;DP=131;FS=0;MQ=60;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:27,32:59:99:1206,0,992:1,26,2,30 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 0/1:19,17:36:99:432,0,572:9,10,8,9 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 0/1:28,36:64:99:994,0,832:5,23,10,26 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 0/2:26:99:7,5,11,3 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 0/1:22,27:49:99:731,0,559:15,7,18,9 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 0/1:22,14:36:99:400,0,680:6,16,3,11 chr1 213164083 . A G 10095.4 PASS AC=2;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 1/1:0,329:329:99:9846,985,0:0,0,162,167 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 1/1:0,94:94:99:4255,291,0:0,0,29,65 chr1 213173457 . C T 254.16 PASS AC=2;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 1/1:0,31:31:93:1051,93,0:0,0,23,8 chr1 213178340 . G A 1158.55 PASS AC=2;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 1/1:0,90:90:99:2864,270,0:0,0,53,37 chr1 213180441 . GA G,GAA 438.87 PASS AC=0,1;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 0/2:47:99:19,7,12,9 chr1 213224719 . T C 1426.16 PASS AC=2;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 1/1:0,89:89:99:2671,266,0:0,0,53,36 chr1 213234933 . G GT,GTT 635.52 PASS AC=2,0;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 1/1:77:22:4,5,28,40 chr1 213405414 . GGCAACTGAGGAT G 340.83 PASS AC=2;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 1/1:0,33:33:99:1487,100,0:0,0,24,9 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 1/1:0,32:32:96:1133,96,0:0,0,17,15 chr1 214454471 . G A 105.9 PASS AC=2;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 1/1:0,16:16:48:450,48,0:0,0,8,8 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 1/1:0,123:123:99:3463,368,0:0,0,64,59 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 1/1:0,20:20:60:691,60,0:0,0,6,14 chr1 214507580 . A G 2877.16 PASS AC=2;AF=1;AN=2;DP=100;FS=0;FractionInformativeReads=0.99;MQ=60;QD=28.77;SOR=0.754;set=variant23 GT:AD:DP:GQ:PL:SB 1/1:0,99:99:99:2905,296,0:0,0,48,51 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 1/1:0,10:10:30:417,30,0:0,0,9,1 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 1/1:0,105:105:99:3235,315,0:0,0,63,42 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 1/1:0,21:21:63:617,63,0:0,0,13,8 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 1/1:0,24:24:72:842,72,0:0,0,5,19 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 1/1:0,214:214:99:6331,641,0:0,0,95,119 chr1 214564442 . C G 923.54 PASS AC=2;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 1/1:0,66:66:99:2271,198,0:0,0,19,47 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 1/1:0,27:27:81:937,81,0:0,0,21,6 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 1/1:0,107:107:99:3241,321,0:0,0,64,43 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 1/1:0,138:138:99:4276,415,0:0,0,66,72 chr1 214571251 . A C 1730.46 PASS AC=2;AF=0.571;AN=2;DP=2590;MQ=60;set=variant-variant2-variant3-variant4-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant23-variant24-variant26-variant28-variant31-variant32-variant34-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3584,368,0:0,0,70,53 chr1 214576482 . C T 461.98 PASS AC=1;AF=0.526;AN=2;DP=698;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant27-variant28-variant36-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,15:34:99:458,0,562:4,15,2,13 chr1 214576513 . C T 476.83 PASS AC=1;AF=0.545;AN=2;DP=443;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant14-variant15-variant18-variant19-variant20-variant21-variant23-variant24-variant27-variant29-variant31-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,9:23:99:323,0,475:2,12,0,9 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 1/1:0,179:179:99:5068,532,0:0,0,75,104 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 1/1:0,35:35:99:1064,105,0:0,0,12,23 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 1/1:0,13:13:39:538,39,0:0,0,1,12 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 1/1:0,4:4:12:181,12,0:0,0,0,4 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 1/1:0,2:2:6:90,6,0:0,0,0,2 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 0/1:10,20:30:99:806,0,652:10,0,13,7 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 0/1:14,24:38:99:854,0,711:12,2,16,8 chr1 214724668 . G A 634.94 PASS AC=1;AF=0.697;AN=2;DP=2843;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,46:92:99:1017,0,985:20,26,22,24 chr1 214776607 . C G 333.8 PASS AC=1;AF=0.5;AN=2;DP=466;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant16-variant22-variant23-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:24,33:57:99:754,0,534:11,13,16,17 chr1 214778910 . G A 334.75 PASS AC=1;AF=0.5;AN=2;DP=72;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:25,14:39:99:298,0,635:14,11,8,6 chr1 214779031 . C A 508.64 PASS AC=1;AF=0.5;AN=2;DP=109;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:25,32:57:99:760,0,582:12,13,18,14 chr1 214779347 . C T 870.5 PASS AC=1;AF=0.5;AN=2;DP=120;FractionInformativeReads=1;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:39,17:56:99:305,0,1037:14,25,7,10 chr1 214787130 . G A 2393.2 PASS AC=1;AF=0.662;AN=2;DP=6803;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,97:182:99:2512,0,1943:38,47,45,52 chr1 214787430 . A G 71.28 PASS AC=1;AF=0.75;AN=2;DP=10;FS=0;MQ=60;MQRankSum=0.406;ReadPosRankSum=0.406;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:64:64,0,75:0,3,0,3 chr1 214788427 . C T 167.95 PASS AC=1;AF=0.5;AN=2;DP=13;FS=0;FractionInformativeReads=1;MQ=60;SOR=1.179;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:16:78,0,16:0,1,0,2 chr1 214792068 . C T 967.36 PASS AC=1;AF=0.5;AN=2;DP=44;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.988;QD=21.99;ReadPosRankSum=-0.354;SOR=0.99;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:16,28:44:99:996,0,495:2,14,3,25 chr1 214804041 . C A 1074.19 PASS AC=1;AF=0.5;AN=2;DP=166;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:45,36:81:99:822,0,1131:17,28,13,23 chr1 214806072 . GAAGT G 1309.51 PASS AC=1;AF=0.5;AN=2;DP=104;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:22,13:35:99:480,0,1215:7,15,1,12 chr1 214811174 . G A 1033.56 PASS AC=1;AF=0.5;AN=2;DP=196;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:48,34:82:99:717,0,1284:29,19,19,15 chr1 214811244 . C G 1323.08 PASS AC=1;AF=0.5;AN=2;DP=863;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant16-variant22-variant23-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:65,39:104:99:857,0,1617:34,31,18,21 chr1 214813487 . A G 510.51 PASS AC=1;AF=0.5;AN=2;DP=85;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:18,20:38:99:577,0,546:9,9,10,10 chr1 214813782 . A G 1010.66 PASS AC=1;AF=0.5;AN=2;DP=123;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:29,33:62:99:845,0,843:17,12,16,17 chr1 214813941 . C G 787.79 PASS AC=1;AF=0.5;AN=2;DP=166;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:46,37:83:99:918,0,1082:21,25,18,19 chr1 214814125 . G A 1195.22 PASS AC=1;AF=0.5;AN=2;DP=150;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:24,30:54:99:852,0,596:11,13,18,12 chr1 214814571 . C T 520.24 PASS AC=1;AF=0.662;AN=2;DP=1928;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,40:72:99:978,0,657:16,16,20,20 chr1 214814582 . G A 645.04 PASS AC=1;AF=0.5;AN=2;DP=138;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:41,30:71:99:580,0,1006:20,21,14,16 chr1 214814733 . T G 631.56 PASS AC=1;AF=0.5;AN=2;DP=106;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:29,22:51:99:513,0,733:14,15,13,9 chr1 214814778 . G A 768.93 PASS AC=1;AF=0.5;AN=2;DP=126;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:33,23:56:99:614,0,803:16,17,12,11 chr1 214814995 . C T 1228.02 PASS AC=1;AF=0.5;AN=2;DP=229;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:43,62:105:99:1392,0,1085:21,22,33,29 chr1 214815916 . T C 727.69 PASS AC=1;AF=0.5;AN=2;DP=120;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:30,11:41:99:274,0,840:14,16,3,8 chr1 214816142 . T G 1566.04 PASS AC=1;AF=0.5;AN=2;DP=191;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:36,45:81:99:1096,0,849:19,17,26,19 chr1 214816224 . G A 1313.36 PASS AC=1;AF=0.5;AN=2;DP=856;MQ=60;set=variant-variant4-variant16-variant22-variant23-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:41,64:105:99:1497,0,901:20,21,33,31 chr1 214816297 . A G 1388.91 PASS AC=1;AF=0.5;AN=2;DP=253;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:50,63:113:99:1696,0,1224:27,23,33,30 chr1 214816715 . G A 1096.11 PASS AC=1;AF=0.5;AN=2;DP=122;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:24,26:50:99:632,0,609:8,16,11,15 chr1 214818215 . G A 1428.88 PASS AC=1;AF=0.5;AN=2;DP=177;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:57,36:93:99:1299,0,2930:26,31,18,18 chr1 214818223 . T A 1300.73 PASS AC=1;AF=0.5;AN=2;DP=543;MQ=60;set=variant4-variant16-variant22-variant23-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:55,35:90:99:1292,0,2928:24,31,17,18 chr1 214818846 . A G 1133.95 PASS AC=1;AF=0.5;AN=2;DP=176;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:40,45:85:99:1136,0,981:21,19,22,23 chr1 214818945 . A C 1090.87 PASS AC=1;AF=0.5;AN=2;DP=151;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:33,34:67:99:816,0,839:16,17,13,21 chr1 214819328 . G A 1205.46 PASS AC=1;AF=0.5;AN=2;DP=213;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:49,49:98:99:1223,0,1273:26,23,24,25 chr1 214819587 . A G 532.92 PASS AC=1;AF=0.5;AN=2;DP=86;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:20,16:36:99:401,0,577:7,13,7,9 chr1 214819980 . C T 1198 PASS AC=1;AF=0.5;AN=2;DP=190;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:37,48:85:99:1215,0,957:18,19,22,26 chr1 214820099 . A G 1697.92 PASS AC=1;AF=0.676;AN=2;DP=1615;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,23:49:99:635,0,624:10,16,9,14 chr1 214820299 . A G 929.77 PASS AC=1;AF=0.5;AN=2;DP=115;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:21,26:47:99:687,0,460:11,10,13,13 chr1 214820494 . G A 1171.18 PASS AC=1;AF=0.5;AN=2;DP=193;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:34,47:81:99:1210,0,890:22,12,27,20 chr1 214820524 . T C 1453 PASS AC=1;AF=0.5;AN=2;DP=245;FS=0;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:55,50:105:99:1331,0,1255:32,23,30,20 chr1 214821415 . A C 292.27 PASS AC=1;AF=0.5;AN=2;DP=50;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:7,13:20:99:352,0,194:1,6,5,8 chr1 214821456 . C G 108.09 PASS AC=1;AF=0.5;AN=2;DP=29;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:85:285,0,85:0,4,3,6 chr1 214821699 . TA T 187.47 PASS AC=2;AF=1;AN=2;DP=6;FS=0;FractionInformativeReads=1;MQ=60;QD=31.25;SOR=2.303;set=variant23 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:225,18,0:0,0,5,1 chr1 214821959 . G A 1213.26 PASS AC=1;AF=0.5;AN=2;DP=151;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:42,36:78:99:917,0,1174:21,21,15,21 chr1 214826196 . G A 1375.88 PASS AC=1;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 0/1:55,56:111:99:1282,0,1353:27,28,30,26 chr1 214826364 . G A 861.04 PASS AC=1;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 0/1:26,21:47:99:557,0,731:9,17,7,14 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 1/1:57:99:1,0,23,33 chr1 214828812 . A G 663.26 PASS AC=1;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 0/1:27,32:59:99:855,0,790:6,21,10,22 chr1 214830617 . A G 1058.07 PASS AC=1;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 0/1:67,43:110:99:983,0,1587:30,37,17,26 chr1 214837110 . C G 624.26 PASS AC=1;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 0/1:20,35:55:99:1132,0,597:10,10,10,25 chr1 215256537 . TC T,TCCCCCCCCCCCCCC,TCCCCCCCCCCCC 219.43 PASS AC=1,0,0;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 0/1:26:99:11,7,2,6 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 0/1:8,12:20:99:423,0,248:1,7,3,9 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 0/1:10,14:24:99:558,0,628:6,4,10,4 chr1 215409388 . AATCTATCT AATCTATCTATCATCTATCTATCTATCTATCTATCT,A,AATCTATCTATCATCTATCT,AATCTATCTATCATCTATCTATCTATCTATCT,AATCTATCTATCT,AATCT,AATCTATCTATCATCTATCTATCTATCT,AATCTATCTATCATCTATCTATCT,AATCTATCTATCATCTATCTATCTATCTATCTATCTATCT,AATCTATCTATCTATCT 2590.75 PASS AC=0,0,0,0,0,0,1,0,0,0;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 0/7:70:99:26,13,18,13 chr1 215409392 . T TATCTATC 3653.07 PASS AC=1;AF=0.5;AN=2;DP=1515;set=variant3-variant6-variant11-variant23-variant24-variant26-variant34-variant43 GT:AD:DP:GQ:PL:SB 0/1:52,39:91:99:1660,0,1895:32,20,26,13 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 1/1:0,85:85:99:2482,254,0:0,0,41,44 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 1/1:0,80:80:99:2429,239,0:0,0,44,36 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 1/1:1,469:470:99:13819,1397,0:1,0,232,237 chr1 215814186 . CAAA CAA,CA,C 82.27 PASS AC=0,1,0;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 0/2:7:82:0,4,1,2 chr1 215848587 . T C 1868.42 PASS AC=1;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 0/1:44,52:96:99:1285,0,1095:18,26,22,30 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 1/1:1,106:107:99:3212,309,0:1,0,51,55 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 1/1:44:99:0,1,16,27 chr1 215914646 . T A 483.22 PASS AC=1;AF=0.583;AN=2;DP=431;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant10-variant11-variant12-variant13-variant17-variant18-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant32-variant33-variant34-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:131,0,150:4,0,4,0 chr1 215914826 . T C 1273.43 PASS AC=1;AF=0.565;AN=2;DP=1971;MQ=60;set=variant3-variant4-variant7-variant10-variant11-variant12-variant13-variant17-variant18-variant20-variant21-variant23-variant26-variant27-variant28-variant32-variant33-variant34-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,34:82:99:712,0,1173:23,25,18,16 chr1 215916563 . G A 1085.7 PASS AC=1;AF=0.565;AN=2;DP=1796;MQ=60;set=variant3-variant4-variant7-variant10-variant11-variant12-variant13-variant17-variant18-variant20-variant21-variant23-variant26-variant27-variant28-variant32-variant33-variant34-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,39:97:99:778,0,1231:28,30,19,20 chr1 215932957 . G A 986.18 PASS AC=1;AF=0.571;AN=2;DP=412;FractionInformativeReads=1;MQ=60;set=variant10-variant15-variant23-variant25-variant36-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:40,24:64:99:605,0,1062:28,12,18,6 chr1 215956304 . A G 492.05 PASS AC=2;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 1/1:0,37:37:99:1218,111,0:0,0,10,27 chr1 215960167 . T G 1381.73 PASS AC=2;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 1/1:0,66:66:99:2188,198,0:0,0,23,43 chr1 216051287 . A G 1700.9 PASS AC=2;AF=0.563;AN=2;DP=2234;MQ=60;set=variant8-variant11-variant13-variant17-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,130:130:99:3851,389,0:0,0,52,78 chr1 216052549 . A G 126.35 PASS AC=2;AF=0.536;AN=2;DP=255;MQ=60;set=variant8-variant11-variant13-variant17-variant23-variant24-variant26-variant28-variant30-variant31-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:305,21,0:0,0,0,7 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 0/1:18,23:41:99:584,0,364:8,10,10,13 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 0/1:26,22:48:99:677,0,720:18,8,17,5 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 0/1:22,28:50:99:678,0,483:10,12,10,18 chr1 216221721 . C T 620.63 PASS AC=1;AF=0.618;AN=2;DP=1463;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,29:47:99:744,0,478:13,5,19,10 chr1 216246675 . AG A 1141.06 PASS AC=1;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 0/1:27,18:45:99:507,0,825:8,19,6,12 chr1 216348764 . C T 1516.97 PASS AC=2;AF=0.614;AN=2;DP=3558;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2661,233,0:0,0,20,58 chr1 216370130 . T G 916.77 PASS AC=2;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 1/1:0,32:32:96:1312,96,0:0,0,3,29 chr1 216390694 . C T 1369.94 PASS AC=2;AF=0.632;AN=2;DP=2678;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant15-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2160,222,0:0,0,45,29 chr1 216592003 . T C 1154.33 PASS AC=2;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 1/1:0,81:81:99:2453,243,0:0,0,43,38 chr1 216595306 . C T 727.26 PASS AC=2;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 1/1:0,88:88:99:2637,264,0:0,0,44,44 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 1/1:0,290:290:99:8778,869,0:0,0,129,161 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 1/1:0,45:45:99:1543,134,0:0,0,19,26 chr1 216679858 . A AT 100.7 PASS AC=2;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 1/1:3,27:30:4:685,4,0:2,1,18,9 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 0/1:87,87:174:99:2109,0,2175:45,42,41,46 chr1 216737861 . G T 229.13 PASS AC=1;AF=0.583;AN=2;DP=330;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant11-variant12-variant14-variant19-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant36-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:264,0,267:0,8,1,7 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 0/1:23,15:38:99:430,0,678:6,17,4,11 chr1 217109912 . T C 301.57 PASS AC=1;AF=0.5;AN=2;DP=220;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant22-variant23-variant29-variant31-variant34-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:213,0,308:8,1,6,1 chr1 217112871 . T C 2752.49 PASS AC=1;AF=0.5;AN=2;DP=3694;MQ=60;set=variant-variant2-variant4-variant5-variant10-variant11-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant32-variant33-variant38 GT:AD:DP:GQ:PL:SB 0/1:106,98:204:99:2379,0,2650:62,44,55,43 chr1 217113033 . G A 2186.97 PASS AC=1;AF=0.5;AN=2;DP=2932;MQ=60;set=variant-variant2-variant4-variant5-variant10-variant11-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant32-variant33-variant38 GT:AD:DP:GQ:PL:SB 0/1:77,63:140:99:1711,0,2102:33,44,26,37 chr1 217113059 . GAA GA,G 1986.66 PASS AC=2,0;AF=0.75,0.045;AN=2;DP=5420;set=Intersection GT:DP:GQ:SB 1/1:87:62:1,6,28,52 chr1 217173648 . T G 2290.61 PASS AC=1;AF=0.724;AN=2;DP=2426;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-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,15:57:99:321,0,1236:31,11,10,5 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 0/1:7,10:17:99:378,0,233:7,0,10,0 chr1 217600603 . T C 3902.75 PASS AC=1;AF=0.577;AN=2;DP=7688;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant23-variant25-variant26-variant27-variant28-variant34-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:145,131:276:99:3234,0,3731:55,90,52,79 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 0/1:58,36:94:99:972,0,1516:26,32,14,22 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 0/1:36,20:56:99:509,0,960:15,21,9,11 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 0/1:35,18:53:99:385,0,1026:16,19,7,11 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 0/1:23,16:39:99:335,0,545:8,15,9,7 chr1 217602392 . T A 3380.55 PASS AC=1;AF=0.577;AN=2;DP=5052;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant23-variant25-variant26-variant27-variant28-variant34-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:113,83:196:99:1956,0,3111:58,55,45,38 chr1 217602811 . T G 600.25 PASS AC=1;AF=0.577;AN=2;DP=936;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant23-variant25-variant26-variant27-variant28-variant34-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,17:30:99:421,0,344:4,9,6,11 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 0/1:6,10:16:99:279,0,123:2,4,2,8 chr1 217602945 . G A 75.8 PASS AC=1;AF=0.652;AN=2;DP=211;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant23-variant25-variant26-variant27-variant28-variant34-variant36-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:37:78,0,37:1,1,0,2 chr1 217603167 . CAAAAAAAAAAAA CAAAAAAAAA,CAAAAAAAA,CAAAAAAAAAAA,CAAAAAAAAAA,C,CAAAAAAAAAAAAA 228.73 PASS AC=0,0,0,1,0,0;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 0/4:24:99:5,7,10,2 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 0/1:81,87:168:99:3297,0,3368:47,34,42,45 chr1 217603506 . T TGC 3827.41 PASS AC=1;AF=0.577;AN=2;DP=5420;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant23-variant25-variant26-variant27-variant28-variant34-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:106,89:195:99:3427,0,5840:46,60,43,46 chr1 217603507 . A C,G 3836.45 PASS AC=1,0;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 0/1:195:99:46,61,43,45 chr1 217603511 . CTTT C 3657.34 PASS AC=1;AF=0.577;AN=2;DP=5158;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant23-variant25-variant26-variant27-variant28-variant34-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:103,82:185:99:3284,0,5818:44,59,39,43 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 0/1:75,76:151:99:1840,0,1943:28,47,34,42 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 0/1:166,148:314:99:3330,0,4217:100,66,87,61 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 0/1:36,29:65:99:749,0,1185:18,18,14,15 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 0/1:18,19:37:99:482,0,410:8,10,6,13 chr1 217671771 . C G 1157.3 PASS AC=1;AF=0.597;AN=2;DP=3292;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant32-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:53,43:96:99:1105,0,1405:25,28,24,19 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 0/1:54,55:109:99:1189,0,1175:35,19,35,20 chr1 217782273 . T C 4691.56 PASS AC=1;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 0/1:156,134:290:99:3318,0,3968:56,100,51,83 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 0/1:29,15:44:99:384,0,764:15,14,3,12 chr1 217804325 . G A 2118.76 PASS AC=1;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 0/1:83,109:192:99:2484,0,1954:35,48,47,62 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 0/1:52,66:118:99:1680,0,1260:29,23,37,29 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 0/1:8,8:16:99:303,0,272:1,7,0,8 chr1 217842180 . T C 1034.76 PASS AC=1;AF=0.5;AN=2;DP=455;FractionInformativeReads=1;MQ=60;set=variant6-variant9-variant23-variant26-variant42 GT:AD:DP:GQ:PL:SB 0/1:42,57:99:99:1289,0,917:22,20,29,28 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 0/1:22,23:45:99:549,0,531:8,14,7,16 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 0/1:7,7:14:99:224,0,204:1,6,1,6 chr1 217947738 . G A 2329.71 PASS AC=1;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 0/1:39,22:61:99:517,0,987:23,16,14,8 chr1 218036237 . T G 738.61 PASS AC=2;AF=0.639;AN=2;DP=512;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant11-variant13-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant27-variant30-variant36 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:771,60,0:0,0,3,17 chr1 218042908 . G A 1384.98 PASS AC=2;AF=0.618;AN=2;DP=2407;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant11-variant13-variant15-variant18-variant21-variant22-variant23-variant24-variant26-variant27-variant30-variant36 GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:3563,385,0:0,0,62,67 chr1 218043988 . A C 7627.03 PASS AC=2;AF=0.6;AN=2;DP=7988;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant11-variant12-variant13-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant30-variant36 GT:AD:DP:GQ:PL:SB 1/1:0,326:326:99:14871,1008,0:0,0,166,160 chr1 218043992 . T C 7646 PASS AC=2;AF=0.6;AN=2;DP=8116;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant11-variant12-variant13-variant15-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant30-variant36 GT:AD:DP:GQ:PL:SB 1/1:0,340:340:99:15078,1029,0:0,0,175,165 chr1 218044052 . A G 5577.07 PASS AC=2;AF=0.619;AN=2;DP=9497;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant11-variant12-variant13-variant15-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant30-variant36 GT:AD:DP:GQ:PL:SB 1/1:0,385:385:99:11567,1151,0:0,0,193,192 chr1 218475533 . C T 308.6 PASS AC=1;AF=0.66;AN=2;DP=729;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,13:22:99:354,0,239:6,3,9,4 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 0/1:101:99:46,33,14,8 chr1 218506744 . CT C 5206.47 PASS AC=1;AF=0.66;AN=2;DP=7380;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:129,145:274:99:4985,0,4347:56,73,67,78 chr1 218520419 . G A 1182.59 PASS AC=1;AF=0.5;AN=2;DP=115;FS=5.845;FractionInformativeReads=1;MQ=60;MQRankSum=-0.553;QD=10.28;ReadPosRankSum=-1.243;SOR=1.142;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:62,53:115:99:1211,0,1438:32,30,21,32 chr1 218578685 . T TTTG,TTTGTTGTTG,TTTGTTG 497.15 PASS AC=1,0,0;AF=0.188,0.063,0.25;AN=2;DP=588;set=variant4-variant5-variant12-variant20-variant23-variant31-variant35-variant36 GT:DP:GQ:SB 0/1:45:99:8,13,9,15 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 0/1:64:99:23,14,17,10 chr1 218617051 . GTTT GTT,GT,GTTTT,G 3025.88 PASS AC=0,0,1,0;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 0/3:92:70:48,29,10,5 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 0/1:80:99:39,22,15,4 chr1 219366400 . T TG,TGGG,TGG 250.22 PASS AC=1,0,0;AF=0.807,0.011,0.034;AN=2;DP=2307;set=Intersection GT:DP:GQ:SB 0/1:39:21:2,3,23,11 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 1/1:0,28:28:93:1353,93,0:0,0,20,8 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 1/1:0,49:49:99:1428,147,0:0,0,28,21 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 1/1:0,62:62:99:1781,185,0:0,0,32,30 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 0/1:35,26:61:99:757,0,870:23,12,21,5 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 0/1:83,103:186:99:2387,0,1868:45,38,55,48 chr1 219783279 . T A 2241.14 PASS AC=1;AF=0.636;AN=2;DP=8400;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:80,106:186:99:2312,0,1617:37,43,41,65 chr1 220089352 . A C 605.8 PASS AC=1;AF=0.595;AN=2;DP=557;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant8-variant10-variant11-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant32-variant34-variant37-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,15:24:99:461,0,282:1,8,4,11 chr1 220101821 . A AGCGCAGCCCACCCCGC 848.84 PASS AC=1;AF=0.5;AN=2;DP=80;FS=1.14;FractionInformativeReads=0.688;MQ=60;MQRankSum=-0.598;QD=10.61;ReadPosRankSum=-0.684;SOR=0.982;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:34,21:55:99:886,0,2172:12,22,6,15 chr1 220145371 . T G 445.5 PASS AC=1;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 0/1:4,10:14:64:252,0,64:3,1,6,4 chr1 220153332 . T TAA 882.2 PASS AC=1;AF=0.841;AN=2;DP=1699;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:27,13:40:99:462,0,1114:16,11,8,5 chr1 220154246 . AT A 92.28 PASS AC=1;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 0/1:8,10:18:99:224,0,160:2,6,2,8 chr1 220154659 . TAAA T 315.43 PASS AC=1;AF=0.841;AN=2;DP=984;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:7,19:26:99:603,0,194:6,1,12,7 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 0/1:49,32:81:99:687,0,1209:27,22,13,19 chr1 220156090 . T C 1265.3 PASS AC=1;AF=0.841;AN=2;DP=5276;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:49,49:98:99:1076,0,1139:26,23,25,24 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 0/1:31,29:60:99:1065,0,1596:9,22,11,18 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 0/1:24,24:48:99:895,0,1375:8,16,8,16 chr1 220160360 . A G 672.02 PASS AC=1;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 0/1:10,4:14:99:138,0,402:10,0,3,1 chr1 220160433 . A G 1226.52 PASS AC=1;AF=0.841;AN=2;DP=3256;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:34,33:67:99:886,0,799:19,15,23,10 chr1 220162195 . T C 380.31 PASS AC=1;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 0/1:4,8:12:99:234,0,143:0,4,2,6 chr1 220178717 . T TA 726.93 PASS AC=1;AF=0.841;AN=2;DP=2450;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:13,30:43:99:876,0,319:5,8,15,15 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 0/1:18:99:9,2,5,2 chr1 220184164 . A G,AG 672.36 PASS AC=1,0;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 0/1:22:99:11,2,7,2 chr1 220191932 . GA GAA,GAAA,G 103.03 PASS AC=1,0,0;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 0/1:18:99:3,7,2,6 chr1 220192171 . T TAAA,TAA 87.37 PASS AC=1,0;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 0/1:7:69:4,1,2,0 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 0/1:11:27:3,0,8,0 chr1 220192495 . C G 1047.96 PASS AC=1;AF=0.841;AN=2;DP=1904;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:25,16:41:99:417,0,719:8,17,4,12 chr1 220197545 . C T 637.19 PASS AC=1;AF=0.807;AN=2;DP=1047;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:13,12:25:99:346,0,352:9,4,10,2 chr1 220197625 . G T 1495.18 PASS AC=1;AF=0.841;AN=2;DP=4207;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:58,48:106:99:981,0,1366:36,22,25,23 chr1 220205943 . G A 253.59 PASS AC=1;AF=0.807;AN=2;DP=772;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:7,13:20:99:455,0,249:1,6,2,11 chr1 220205980 . A C 118.65 PASS AC=1;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 0/1:5,9:14:99:303,0,145:1,4,1,8 chr1 220207017 . C T 702.66 PASS AC=1;AF=0.841;AN=2;DP=2295;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:17,25:42:99:604,0,418:6,11,9,16 chr1 220208154 . C A 402.22 PASS AC=1;AF=0.807;AN=2;DP=1974;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:26,16:42:99:533,0,802:21,5,15,1 chr1 220231447 . G A 1419.25 PASS AC=1;AF=0.909;AN=2;DP=1906;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:25,9:34:99:244,0,781:18,7,8,1 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 0/1:43,28:71:99:713,0,1001:18,25,9,19 chr1 220263059 . G A 430.13 PASS AC=1;AF=0.5;AN=2;DP=313;FractionInformativeReads=1;MQ=60;set=variant16-variant17-variant23-variant28-variant31-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,24:57:99:618,0,822:20,13,17,7 chr1 220267669 . G C 3782.85 PASS AC=1;AF=0.5;AN=2;DP=345;FS=2.854;FractionInformativeReads=0.997;MQ=60;MQRankSum=0.97;QD=10.96;ReadPosRankSum=0.739;SOR=0.826;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:181,163:344:99:3811,0,4308:90,91,87,76 chr1 220321913 . ATGAAGT A 3276.51 PASS AC=1;AF=0.5;AN=2;DP=186;FS=0;FractionInformativeReads=0.995;MQ=60;MQRankSum=1.188;QD=17.62;ReadPosRankSum=2.366;SOR=0.715;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:99,86:185:99:3314,0,4442:42,57,36,50 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 0/1:83:99:19,37,8,19 chr1 220323793 . CTT CT,CTTT,C 441.22 PASS AC=1,0,0;AF=0.4,0.05,0.088;AN=2;DP=4385;set=variant-variant2-variant3-variant4-filterInvariant6-variant7-filterInvariant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-filterInvariant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:76:99:13,21,15,27 chr1 220374047 . A C 398.36 PASS AC=1;AF=0.5;AN=2;DP=158;FractionInformativeReads=1;MQ=60;set=variant16-variant17-variant23-variant28-variant31-variant33-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:287,0,352:4,9,1,8 chr1 220603310 . TGTGA T 948.83 PASS AC=1;AF=0.795;AN=2;DP=2013;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:4,32:36:24:686,0,24:3,1,24,8 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 1/1:0,64:64:99:2076,192,0:0,0,27,37 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 1/1:0,49:49:99:1796,147,0:0,0,35,14 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 1/1:1,72:73:99:2019,208,0:0,1,35,37 chr1 220789362 . T A 226.77 PASS AC=1;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 0/1:3,11:14:43:251,0,43:1,2,2,9 chr1 220808666 . CTTT CTT,CT,C 258.57 PASS AC=1,0,0;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 0/1:27:98:11,5,8,3 chr1 220808921 . T C 2811.34 PASS AC=2;AF=0.838;AN=2;DP=3562;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:2771,282,0:0,0,40,54 chr1 220824115 . G C 1996.17 PASS AC=2;AF=0.62;AN=2;DP=3534;MQ=60;set=variant3-variant7-variant10-variant12-variant13-variant16-variant17-variant18-variant19-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,102:102:99:2950,306,0:0,0,47,55 chr1 220825523 . A G 3859.31 PASS AC=2;AF=0.838;AN=2;DP=4848;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:2955,302,0:0,0,42,59 chr1 220970028 . A G 1535.21 PASS AC=1;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 0/1:35,32:67:99:817,0,933:14,21,14,18 chr1 220986516 . C T,G 543.46 PASS AC=1,0;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 0/1:38:99:12,5,19,2 chr1 220986546 . G A 967.65 PASS AC=1;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 0/1:22,40:62:99:1078,0,592:16,6,29,11 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 1/1:0,53:53:99:1831,159,0:0,0,25,28 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 0/1:26,21:47:99:477,0,747:18,8,13,8 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 1/1:0,56:56:99:1650,168,0:0,0,27,29 chr1 221052640 . T C 1032.56 PASS AC=1;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 0/1:14,9:23:99:249,0,442:10,4,7,2 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 0/1:50,34:84:99:1254,0,3728:25,25,16,18 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 0/1:84:99:24,25,17,18 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 0/1:57,37:94:99:1365,0,3971:30,27,17,20 chr1 221052937 . A C 1128.19 PASS AC=1;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 0/1:20,22:42:99:540,0,664:10,10,12,10 chr1 221053574 . A C 2736.87 PASS AC=1;AF=0.5;AN=2;DP=782;MQ=60;set=variant11-variant23-variant30-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,89:175:99:2137,0,2121:44,42,47,42 chr1 221055105 . AACACACACACACACAC AACAC,AACACACACACAC,AACACAC,AACACACACACACAC,AACACACAC,AACACACACAC,AAC,AACACACACACACACACACACAC,A,AACACACACACACACACACAC 143.06 PASS AC=1,0,0,0,0,0,0,0,0,0;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 0/1:6:18:2,0,3,1 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 0/1:74,62:136:99:1491,0,1927:40,34,34,28 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 0/1:102,87:189:99:2051,0,2451:45,57,35,52 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 0/1:77,57:134:99:1566,0,2061:37,40,23,34 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 0/1:110,85:195:99:1968,0,2584:54,56,40,45 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 0/1:41,15:56:99:268,0,1064:22,19,7,8 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 1/1:0,38:38:99:1362,114,0:0,0,30,8 chr1 221509219 . C G 762.2 PASS AC=1;AF=0.5;AN=2;DP=53;FS=4.135;FractionInformativeReads=1;MQ=60;MQRankSum=1.44;QD=14.38;ReadPosRankSum=-1.844;SOR=0.268;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:20,33:53:99:790,0,500:14,6,18,15 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 0/1:84,54:138:99:1214,0,2110:43,41,26,28 chr1 221874929 . GA G,GAA 121.57 PASS AC=1,0;AF=0.458,0.042;AN=2;DP=1471;MQ=60;set=variant-filterInvariant2-filterInvariant5-variant8-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant18-filterInvariant22-filterInvariant23-variant24-filterInvariant26-filterInvariant27-filterInvariant29-variant31-filterInvariant32-filterInvariant33-variant34-variant36-filterInvariant38-filterInvariant39-filterInvariant40-variant42-filterInvariant44 GT:DP:GQ:SB 0/1:61:99:33,14,10,4 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 0/1:40,28:68:99:698,0,987:21,19,14,14 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 0/1:59,67:126:99:1710,0,1515:23,36,26,41 chr1 222645515 . C T 143.29 PASS AC=1;AF=0.75;AN=2;DP=99;FS=0;FractionInformativeReads=1;set=variant-variant5-variant6-variant9-variant12-variant13-variant14-variant16-filterInvariant17-variant19-variant22-variant23-variant25-variant26-variant31-variant36-variant37-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:71:71,0,90:2,1,2,2 chr1 222645528 . A G 106.77 PASS AC=2;AF=0.912;AN=2;DP=175;FractionInformativeReads=1;set=variant-variant3-filterInvariant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:168,12,0:0,0,3,1 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 1/1:0,3:3:12:168,12,0:0,0,2,1 chr1 222646973 . G A 61.77 PASS AC=1;AF=0.672;AN=2;DP=406;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant31-variant33-variant34-variant36-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,9:21:99:159,0,262:6,6,5,4 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 1/1:0,19:19:57:670,57,0:0,0,10,9 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 1/1:0,21:21:63:628,63,0:0,0,15,6 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 0/1:9,17:26:99:454,0,198:3,6,9,8 chr1 222650112 . T G 981.29 PASS AC=1;AF=0.5;AN=2;DP=823;FractionInformativeReads=1;set=variant3-variant7-variant23-variant27-variant30-variant36-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:55,23:78:99:763,0,3141:24,31,1,22 chr1 222650120 . C G 846.68 PASS AC=1;AF=0.5;AN=2;DP=460;FractionInformativeReads=1;set=variant3-variant7-variant23-variant27-variant30 GT:AD:DP:GQ:PL:SB 0/1:55,19:74:99:630,0,3170:24,31,1,18 chr1 222650305 . C T 772.8 PASS AC=1;AF=0.65;AN=2;DP=1430;set=variant-filterInvariant2-filterInvariant3-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-variant13-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-variant19-filterInvariant21-variant22-filterInvariant23-variant24-variant25-variant26-variant31-filterInvariant33-variant34-filterInvariant36-filterInvariant37-variant39-filterInvariant40-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:20,29:49:99:718,0,387:7,13,9,20 chr1 222650534 . T C 268.59 PASS AC=1;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 0/1:20,11:31:99:241,0,500:7,13,4,7 chr1 222721288 . C T 2543.54 PASS AC=2;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 1/1:0,95:95:99:3126,283,0:0,0,48,47 chr1 222734803 . G C 801.79 PASS AC=2;AF=0.667;AN=2;DP=2325;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:1914,195,0:0,0,31,34 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 1/1:0,25:25:75:797,75,0:0,0,16,9 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 1/1:0,19:19:57:686,57,0:0,0,4,15 chr1 222742676 . T C 352.46 PASS AC=2;AF=0.697;AN=2;DP=2308;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-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1803,182,0:0,0,35,26 chr1 222751034 . T C 1656.56 PASS AC=2;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 1/1:0,50:50:99:1882,150,0:0,0,11,39 chr1 222761649 . C A 1349.32 PASS AC=2;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 1/1:0,13:13:39:567,39,0:0,0,13,0 chr1 222763026 . C T 369.47 PASS AC=2;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 1/1:0,18:18:54:618,54,0:0,0,13,5 chr1 222763235 . T G 1478.84 PASS AC=2;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 1/1:0,45:45:99:1348,135,0:0,0,16,29 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 1/1:0,33:33:98:963,98,0:0,0,12,21 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 1/1:0,110:110:99:2971,329,0:0,0,51,59 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 1/1:0,78:78:99:2236,233,0:0,0,41,37 chr1 222802803 . T G 2411.21 PASS AC=2;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 1/1:0,78:78:99:2345,234,0:0,0,43,35 chr1 222802926 . C T 2818.59 PASS AC=2;AF=0.898;AN=2;DP=3977;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2525,266,0:0,0,45,44 chr1 222821211 . C T 283.69 PASS AC=2;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 1/1:0,28:28:84:845,84,0:0,0,13,15 chr1 222823529 . A C 1264.65 PASS AC=2;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 1/1:0,41:41:99:1352,123,0:0,0,26,15 chr1 222823743 . T G 1072.42 PASS AC=2;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 1/1:0,39:39:99:1278,117,0:0,0,11,28 chr1 222825403 . G A 1159.26 PASS AC=2;AF=0.989;AN=2;DP=1688;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1040,102,0:0,0,13,21 chr1 222825717 . T C 1632.65 PASS AC=2;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 1/1:0,91:91:99:2757,273,0:0,0,37,54 chr1 222825761 . G A 1023.06 PASS AC=2;AF=0.989;AN=2;DP=2548;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1728,150,0:0,0,14,36 chr1 222826481 . G A 3182.62 PASS AC=2;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 1/1:2,70:72:99:2124,166,0:1,1,37,33 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 0/1:13,21:34:99:573,0,386:11,2,14,7 chr1 222832295 . T C 567.11 PASS AC=2;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 1/1:0,17:17:51:663,51,0:0,0,4,13 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 1/1:0,103:103:99:3305,309,0:0,0,56,47 chr1 222833778 . A G 1081.8 PASS AC=1;AF=0.5;AN=2;DP=192;FractionInformativeReads=1;MQ=60;set=variant7-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:23,28:51:99:780,0,714:5,18,9,19 chr1 222837594 . G A 1195.04 PASS AC=2;AF=0.784;AN=2;DP=1831;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1193,99,0:0,0,6,27 chr1 222838216 . C T 2969.91 PASS AC=2;AF=0.989;AN=2;DP=3855;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:1982,195,0:0,0,28,37 chr1 222839838 . A G 8720.25 PASS AC=2;AF=0.898;AN=2;DP=12288;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,282:283:99:8793,807,0:1,0,99,183 chr1 222840043 . T TGGG,TGGGG 936.21 PASS AC=2,0;AF=0.898,0.091;AN=2;DP=1456;MQ=60;set=Intersection GT:DP:GQ:SB 1/1:21:62:0,0,17,4 chr1 222846882 . G A 135.97 PASS AC=2;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 1/1:0,6:6:18:186,18,0:0,0,1,5 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 1/1:0,330:330:99:10086,988,0:0,0,170,160 chr1 222906294 . A G 12588.5 PASS AC=2;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 1/1:0,326:326:99:9415,975,0:0,0,137,189 chr1 222908112 . A G 4462.96 PASS AC=1;AF=0.5;AN=2;DP=1067;FractionInformativeReads=1;MQ=60;set=variant7-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:181,175:356:99:4262,0,4101:94,87,97,78 chr1 222919748 . G A 247.51 PASS AC=2;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 1/1:0,7:7:21:196,21,0:0,0,4,3 chr1 222919895 . T G 1975.15 PASS AC=2;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 1/1:0,35:35:99:1125,105,0:0,0,25,10 chr1 222920085 . G A 1015.05 PASS AC=1;AF=0.5;AN=2;DP=82;FS=0.845;FractionInformativeReads=1;MQ=60;MQRankSum=1.123;QD=12.38;ReadPosRankSum=0.492;SOR=0.866;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:39,43:82:99:1043,0,865:17,22,17,26 chr1 222923001 . A G 2148.17 PASS AC=2;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 1/1:0,44:44:99:1440,132,0:0,0,21,23 chr1 222923351 . A G 1800.59 PASS AC=2;AF=0.807;AN=2;DP=3244;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,59:59:99:1756,177,0:0,0,26,33 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 1/1:0,68:68:99:1990,204,0:0,0,37,31 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 0/1:14,7:21:99:217,0,363:5,9,1,6 chr1 223116109 . C T 2366.1 PASS AC=1;AF=0.563;AN=2;DP=3658;MQ=60;set=variant-variant3-variant4-variant9-variant13-variant14-variant17-variant18-variant23-variant24-variant25-variant33-variant34-variant36-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:86,110:196:99:2668,0,2093:54,32,64,46 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 1/1:0,30:30:90:1085,90,0:0,0,24,6 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 1/1:0,60:60:99:1925,180,0:0,0,42,18 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 0/1:21,23:44:99:530,0,589:12,9,14,9 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 0/1:79,64:143:99:1583,0,1987:37,42,32,32 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 0/1:45,49:94:99:1309,0,1255:22,23,23,26 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 0/1:120,120:240:99:2808,0,3076:57,63,62,58 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 1/1:0,89:89:99:2721,266,0:0,0,53,36 chr1 223284528 . A G 1735.81 PASS AC=1;AF=0.571;AN=2;DP=2668;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,27:78:99:524,0,1310:28,23,13,14 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 0/1:33,36:69:99:1017,0,861:17,16,19,17 chr1 223537285 . CA C,CAA 101.87 PASS AC=0,1;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 0/2:50:89:26,13,6,5 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 1/1:0,142:142:99:4128,426,0:0,0,72,70 chr1 223568757 . T C 1006.91 PASS AC=1;AF=0.5;AN=2;DP=277;MQ=60;set=variant15-variant19-variant23 GT:AD:DP:GQ:PL:SB 0/1:39,32:71:99:664,0,832:17,22,13,19 chr1 223712863 . C A 1139.76 PASS AC=1;AF=0.5;AN=2;DP=428;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant12-variant23-variant26-variant34-variant37 GT:AD:DP:GQ:PL:SB 0/1:35,21:56:99:506,0,1393:20,15,10,11 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 0/1:20,33:53:99:954,0,741:9,11,20,13 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 1/1:0,17:17:51:562,51,0:0,0,12,5 chr1 223715248 . GT G 949.48 PASS AC=1;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 0/1:49,34:83:99:1024,0,1565:24,25,18,16 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 1/1:0,110:110:99:3392,330,0:0,0,69,41 chr1 223716508 . C T 2249.61 PASS AC=1;AF=0.5;AN=2;DP=1472;MQ=60;set=variant9-variant11-variant13-variant16-variant19-variant21-variant23-variant25-variant27-variant28-variant32 GT:AD:DP:GQ:PL:SB 0/1:45,52:97:99:1200,0,1290:16,29,22,30 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 1/1:0,49:49:99:1670,147,0:0,0,32,17 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 1/1:0,69:69:99:2141,207,0:0,0,33,36 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 1/1:0,38:38:99:1176,113,0:0,0,27,11 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 1/1:0,66:66:99:1986,197,0:0,0,41,25 chr1 223718651 . G A 1045.79 PASS AC=1;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 0/1:38,44:82:99:1119,0,974:19,19,23,21 chr1 223718670 . G A 1155.94 PASS AC=1;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 0/1:34,42:76:99:1186,0,809:15,19,18,24 chr1 223722609 . G A 84.47 PASS AC=1;AF=0.571;AN=2;DP=40;FractionInformativeReads=1;MQ=60;set=variant9-variant11-variant13-variant23-variant25-variant27-variant32 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:67:112,0,67:2,0,3,0 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 1/1:0,12:12:39:343,39,0:0,0,9,3 chr1 223722780 . G A 554.78 PASS AC=1;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 0/1:38,19:57:99:380,0,1006:22,16,10,9 chr1 223799857 . C T 1206.46 PASS AC=2;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 1/1:0,151:151:99:4292,452,0:0,0,74,77 chr1 223799871 . C T 1373.02 PASS AC=2;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 1/1:0,155:155:99:4490,464,0:0,0,77,78 chr1 223804932 . A T 537.67 PASS AC=2;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 1/1:0,13:13:39:499,39,0:0,0,8,5 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 0/1:16:2:2,0,9,5 chr1 223805032 . T TTTTG 1199.53 PASS AC=2;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 1/1:0,58:58:99:2651,180,0:0,0,39,19 chr1 223805231 . T G 1875.73 PASS AC=2;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 1/1:0,106:106:99:3731,318,0:0,0,52,54 chr1 223805504 . T C 808.97 PASS AC=2;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 1/1:0,51:51:99:1722,153,0:0,0,22,29 chr1 223810318 . G A 1518.83 PASS AC=2;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 1/1:0,68:68:99:2274,204,0:0,0,46,22 chr1 223813586 . G T 1154.33 PASS AC=2;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 1/1:0,105:105:99:3245,315,0:0,0,40,65 chr1 223814671 . A T 1246.44 PASS AC=2;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 1/1:0,32:32:96:1069,96,0:0,0,24,8 chr1 223815575 . G A 108.47 PASS AC=2;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 1/1:0,25:25:74:762,74,0:0,0,17,8 chr1 223815851 . AG A 793.65 PASS AC=1;AF=0.5;AN=2;DP=481;MQ=60;set=variant5-variant14-variant23-variant32-variant33-variant34 GT:AD:DP:GQ:PL:SB 0/1:26,21:47:99:527,0,684:6,20,6,15 chr1 223816322 . A G 921.14 PASS AC=2;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 1/1:0,91:91:99:2719,272,0:0,0,41,50 chr1 223816347 . A G 793.88 PASS AC=2;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 1/1:0,87:87:99:2666,261,0:0,0,40,47 chr1 223830566 . G A 1038.62 PASS AC=1;AF=0.621;AN=2;DP=2513;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant33-variant34-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,33:72:99:643,0,984:20,19,16,17 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 0/1:4,6:10:99:196,0,109:3,1,5,1 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 0/1:13,17:30:99:496,0,281:8,5,13,4 chr1 223841913 . C A 783.17 PASS AC=1;AF=0.625;AN=2;DP=1458;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant33-variant34-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,21:58:99:444,0,995:25,12,13,8 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 1/1:0,34:34:99:1219,102,0:0,0,8,26 chr1 223853473 . C T 450.77 PASS AC=1;AF=0.5;AN=2;DP=233;FractionInformativeReads=1;MQ=60;set=variant3-variant14-variant23-variant32-variant33-variant34-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,18:25:99:545,0,159:2,5,4,14 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 1/1:0,356:356:99:10499,1065,0:0,0,187,169 chr1 223905532 . G A 2095.33 PASS AC=1;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 0/1:54,31:85:99:748,0,1355:27,27,17,14 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 1/1:0,37:37:99:1129,111,0:0,0,22,15 chr1 223932743 . CAAA C,CAA 192.14 PASS AC=1,0;AF=0.438,0.125;AN=2;DP=79;MQ=60;set=variant8-variant14-variant18-variant23-variant27-variant32-variant33-variant37 GT:DP:GQ:SB 0/1:11:99:7,1,3,0 chr1 223932894 . C G 706.83 PASS AC=1;AF=0.5;AN=2;DP=468;FractionInformativeReads=1;MQ=60;set=variant8-variant14-variant18-variant23-variant32-variant33-variant34-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:19,17:36:99:450,0,574:9,10,9,8 chr1 223933061 . C T 1483.5 PASS AC=1;AF=0.5;AN=2;DP=886;FractionInformativeReads=1;MQ=60;set=variant8-variant14-variant18-variant23-variant32-variant33-variant34 GT:AD:DP:GQ:PL:SB 0/1:61,60:121:99:1404,0,1512:31,30,30,30 chr1 223933079 . C T 1300.96 PASS AC=1;AF=0.5;AN=2;DP=1139;FractionInformativeReads=1;MQ=60;set=variant8-variant14-variant18-variant23-variant32-variant33-variant34-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:58,57:115:99:1370,0,1422:30,28,25,32 chr1 223934720 . G A 5105.78 PASS AC=1;AF=0.898;AN=2;DP=9016;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:105,77:182:99:1987,0,2585:52,53,36,41 chr1 223936864 . G A 1385.15 PASS AC=1;AF=0.5;AN=2;DP=785;FractionInformativeReads=1;MQ=60;set=variant8-variant18-variant23-variant32-variant33-variant34-variant37 GT:AD:DP:GQ:PL:SB 0/1:44,58:102:99:1463,0,1065:19,25,26,32 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 1/1:0,139:139:99:4199,417,0:0,0,73,66 chr1 223944173 . T C 812.39 PASS AC=1;AF=0.5;AN=2;DP=508;MQ=60;set=variant8-variant14-variant18-variant23-variant32-variant33-variant34-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,20:38:99:518,0,516:12,6,12,8 chr1 223949762 . G A 135.15 PASS AC=1;AF=0.5;AN=2;DP=101;FractionInformativeReads=1;MQ=60;set=variant8-variant14-variant18-variant23-variant32-variant33-variant34-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:99:226,0,106:3,0,6,0 chr1 223951841 . T C 2534.66 PASS AC=1;AF=0.588;AN=2;DP=6293;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-variant30-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:91,69:160:99:1508,0,2192:54,37,38,31 chr1 223958272 . G A 1192.8 PASS AC=1;AF=0.5;AN=2;DP=523;FractionInformativeReads=1;MQ=60;set=variant8-variant14-variant18-variant23-variant32-variant33-variant34 GT:AD:DP:GQ:PL:SB 0/1:40,33:73:99:803,0,1026:15,25,12,21 chr1 223959452 . G A 495.67 PASS AC=1;AF=0.5;AN=2;DP=282;FractionInformativeReads=1;MQ=60;set=variant8-variant14-variant18-variant23-variant32-variant33-variant34 GT:AD:DP:GQ:PL:SB 0/1:26,15:41:99:403,0,738:18,8,10,5 chr1 223959796 . G A 991.09 PASS AC=1;AF=0.577;AN=2;DP=920;FractionInformativeReads=1;MQ=60;set=variant8-variant14-variant18-variant22-variant23-variant24-variant29-variant31-variant32-variant33-variant34-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:33,16:49:99:465,0,863:17,16,7,9 chr1 223959994 . G A 525.78 PASS AC=1;AF=0.5;AN=2;DP=258;MQ=60;set=variant8-variant14-variant18-variant23-variant32-variant33-variant34 GT:AD:DP:GQ:PL:SB 0/1:17,24:41:99:618,0,420:6,11,8,16 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 0/1:37,47:84:99:1318,0,1019:12,25,17,30 chr1 223963468 . T C 500.01 PASS AC=1;AF=0.5;AN=2;DP=221;FractionInformativeReads=1;MQ=60;set=variant8-variant14-variant18-variant23-variant32-variant33-variant34 GT:AD:DP:GQ:PL:SB 0/1:17,6:23:99:105,0,537:12,5,3,3 chr1 223967953 . C T 2830 PASS AC=1;AF=0.538;AN=2;DP=3089;set=variant8-variant14-variant18-variant22-variant23-variant24-variant29-variant31-variant32-variant33-variant34-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:128,101:229:99:2452,0,3372:53,75,41,60 chr1 223989712 . G T 517.94 PASS AC=1;AF=0.5;AN=2;DP=340;MQ=60;set=variant8-variant14-variant18-variant23-variant32-variant33-variant34 GT:AD:DP:GQ:PL:SB 0/1:31,27:58:99:546,0,726:19,12,15,12 chr1 223991119 . G T 685.39 PASS AC=1;AF=0.5;AN=2;DP=502;FractionInformativeReads=1;MQ=60;set=variant8-variant14-variant23-variant32-variant33-variant34 GT:AD:DP:GQ:PL:SB 0/1:29,31:60:99:783,0,729:15,14,12,19 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 0/1:34,15:49:99:377,0,824:21,13,5,10 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 0/1:34,11:45:99:264,0,852:16,18,2,9 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 1/1:0,3:3:9:94,9,0:0,0,1,2 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 0/1:9,12:21:99:269,0,178:5,4,6,6 chr1 224301749 . C T 325.85 PASS AC=2;AF=0.667;AN=2;DP=2798;MQ=60;set=variant-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-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,60:60:99:1732,177,0:0,0,37,23 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 1/1:0,48:48:99:2129,144,0:0,0,16,32 chr1 224302230 . C G 124.69 PASS AC=2;AF=0.667;AN=2;DP=470;FractionInformativeReads=1;MQ=60;set=variant-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-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:312,24,0:0,0,1,7 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 1/1:0,38:38:99:1704,114,0:0,0,28,10 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 1/1:0,36:36:99:1061,108,0:0,0,13,23 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 1/1:0,23:23:69:758,69,0:0,0,18,5 chr1 224346959 . G A 4561.57 PASS AC=1;AF=0.653;AN=2;DP=10861;MQ=60;set=variant-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-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:147,136:283:99:3317,0,3538:72,75,63,73 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 1/1:0,146:146:99:4434,437,0:0,0,73,73 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 1/1:0,137:137:99:4582,410,0:0,0,76,61 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 1/1:0,210:210:99:6686,629,0:0,0,119,91 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 1/1:0,379:379:99:11657,1134,0:0,0,172,207 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 1/1:0,278:278:99:8624,832,0:0,0,126,152 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 1/1:0,236:236:99:7558,708,0:0,0,119,117 chr1 224348818 . T C 3993.41 PASS AC=1;AF=0.653;AN=2;DP=11497;MQ=60;set=variant-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-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:140,127:267:99:2996,0,3371:58,82,59,68 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 1/1:0,258:258:99:9350,775,0:0,0,113,145 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 1/1:0,174:174:99:5469,521,0:0,0,80,94 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 0/1:44,66:110:99:1531,0,1077:22,22,30,36 chr1 224380478 . A G 267.67 PASS AC=1;AF=0.5;AN=2;DP=141;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant8-variant9-variant16-variant17-variant23-variant29-variant31-variant32-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:77:79,0,77:0,2,1,2 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 0/1:99,92:191:99:2209,0,2344:45,54,39,53 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 1/1:0,89:89:99:2579,265,0:0,0,52,37 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 1/1:0,9:9:27:361,27,0:0,0,1,8 chr1 224468986 . CGT CGTGTGTGT,CGTGT,CGTGTGT,C 310.05 PASS AC=0,1,1,0;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 2/3:10:96:0,1,2,7 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 1/1:0,24:24:72:868,72,0:0,0,6,18 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 1/1:0,18:18:54:797,54,0:0,0,18,0 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 1/1:0,46:46:99:1371,138,0:0,0,29,17 chr1 224492746 . C T 4419.33 PASS AC=2;AF=0.943;AN=2;DP=6274;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,123:123:99:3566,368,0:0,0,61,62 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 1/1:0,112:112:99:3264,335,0:0,0,55,57 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 1/1:0,37:37:99:1643,111,0:0,0,13,24 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 1/1:0,5:5:15:184,15,0:0,0,1,4 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 1/1:0,10:10:30:431,30,0:0,0,0,10 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 1/1:0,150:150:99:4127,448,0:0,0,74,76 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 1/1:0,90:90:99:2727,268,0:0,0,38,52 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 1/1:0,26:26:78:797,78,0:0,0,10,16 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 1/1:0,12:12:36:410,36,0:0,0,3,9 chr1 224544529 . A G 3274.98 PASS AC=1;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 0/1:61,71:132:99:1992,0,1754:43,18,51,20 chr1 224564374 . C T 614.71 PASS AC=1;AF=0.6;AN=2;DP=982;MQ=60;set=variant2-variant6-variant8-variant9-variant12-variant13-variant14-variant15-variant23-variant24-variant26-variant29-variant31-variant34-variant42 GT:AD:DP:GQ:PL:SB 0/1:41,34:75:99:896,0,1032:21,20,17,17 chr1 224564490 . TTA T 596.74 PASS AC=1;AF=0.6;AN=2;DP=711;MQ=60;set=variant2-variant6-variant8-variant9-variant12-variant13-variant14-variant15-variant23-variant24-variant26-variant29-variant31-variant34-variant42 GT:AD:DP:GQ:PL:SB 0/1:33,18:51:99:647,0,1256:16,17,5,13 chr1 224566216 . A G 2636.63 PASS AC=1;AF=0.6;AN=2;DP=3749;set=variant2-variant6-variant8-variant9-variant12-variant13-variant14-variant15-variant23-variant24-variant26-variant29-variant31-variant34-variant42 GT:AD:DP:GQ:PL:SB 0/1:107,120:227:99:2968,0,2557:43,64,52,68 chr1 224567004 . G A 989.51 PASS AC=1;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 0/1:14,19:33:99:474,0,440:2,12,8,11 chr1 224567136 . T C 96.15 PASS AC=1;AF=0.6;AN=2;DP=67;FractionInformativeReads=1;MQ=60;set=variant14-variant15-variant23-variant29-variant34 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:137,0,243:2,6,2,3 chr1 224573601 . C T 3261.69 PASS AC=1;AF=0.611;AN=2;DP=4965;MQ=60;set=variant2-variant6-variant8-variant9-variant12-variant13-variant14-variant15-variant18-variant23-variant24-variant26-variant29-variant31-variant34-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:148,120:268:99:3243,0,3873:72,76,57,63 chr1 224575018 . C T 1541.16 PASS AC=1;AF=0.6;AN=2;DP=2136;MQ=60;set=variant2-variant6-variant8-variant9-variant12-variant13-variant14-variant15-variant23-variant24-variant26-variant29-variant31-variant34-variant42 GT:AD:DP:GQ:PL:SB 0/1:71,58:129:99:1497,0,1936:24,47,22,36 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 1/1:0,131:131:99:4278,393,0:0,0,65,66 chr1 224575831 . C CT 2667.01 PASS AC=1;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 0/1:39,39:78:99:1179,0,1139:26,13,25,14 chr1 224585958 . A C 731.6 PASS AC=1;AF=0.611;AN=2;DP=1131;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant8-variant9-variant12-variant13-variant14-variant15-variant18-variant23-variant24-variant26-variant29-variant31-variant34-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,27:54:99:722,0,686:10,17,11,16 chr1 224588825 . T A 250.4 PASS AC=1;AF=0.639;AN=2;DP=200;MQ=60;set=variant2-variant6-variant8-variant9-variant12-variant13-variant14-variant15-variant18-variant23-variant24-variant26-variant29-variant31-variant34-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,9:12:56:207,0,56:2,1,3,6 chr1 224600910 . C A 2558.04 PASS AC=2;AF=0.909;AN=2;DP=3701;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,86:86:99:3596,273,0:0,0,47,39 chr1 224600920 . C A 2613.74 PASS AC=2;AF=0.989;AN=2;DP=3778;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,88:88:99:3558,264,0:0,0,43,45 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 1/1:0,77:77:99:2635,231,0:0,0,57,20 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 0/1:43,38:81:99:1471,0,1614:22,21,16,22 chr1 224621934 . G C 1045.12 PASS AC=1;AF=0.6;AN=2;DP=1664;MQ=60;set=variant2-variant6-variant8-variant9-variant12-variant13-variant14-variant15-variant23-variant24-variant26-variant29-variant31-variant34-variant42 GT:AD:DP:GQ:PL:SB 0/1:40,49:89:99:1041,0,824:16,24,23,26 chr1 224868596 . A C 1671.38 PASS AC=1;AF=0.542;AN=2;DP=1522;MQ=60;set=variant4-variant7-variant8-variant11-variant12-variant13-variant23-variant26-variant30-variant36-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,55:122:99:1382,0,1624:37,30,35,20 chr1 224872443 . A G 2270.1 PASS AC=1;AF=0.538;AN=2;DP=2245;MQ=60;set=variant4-variant7-variant8-variant11-variant12-variant13-variant19-variant23-variant26-variant30-variant36-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,80:159:99:1882,0,1988:43,36,43,37 chr1 224872473 . A G 2580.28 PASS AC=1;AF=0.542;AN=2;DP=2418;MQ=60;set=variant4-variant7-variant8-variant11-variant12-variant13-variant23-variant26-variant30-variant36-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,87:170:99:2146,0,1910:39,44,47,40 chr1 224927217 . C T 879.76 PASS AC=1;AF=0.603;AN=2;DP=1845;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant14-variant15-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,22:43:99:593,0,575:9,12,10,12 chr1 225156457 . G A 439.06 PASS AC=1;AF=0.5;AN=2;DP=333;FractionInformativeReads=1;MQ=60;set=variant7-variant10-variant11-variant18-variant20-variant21-variant23-variant25-variant26-variant29-variant36 GT:AD:DP:GQ:PL:SB 0/1:13,8:21:99:213,0,309:8,5,6,2 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 1/1:0,123:123:99:3321,367,0:0,0,63,60 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 1/1:0,56:56:99:1721,167,0:0,0,30,26 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 1/1:0,100:100:99:3239,299,0:0,0,66,34 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 1/1:0,141:141:99:4210,423,0:0,0,74,67 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 1/1:0,13:13:39:538,39,0:0,0,12,1 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 1/1:0,60:60:99:1752,179,0:0,0,30,30 chr1 225267374 . CTTTTTTTT C,CTTTTTTTTTT,CTTTTTTTTTTT,CTTTTTTTTT 90.5 PASS AC=0,0,2,0;AF=0.125,0.438,0.188,0.063;AN=2;DP=53;FS=0;MQ=60;set=variant-variant3-variant12-variant21-variant22-variant23-variant29-variant42 GT:DP:GQ:SB 3/3:4:2:0,1,1,2 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 1/1:0,117:117:99:5240,352,0:0,0,51,66 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 1/1:0,117:117:99:5240,352,0:0,0,51,66 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 1/1:0,61:61:99:1847,182,0:0,0,24,37 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 1/1:0,38:38:99:1267,114,0:0,0,27,11 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 1/1:0,3:3:9:96,9,0:0,0,1,2 chr1 225311160 . G C 561.02 PASS AC=1;AF=0.5;AN=2;DP=190;FractionInformativeReads=1;MQ=60;set=variant7-variant10-variant18-variant20-variant21-variant23-variant25-variant26-variant29-variant36 GT:AD:DP:GQ:PL:SB 0/1:10,7:17:99:183,0,271:7,3,4,3 chr1 225346975 . C G 925.26 PASS AC=1;AF=0.5;AN=2;DP=776;FractionInformativeReads=1;MQ=60;set=variant7-variant10-variant11-variant18-variant20-variant21-variant23-variant25-variant26-variant29-variant36 GT:AD:DP:GQ:PL:SB 0/1:38,34:72:99:906,0,974:17,21,19,15 chr1 225355525 . G T 74.4 PASS AC=1;AF=0.563;AN=2;DP=54;FS=0;FractionInformativeReads=1;MQ=60;set=variant7-variant11-variant18-variant23-variant25-variant26-variant29-variant36 GT:AD:DP:GQ:PL:SB 0/1:6,2:8:66:66,0,183:6,0,2,0 chr1 225373072 . C T 932.93 PASS AC=1;AF=0.5;AN=2;DP=1142;FractionInformativeReads=1;MQ=60;set=variant7-variant10-variant11-variant18-variant20-variant21-variant23-variant25-variant26-variant29-variant36 GT:AD:DP:GQ:PL:SB 0/1:32,41:73:99:983,0,774:16,16,19,22 chr1 225393587 . C T 499.03 PASS AC=1;AF=0.5;AN=2;DP=200;FractionInformativeReads=1;MQ=60;set=variant7-variant10-variant11-variant18-variant20-variant21-variant23-variant25-variant26-variant29-variant36 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:99:139,0,263:7,0,4,0 chr1 225439988 . T C 1391.04 PASS AC=1;AF=0.587;AN=2;DP=2690;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant29-variant30-variant32-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:44,54:98:99:1278,0,1010:20,24,29,25 chr1 225445652 . G T 346.79 PASS AC=1;AF=0.591;AN=2;DP=519;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant29-variant32-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:17,15:32:99:373,0,382:10,7,10,5 chr1 225460626 . T A 179.24 PASS AC=1;AF=0.583;AN=2;DP=516;MQ=60;set=variant2-variant3-variant4-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant28-variant29-variant30-variant32-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:4,8:12:99:196,0,105:2,2,7,1 chr1 225463772 . A G 416.79 PASS AC=1;AF=0.5;AN=2;DP=243;FractionInformativeReads=1;MQ=60;set=variant7-variant10-variant11-variant18-variant20-variant21-variant23-variant25-variant26-variant29-variant36 GT:AD:DP:GQ:PL:SB 0/1:5,14:19:99:435,0,136:0,5,3,11 chr1 225477869 . A G 85.3 PASS AC=1;AF=0.615;AN=2;DP=99;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant10-variant15-variant20-variant21-variant23-variant25-variant26-variant29-variant30-variant32-variant36 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:72:72,0,115:0,4,0,2 chr1 225506262 . G A 1147.52 PASS AC=1;AF=0.563;AN=2;DP=1722;MQ=60;set=variant2-variant9-variant10-variant13-variant15-variant18-variant20-variant21-variant23-variant25-variant26-variant29-variant32-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,41:97:99:1099,0,1451:34,22,28,13 chr1 225512402 . GT G 1506.54 PASS AC=1;AF=0.563;AN=2;DP=2096;MQ=60;set=variant2-variant9-variant10-variant13-variant15-variant18-variant20-variant21-variant23-variant25-variant26-variant29-variant32-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,61:122:99:1611,0,1618:38,23,37,24 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 0/1:63,62:125:99:1401,0,1602:40,23,33,29 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 0/1:27,34:61:99:813,0,647:14,13,19,15 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 0/1:45,47:92:99:1224,0,1130:16,29,20,27 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 0/1:14,17:31:99:544,0,295:6,8,3,14 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 0/1:4,6:10:99:146,0,153:0,4,2,4 chr1 225541372 . A G 145.15 PASS AC=1;AF=0.714;AN=2;DP=67;FS=0;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant15-variant16-variant17-variant19-variant20-variant21-variant23-variant25-variant29-variant32-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:37:81,0,37:1,0,2,0 chr1 225545580 . A C 2057.04 PASS AC=1;AF=0.583;AN=2;DP=1485;MQ=60;set=variant2-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant28-variant29-variant32-variant36-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,23:45:99:896,0,1300:5,17,5,18 chr1 225545588 . A G 603.69 PASS AC=1;AF=0.563;AN=2;DP=860;FractionInformativeReads=1;MQ=60;set=variant2-variant9-variant10-variant13-variant15-variant18-variant20-variant21-variant23-variant25-variant26-variant29-variant32-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,21:40:99:860,0,1231:4,15,5,16 chr1 225546172 . C G 835.68 PASS AC=1;AF=0.583;AN=2;DP=407;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant28-variant29-variant32-variant36-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,7:17:99:183,0,350:9,1,5,2 chr1 225552624 . G A 724.18 PASS AC=1;AF=0.63;AN=2;DP=859;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant28-variant29-variant32-variant36-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,11:28:99:249,0,410:7,10,4,7 chr1 225552650 . C T 565.24 PASS AC=1;AF=0.63;AN=2;DP=699;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant28-variant29-variant32-variant36-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:129,0,283:3,7,2,4 chr1 225555512 . C T 4988.56 PASS AC=1;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 0/1:76,63:139:99:1493,0,2122:42,34,34,29 chr1 225555602 . T G 4399.21 PASS AC=1;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 0/1:66,44:110:99:1037,0,1500:27,39,17,27 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 1/1:0,67:67:99:2123,201,0:0,0,41,26 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 1/1:0,44:44:99:1418,132,0:0,0,24,20 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 1/1:0,36:36:99:1047,107,0:0,0,16,20 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 1/1:0,62:62:99:1869,186,0:0,0,26,36 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 1/1:0,47:47:99:1509,141,0:0,0,32,15 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 1/1:0,25:25:75:841,75,0:0,0,7,18 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 1/1:0,31:31:93:1102,93,0:0,0,7,24 chr1 225586274 . G T 966.47 PASS AC=1;AF=0.5;AN=2;DP=87;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.786;QD=11.11;ReadPosRankSum=1.27;SOR=0.719;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:42,45:87:99:995,0,946:24,18,26,19 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 1/1:1,82:83:99:2271,237,0:1,0,41,41 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 1/1:0,18:18:54:582,54,0:0,0,6,12 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 1/1:0,48:48:99:1618,144,0:0,0,15,33 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 1/1:0,89:89:99:2981,267,0:0,0,53,36 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 1/1:0,77:77:99:2192,231,0:0,0,42,35 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 1/1:0,30:30:90:1014,90,0:0,0,10,20 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 1/1:0,37:37:99:1263,111,0:0,0,24,13 chr1 225615680 . C G 1784.09 PASS AC=1;AF=0.5;AN=2;DP=158;FS=1.241;FractionInformativeReads=1;MQ=60;MQRankSum=-0.606;QD=11.29;ReadPosRankSum=4.858;SOR=0.591;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:72,86:158:99:1812,0,1572:38,34,43,43 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 1/1:0,52:52:99:2377,162,0:0,0,41,11 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 1/1:0,216:216:99:6621,646,0:0,0,103,113 chr1 225681766 . CAAA CAAAAAAA,CAAAAAAAA,CAAAAAA,CAAAAAAAAA,CAAAAA,CAAAA,CAAAAAAAAAAA,CAA,CAAAAAAAAAA,CAAAAAAAAAAAA,C,CA 1161.28 PASS AC=1,0,1,0,0,0,0,0,0,0,0,0;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 3/1:32:99:1,1,21,9 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 1/1:0,357:357:99:11010,1066,0:0,0,188,169 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 1/1:0,92:92:99:2737,275,0:0,0,39,53 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 0/1:124:99:33,13,17,61 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 1/1:0,32:32:97:1441,97,0:0,0,7,25 chr1 225707398 . C T 179.62 PASS AC=1;AF=0.5;AN=2;DP=12;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.289;QD=14.97;ReadPosRankSum=2.18;SOR=0.859;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:4,8:12:99:208,0,105:1,3,2,6 chr1 225965527 . C A 1094.12 PASS AC=1;AF=0.5;AN=2;DP=787;set=variant4-variant5-variant7-variant9-variant20-variant23-variant24-variant26 GT:AD:DP:GQ:PL:SB 0/1:49,46:95:99:1087,0,1240:25,24,24,22 chr1 225965550 . G A 597.19 PASS AC=1;AF=0.5;AN=2;DP=164;FS=0;FractionInformativeReads=1;set=variant5-variant23 GT:AD:DP:GQ:PL:SB 0/1:47,48:95:99:1184,0,1239:26,21,26,22 chr1 225965803 . C A 1483.67 PASS AC=1;AF=0.55;AN=2;DP=1391;FractionInformativeReads=1;MQ=60;set=variant13-variant14-variant18-variant19-variant23-variant25-variant27-variant32-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:66,49:115:99:994,0,1694:23,43,20,29 chr1 225974486 . T TG 1080.13 PASS AC=2;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 1/1:0,61:61:99:2294,184,0:0,0,34,27 chr1 225974531 . A G 1158.91 PASS AC=2;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 1/1:0,59:59:99:1735,177,0:0,0,29,30 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 0/1:8,9:17:99:265,0,191:5,3,7,2 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 0/1:25,22:47:99:445,0,545:13,12,14,8 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 0/1:2,6:8:68:162,0,68:0,2,2,4 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 0/1:2,5:7:70:147,0,70:0,2,1,4 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 0/1:18,32:50:99:1266,0,1015:14,4,23,9 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 0/1:32,40:72:99:1466,0,1357:21,11,28,12 chr1 226019774 . G C 191.3 PASS AC=2;AF=0.744;AN=2;DP=772;MQ=60;set=variant-variant2-variant4-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-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:901,75,0:0,0,5,20 chr1 226033083 . A C 305.2 PASS AC=1;AF=0.5;AN=2;DP=101;MQ=60;set=variant-variant7-variant21-variant23-variant33 GT:AD:DP:GQ:PL:SB 0/1:11,4:15:99:101,0,288:4,7,1,3 chr1 226040404 . C T 953.76 PASS AC=1;AF=0.5;AN=2;DP=369;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant21-variant23-variant33 GT:AD:DP:GQ:PL:SB 0/1:28,28:56:99:715,0,712:19,9,19,9 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 1/1:0,38:38:99:1220,114,0:0,0,13,25 chr1 226048744 . CA C 1527.25 PASS AC=2;AF=0.58;AN=2;DP=3478;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant13-variant14-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant31-variant32-variant33-variant34-variant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,118:119:99:4382,321,0:1,0,58,60 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 1/1:0,6:6:18:270,18,0:0,0,0,6 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 1/1:0,3:3:12:180,12,0:0,0,0,3 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 1/1:0,15:15:45:569,45,0:0,0,13,2 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 1/1:0,15:15:45:569,45,0:0,0,14,1 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 1/1:0,16:16:48:519,48,0:0,0,11,5 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 1/1:0,50:50:99:1475,150,0:0,0,20,30 chr1 226065455 . G A 279.69 PASS AC=1;AF=0.5;AN=2;DP=19;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.041;QD=14.72;ReadPosRankSum=0.367;SOR=0.368;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:308,0,325:1,8,2,8 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 1/1:0,13:13:39:382,39,0:0,0,8,5 chr1 226074563 . T G 2197.68 PASS AC=2;AF=0.609;AN=2;DP=5754;set=variant-variant3-variant5-variant7-variant8-variant9-variant11-variant13-variant14-variant17-variant19-variant20-variant21-variant22-variant23-variant26-variant28-variant31-variant32-variant34-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,211:211:99:6907,633,0:0,0,106,105 chr1 226075358 . C T 2990.79 PASS AC=1;AF=0.5;AN=2;DP=275;FS=0;FractionInformativeReads=0.996;MQ=59.42;MQRankSum=-1.333;QD=10.88;ReadPosRankSum=1.034;SOR=0.723;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:137,137:274:99:3019,0,3246:60,77,59,78 chr1 226075410 . GC G 1628.88 PASS AC=2;AF=0.587;AN=2;DP=3203;set=variant-variant3-variant5-variant7-variant8-variant9-variant11-variant13-variant14-variant17-variant19-variant20-variant21-variant22-variant23-variant26-variant28-variant31-variant32-variant34-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:3552,351,0:0,0,30,87 chr1 226076919 . G T 347.17 PASS AC=2;AF=0.587;AN=2;DP=970;MQ=60;set=variant-variant3-variant5-variant7-variant8-variant9-variant11-variant13-variant14-variant17-variant19-variant20-variant21-variant22-variant23-variant26-variant28-variant31-variant32-variant34-variant36-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,38:38:99:1065,112,0:0,0,15,23 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 0/1:18,29:47:99:793,0,451:11,7,18,11 chr1 226108894 . C T 328.6 PASS AC=1;AF=0.5;AN=2;DP=597;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant12-variant15-variant18-variant19-variant22-variant23-variant25-variant29-variant36-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:20,23:43:99:963,0,1127:12,8,14,9 chr1 226108899 . T G 328.6 PASS AC=1;AF=0.5;AN=2;DP=561;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant15-variant18-variant19-variant22-variant23-variant25-variant29-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:21,25:46:99:963,0,1127:13,8,15,10 chr1 226110243 . G A 587.03 PASS AC=1;AF=0.5;AN=2;DP=810;MQ=60;set=variant-variant2-variant6-variant12-variant15-variant18-variant19-variant22-variant23-variant25-variant29-variant36-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:21,40:61:99:906,0,434:11,10,19,21 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 1/1:0,84:84:99:2967,253,0:0,0,21,63 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 1/1:0,40:40:99:1484,120,0:0,0,9,31 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 0/1:85,54:139:99:1439,0,2413:35,50,22,32 chr1 226171475 . G C 2918.24 PASS AC=1;AF=0.605;AN=2;DP=3679;MQ=60;set=variant-variant6-variant9-variant10-variant12-variant14-variant17-variant19-variant20-variant23-variant26-variant28-variant31-variant32-variant36-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:85,83:168:99:2013,0,2293:48,37,43,40 chr1 226179909 . A G 436.9 PASS AC=2;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 1/1:0,10:10:30:403,30,0:0,0,8,2 chr1 226179924 . T A 107.06 PASS AC=1;AF=0.5;AN=2;DP=19;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant28 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:135,0,153:4,2,4,2 chr1 226180813 . TTTC T 304.79 PASS AC=1;AF=0.517;AN=2;DP=857;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-filterInvariant10-variant11-variant13-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant33-variant34-variant37-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,9:19:99:322,0,308:3,7,0,9 chr1 226249752 . G A 1109.45 PASS AC=1;AF=0.5;AN=2;DP=113;FS=0.712;FractionInformativeReads=1;MQ=60;MQRankSum=-0.589;QD=9.82;ReadPosRankSum=0.014;SOR=0.598;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:57,56:113:99:1138,0,1424:22,35,23,33 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 1/1:0,43:43:99:1423,129,0:0,0,16,27 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 1/1:0,9:9:26:311,26,0:0,0,8,1 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 1/1:0,52:52:99:1585,156,0:0,0,22,30 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 1/1:0,67:67:99:2240,200,0:0,0,31,36 chr1 226332993 . C T 4064.66 PASS AC=1;AF=0.5;AN=2;DP=3465;MQ=60;set=variant6-variant8-variant9-variant16-variant20-variant23-variant28-variant31-variant32-variant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:149,144:293:99:3611,0,3832:85,64,80,64 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 0/1:122,70:192:99:2534,0,7261:70,52,45,25 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 1/1:0,35:35:99:1133,105,0:0,0,8,27 chr1 226352498 . T G 1912.2 PASS AC=2;AF=0.672;AN=2;DP=3985;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:3992,398,0:0,0,74,59 chr1 226353521 . T A 715.67 PASS AC=1;AF=0.646;AN=2;DP=1534;MQ=60;set=variant-variant2-variant5-variant7-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant25-variant26-variant28-variant29-variant30-variant34-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:30,48:78:99:1128,0,628:18,12,28,20 chr1 226411135 . G A 192.99 PASS AC=2;AF=0.887;AN=2;DP=234;FS=0;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:317,30,0:0,0,7,3 chr1 226411317 . C T 569.98 PASS AC=2;AF=0.714;AN=2;DP=3147;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2155,219,0:0,0,39,35 chr1 226419166 . G C 843.28 PASS AC=2;AF=0.703;AN=2;DP=2336;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1559,153,0:0,0,30,21 chr1 226419237 . C G 1800.08 PASS AC=2;AF=0.703;AN=2;DP=5752;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,146:146:99:4307,437,0:0,0,88,58 chr1 226420040 . T C 2121.82 PASS AC=1;AF=0.5;AN=2;DP=1644;MQ=60;set=variant4-variant8-variant9-variant17-variant23-variant29-variant32-variant34-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:70,83:153:99:2084,0,1660:42,28,45,38 chr1 226420412 . T C 138.27 PASS AC=1;AF=0.5;AN=2;DP=12;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.529;QD=11.52;ReadPosRankSum=-1.461;SOR=1.371;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:167,0,284:6,1,5,0 chr1 226420536 . C G 1721.05 PASS AC=1;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 0/1:56,51:107:99:1210,0,1390:36,20,29,22 chr1 226420722 . A G 1323.02 PASS AC=1;AF=0.571;AN=2;DP=2518;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant32-variant34-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,41:83:99:1004,0,1215:17,25,19,22 chr1 226438449 . T C 1013.03 PASS AC=2;AF=0.866;AN=2;DP=725;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-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:905,81,0:0,0,20,7 chr1 226474132 . G A 342.14 PASS AC=2;AF=0.716;AN=2;DP=1642;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1060,119,0:0,0,17,23 chr1 226485327 . A AT 1270.46 PASS AC=2;AF=0.729;AN=2;DP=2159;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1456,141,0:0,0,34,13 chr1 226488826 . A G 876.58 PASS AC=1;AF=0.559;AN=2;DP=955;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant7-variant8-variant11-variant12-variant16-variant20-variant23-variant25-variant28-variant31-variant36-variant37-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,26:54:99:537,0,634:16,12,16,10 chr1 226550553 . ATT A,AT 767.33 PASS AC=0,1;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 0/2:37:99:6,4,16,11 chr1 226550741 . C T 1535.33 PASS AC=1;AF=0.583;AN=2;DP=1212;MQ=60;set=variant3-variant7-variant8-variant9-variant19-variant23-variant29-variant31-variant32-variant34-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:49,44:93:99:1091,0,1309:24,25,21,23 chr1 226553485 . A C 1186.77 PASS AC=1;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 0/1:4,5:9:99:240,0,405:4,0,4,1 chr1 226553486 . C A 1186.77 PASS AC=1;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 0/1:4,5:9:99:240,0,405:4,0,4,1 chr1 226553490 . C A 1186.77 PASS AC=1;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 0/1:4,6:10:99:237,0,430:4,0,5,1 chr1 226553494 . C A,CA 1070.14 PASS AC=0,1;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 0/2:11:99:4,1,5,1 chr1 226555302 . A G 2276.36 PASS AC=1;AF=0.5;AN=2;DP=2435;MQ=60;set=variant5-variant7-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant23-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,72:147:99:1737,0,1824:41,34,40,32 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 1/1:0,28:28:84:875,84,0:0,0,11,17 chr1 226566726 . A C 1231.79 PASS AC=1;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 0/1:18,11:29:99:356,0,588:14,4,9,2 chr1 226567008 . C G 1529.39 PASS AC=1;AF=0.583;AN=2;DP=1215;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant8-variant9-variant19-variant23-variant29-variant31-variant32-variant34-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:48,49:97:99:1229,0,1166:20,28,23,26 chr1 226567563 . C G 320.08 PASS AC=1;AF=0.6;AN=2;DP=144;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant19-variant23-variant29-variant31-variant32-variant34-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:196,0,149:2,2,2,4 chr1 226570840 . T C 2558.82 PASS AC=1;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 0/1:34,38:72:99:1089,0,865:14,20,16,22 chr1 226573364 . A G 1975.2 PASS AC=2;AF=0.636;AN=2;DP=3661;MQ=60;set=variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant23-variant29-variant31-variant32-variant34-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,132:132:99:3933,396,0:0,0,63,69 chr1 226573402 . T C 1843.87 PASS AC=1;AF=0.583;AN=2;DP=1915;MQ=60;set=variant3-variant7-variant8-variant9-variant19-variant23-variant29-variant31-variant32-variant34-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:58,72:130:99:1675,0,1395:27,31,33,39 chr1 226576270 . A G 450.35 PASS AC=1;AF=0.538;AN=2;DP=510;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant23-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,19:39:99:576,0,471:11,9,15,4 chr1 226576296 . G A 416.89 PASS AC=1;AF=0.583;AN=2;DP=610;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant8-variant9-variant19-variant23-variant29-variant31-variant32-variant34-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:23,21:44:99:489,0,648:16,7,12,9 chr1 226580021 . G T 1751.42 PASS AC=1;AF=0.583;AN=2;DP=1045;MQ=60;set=variant3-variant7-variant8-variant9-variant19-variant23-variant29-variant31-variant32-variant34-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:51,23:74:99:616,0,1409:25,26,8,15 chr1 226580093 . C T 1188.73 PASS AC=1;AF=0.583;AN=2;DP=948;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant8-variant9-variant19-variant23-variant29-variant31-variant32-variant34-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:49,21:70:99:487,0,1378:20,29,9,12 chr1 226580187 . T C 978.64 PASS AC=1;AF=0.583;AN=2;DP=746;MQ=60;set=variant3-variant7-variant8-variant9-variant19-variant23-variant29-variant31-variant32-variant34-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:28,23:51:99:473,0,763:12,16,10,13 chr1 226589709 . C T 1127.53 PASS AC=2;AF=0.636;AN=2;DP=1387;MQ=60;set=variant3-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant23-variant29-variant31-variant32-variant34-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1518,159,0:0,0,31,22 chr1 226589833 . T C 1483.42 PASS AC=1;AF=0.583;AN=2;DP=1122;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant8-variant9-variant19-variant23-variant29-variant31-variant32-variant34-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:42,53:95:99:1293,0,910:18,24,26,27 chr1 226589958 . G A 1466.77 PASS AC=1;AF=0.538;AN=2;DP=1110;MQ=60;set=variant5-variant7-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant23-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,22:64:99:631,0,1160:23,19,15,7 chr1 226595647 . C G 3842.08 PASS AC=1;AF=0.5;AN=2;DP=4470;MQ=60;set=variant5-variant7-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant23-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:183,179:362:99:4085,0,4442:94,89,81,98 chr1 226725814 . G A 1465.04 PASS AC=1;AF=0.635;AN=2;DP=3381;set=variant2-variant3-variant5-variant7-variant10-variant12-variant14-variant15-variant18-variant19-variant20-variant21-variant23-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,74:140:99:1890,0,1747:30,36,38,36 chr1 226790001 . C T 807.42 PASS AC=1;AF=0.533;AN=2;DP=1872;MQ=60;set=variant2-variant3-variant5-variant8-variant10-variant11-variant13-variant14-variant15-variant19-variant21-variant23-variant27-variant29-variant31 GT:AD:DP:GQ:PL:SB 0/1:42,48:90:99:1163,0,977:24,18,30,18 chr1 226790951 . A G 451.98 PASS AC=1;AF=0.563;AN=2;DP=669;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant8-variant10-variant15-variant16-variant21-variant23-variant26-variant27-variant28-variant29-variant30-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,22:32:99:590,0,301:1,9,10,12 chr1 226791238 . C T 2181.71 PASS AC=1;AF=0.684;AN=2;DP=2722;MQ=60;set=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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,28:51:99:769,0,545:13,10,16,12 chr1 226792034 . TTG T 1625.35 PASS AC=1;AF=0.563;AN=2;DP=1720;MQ=60;set=variant2-variant4-variant5-variant8-variant10-variant15-variant16-variant21-variant23-variant26-variant27-variant28-variant29-variant30-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,41:80:99:1409,0,1319:19,20,15,26 chr1 226792088 . C T 861.46 PASS AC=1;AF=0.559;AN=2;DP=1189;MQ=60;set=variant2-variant4-variant5-variant8-variant10-variant15-variant16-variant21-variant23-variant26-variant27-variant28-variant29-variant30-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,31:63:99:834,0,816:15,17,11,20 chr1 226793428 . C T 1038.98 PASS AC=1;AF=0.559;AN=2;DP=1105;MQ=60;set=variant2-variant4-variant5-variant8-variant10-variant15-variant16-variant21-variant23-variant26-variant27-variant28-variant29-variant30-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,28:55:99:641,0,607:14,13,16,12 chr1 226793899 . T TGAG 304.38 PASS AC=1;AF=0.738;AN=2;DP=1454;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,16:26:99:642,0,423:6,4,12,4 chr1 226795975 . T C 1067.85 PASS AC=1;AF=0.694;AN=2;DP=3188;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,32:73:99:863,0,1035:16,25,15,17 chr1 226796517 . C A 1433.95 PASS AC=1;AF=0.646;AN=2;DP=3478;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant15-variant16-variant17-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:96,66:162:99:2375,0,4753:48,48,30,36 chr1 226796537 . T C 2096.43 PASS AC=1;AF=0.595;AN=2;DP=2777;MQ=60;set=variant2-variant4-variant5-variant8-variant10-variant15-variant16-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:88,61:149:99:2267,0,4491:43,45,30,31 chr1 226796968 . T TCTGA 3264.45 PASS AC=1;AF=0.646;AN=2;DP=4048;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant15-variant16-variant17-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:73,56:129:99:2079,0,4202:21,52,15,41 chr1 226819524 . CG C 200.11 PASS AC=1;AF=0.737;AN=2;DP=1588;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,8:34:99:141,0,688:15,11,4,4 chr1 226820605 . T C 583.06 PASS AC=1;AF=0.5;AN=2;DP=42;FS=2.587;FractionInformativeReads=1;MQ=60;MQRankSum=0.038;QD=13.88;ReadPosRankSum=1.196;SOR=0.392;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:20,22:42:99:611,0,577:8,12,11,11 chr1 226923505 . G T 1949.5 PASS AC=1;AF=0.953;AN=2;DP=9704;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:98,99:197:99:2431,0,2429:48,50,49,50 chr1 227058344 . A G 76.53 PASS AC=2;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 1/1:0,12:12:36:334,36,0:0,0,7,5 chr1 227058440 . T G 49.69 PASS AC=1;AF=0.545;AN=2;DP=100;FractionInformativeReads=1;MQ=60;set=variant15-variant16-variant21-variant22-variant23-variant25-variant28-variant36-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,9:14:99:190,0,145:2,3,4,5 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 0/1:24,16:40:99:351,0,554:12,12,6,10 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 0/1:111,111:222:99:2519,0,2680:51,60,50,61 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 0/1:11,11:22:99:332,0,356:9,2,10,1 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 0/1:38,42:80:99:1014,0,936:12,26,18,24 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 0/1:23,23:46:99:526,0,593:15,8,14,9 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 0/1:32,37:69:99:1017,0,825:22,10,23,14 chr1 227085462 . T C 1346.16 PASS AC=1;AF=0.5;AN=2;DP=2205;MQ=60;set=variant7-variant12-variant15-variant16-variant18-variant21-variant22-variant23-variant25-variant28-variant30-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,45:109:99:1145,0,1543:31,33,14,31 chr1 227086195 . T C 3256.17 PASS AC=1;AF=0.5;AN=2;DP=2446;MQ=60;set=variant7-variant12-variant15-variant16-variant18-variant21-variant22-variant23-variant25-variant28-variant30-variant36-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:86,61:147:99:2312,0,4388:40,46,27,34 chr1 227086197 . T A 3256.17 PASS AC=1;AF=0.5;AN=2;DP=2459;FractionInformativeReads=1;MQ=60;set=variant7-variant12-variant15-variant16-variant18-variant21-variant22-variant23-variant25-variant28-variant30-variant36-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,62:149:99:2312,0,4388:40,47,27,35 chr1 227087243 . G T 135.18 PASS AC=1;AF=0.5;AN=2;DP=252;MQ=60;set=variant7-variant15-variant16-variant18-variant21-variant22-variant23-variant25-variant28-variant30-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:62:62,0,121:3,2,1,2 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 0/1:22,34:56:99:832,0,447:12,10,20,14 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 1/1:0,6:6:18:264,18,0:0,0,0,6 chr1 227170768 . T C 156.67 PASS AC=1;AF=0.536;AN=2;DP=313;MQ=60;set=variant-variant3-variant8-variant10-variant12-variant14-variant23-variant26-variant27-variant29-variant31-variant34-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:13,8:21:99:267,0,486:1,12,1,7 chr1 227171210 . G A 1030.02 PASS AC=1;AF=0.563;AN=2;DP=595;FractionInformativeReads=1;MQ=60;set=variant8-variant14-variant21-variant22-variant23-variant28-variant30-variant38 GT:AD:DP:GQ:PL:SB 0/1:31,37:68:99:939,0,839:23,8,22,15 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 0/1:67,52:119:99:1344,0,1837:27,40,20,32 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 0/1:52,52:104:99:1215,0,1285:25,27,27,25 chr1 227178948 . G A 13596.2 PASS AC=1;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 0/1:144,155:299:99:3853,0,3497:60,84,66,89 chr1 227179047 . C T 2306.02 PASS AC=1;AF=0.545;AN=2;DP=1315;MQ=60;set=variant6-variant8-variant12-variant21-variant22-variant23-variant28-variant30-variant31-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,36:90:99:912,0,1620:18,36,14,22 chr1 227179358 . T C 1016.19 PASS AC=2;AF=0.92;AN=2;DP=2310;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1289,117,0:0,0,18,21 chr1 227180805 . A G 243.01 PASS AC=1;AF=0.5;AN=2;DP=125;FractionInformativeReads=1;MQ=60;set=variant23-variant27-variant39 GT:AD:DP:GQ:PL:SB 0/1:25,11:36:99:271,0,685:14,11,7,4 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 1/1:1,93:94:99:2595,269,0:0,1,47,46 chr1 227182575 . A G 1839.74 PASS AC=1;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 0/1:32,29:61:99:660,0,660:18,14,18,11 chr1 227191755 . ATT AT,ATTT,ATTTT,A 342.89 PASS AC=2,0,0,0;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 1/1:20:34:1,0,13,6 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 0/1:14,18:32:99:571,0,372:6,8,10,8 chr1 227203642 . G C 118.69 PASS AC=1;AF=0.538;AN=2;DP=167;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant11-variant12-variant21-variant22-variant23-variant25-variant28-variant30-variant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:236,0,144:5,0,6,1 chr1 227217005 . C T 209.82 PASS AC=1;AF=0.545;AN=2;DP=214;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant12-variant21-variant22-variant23-variant28-variant31-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,5:16:99:101,0,410:2,9,1,4 chr1 227218069 . C CAT 1349.92 PASS AC=2;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 1/1:0,20:20:60:900,60,0:0,0,12,8 chr1 227221222 . C G 691.01 PASS AC=1;AF=0.542;AN=2;DP=675;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant12-variant21-variant22-variant23-variant28-variant30-variant31-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,20:56:99:516,0,905:14,22,5,15 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 0/1:13,22:35:99:631,0,369:2,11,7,15 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 1/1:0,51:51:99:2243,153,0:0,0,18,33 chr1 227223367 . G A 490.42 PASS AC=1;AF=0.545;AN=2;DP=336;MQ=60;set=variant6-variant8-variant12-variant21-variant23-variant28-variant30-variant31-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,14:27:99:427,0,341:3,10,3,11 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 0/1:15,13:28:99:363,0,445:12,3,10,3 chr1 227239746 . G T 1186.77 PASS AC=2;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 1/1:0,28:28:84:862,84,0:0,0,9,19 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 0/1:16,7:23:99:153,0,379:12,4,5,2 chr1 227288655 . G A 542.78 PASS AC=2;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 1/1:0,10:10:30:357,30,0:0,0,7,3 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 1/1:1,92:93:99:2856,242,0:1,0,33,59 chr1 227335329 . T C 37.47 PASS AC=1;AF=0.6;AN=2;DP=67;FS=0;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant19-variant23-variant25-variant32-variant33-variant34-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:99:103,0,231:2,5,1,3 chr1 227348349 . A C 729.03 PASS AC=1;AF=0.5;AN=2;DP=369;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant23-variant25-variant27-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,14:32:99:291,0,462:5,13,6,8 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 1/1:0,8:8:24:319,24,0:0,0,7,1 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 1/1:0,18:18:54:635,54,0:0,0,15,3 chr1 227381442 . A G 831.25 PASS AC=1;AF=0.545;AN=2;DP=754;MQ=60;set=variant6-variant8-variant12-variant21-variant22-variant23-variant28-variant30-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,33:57:99:853,0,653:16,8,19,14 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 0/1:11,13:24:99:415,0,326:4,7,3,10 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 1/1:0,9:9:27:335,27,0:0,0,8,1 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 1/1:0,37:37:99:1096,111,0:0,0,14,23 chr1 227505088 . A C 1467.72 PASS AC=1;AF=0.5;AN=2;DP=796;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant23-variant25-variant27-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:43,55:98:99:1225,0,955:19,24,23,32 chr1 227505212 . TAAAA TAAA,T,TAAAAA 91.3 PASS AC=1,0,1;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 1/3:71:99:5,4,39,23 chr1 227505361 . G GA 1577.49 PASS AC=1;AF=0.542;AN=2;DP=1829;MQ=60;set=variant6-variant8-variant12-variant21-variant22-variant23-variant28-variant30-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,64:128:99:1523,0,1549:29,35,34,30 chr1 227505713 . A C 614.64 PASS AC=1;AF=0.545;AN=2;DP=505;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant12-variant21-variant22-variant23-variant28-variant30-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,21:56:99:473,0,875:13,22,7,14 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 1/1:0,37:37:99:1491,111,0:0,0,24,13 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 1/1:0,137:137:99:5507,412,0:0,0,67,70 chr1 227834228 . AT A 2339.56 PASS AC=1;AF=0.5;AN=2;DP=3140;MQ=60;set=variant4-variant17-variant20-variant23-variant24-variant27-variant28-variant29-variant32-variant34-variant37-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:97,71:168:99:1315,0,2355:56,41,39,32 chr1 227834233 . TC T 1989.36 PASS AC=1;AF=0.652;AN=2;DP=7280;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant29-variant30-variant31-variant33-variant34-variant36-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,86:165:99:1696,0,1908:44,35,47,39 chr1 227834400 . G A 1673.6 PASS AC=2;AF=0.713;AN=2;DP=6177;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:4091,384,0:0,0,46,82 chr1 227844182 . A T 52.74 PASS AC=1;AF=0.667;AN=2;DP=49;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant11-variant16-variant20-variant23-variant31-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:33:81,0,33:0,1,0,2 chr1 227919190 . G A 504.35 PASS AC=1;AF=0.58;AN=2;DP=1816;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant36-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,37:69:99:987,0,858:18,14,23,14 chr1 227920061 . T G 789.66 PASS AC=2;AF=0.724;AN=2;DP=2016;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1806,168,0:0,0,20,36 chr1 227920103 . G A 501.33 PASS AC=1;AF=0.5;AN=2;DP=617;MQ=60;set=variant4-variant17-variant20-variant23-variant27-variant28-variant29-variant32-variant34-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,32:58:99:843,0,718:11,15,15,17 chr1 227920447 . C T 609.45 PASS AC=1;AF=0.5;AN=2;DP=550;FractionInformativeReads=1;MQ=60;set=variant4-variant17-variant20-variant23-variant27-variant28-variant29-variant32-variant34-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,14:32:99:363,0,500:5,13,5,9 chr1 227922918 . A C 2394.03 PASS AC=2;AF=0.586;AN=2;DP=9052;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,238:238:99:6988,713,0:0,0,131,107 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 1/1:0,301:301:99:8162,897,0:0,0,140,161 chr1 227935280 . C T 193.96 PASS AC=2;AF=0.724;AN=2;DP=1228;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1051,84,0:0,0,24,4 chr1 227935355 . T C 385.55 PASS AC=2;AF=0.724;AN=2;DP=3342;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2180,210,0:0,0,41,29 chr1 227935444 . A G 629.07 PASS AC=2;AF=0.586;AN=2;DP=4678;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,136:136:99:4170,408,0:0,0,69,67 chr1 227946501 . G GCC 142.73 PASS AC=2;AF=0.803;AN=2;DP=257;MQ=60;set=variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant29-variant30-variant31-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:264,18,0:0,0,3,3 chr1 227954742 . C T 1819.82 PASS AC=1;AF=0.5;AN=2;DP=833;FractionInformativeReads=1;MQ=60;set=variant8-variant21-variant23-variant43 GT:AD:DP:GQ:PL:SB 0/1:103,95:198:99:2091,0,2450:50,53,48,47 chr1 227963491 . G T 1644.93 PASS AC=1;AF=0.5;AN=2;DP=1278;FractionInformativeReads=1;MQ=60;set=variant4-variant17-variant20-variant23-variant27-variant28-variant29-variant32-variant34-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:68,31:99:99:719,0,1743:37,31,18,13 chr1 227963880 . A C 931.68 PASS AC=1;AF=0.5;AN=2;DP=115;FractionInformativeReads=1;MQ=60;set=variant21-variant23 GT:AD:DP:GQ:PL:SB 0/1:16,20:36:99:635,0,454:9,7,9,11 chr1 227964399 . T C 529.18 PASS AC=2;AF=0.724;AN=2;DP=1946;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:98:877,98,0:0,0,17,16 chr1 227968033 . T C 191.76 PASS AC=2;AF=0.724;AN=2;DP=919;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:777,60,0:0,0,16,4 chr1 227968107 . G A 619.33 PASS AC=2;AF=0.658;AN=2;DP=2514;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2023,195,0:0,0,42,23 chr1 228003247 . G A 1028.86 PASS AC=1;AF=0.5;AN=2;DP=345;MQ=60;set=variant5-variant12-variant20-variant23-variant27-variant33-variant40 GT:AD:DP:GQ:PL:SB 0/1:31,19:50:99:515,0,918:22,9,16,3 chr1 228003839 . C T 1350.81 PASS AC=1;AF=0.5;AN=2;DP=983;FractionInformativeReads=1;MQ=60;set=variant5-variant12-variant20-variant23-variant27-variant33-variant40 GT:AD:DP:GQ:PL:SB 0/1:78,66:144:99:1609,0,1874:42,36,40,26 chr1 228003967 . G A 1254.68 PASS AC=1;AF=0.635;AN=2;DP=3573;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant26-variant28-variant29-variant30-variant31-variant32-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,76:158:99:1650,0,1906:36,46,32,44 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 1/1:0,77:77:99:2485,230,0:0,0,47,30 chr1 228033333 . T A 1248.4 PASS AC=1;AF=0.5;AN=2;DP=983;MQ=60;set=variant5-variant12-variant20-variant23-variant27-variant33-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:71,44:115:99:828,0,1765:33,38,20,24 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 0/1:17,33:50:99:871,0,477:7,10,16,17 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 0/1:22,18:40:99:475,0,491:9,13,7,11 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 0/1:6,13:19:99:489,0,206:1,5,4,9 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 0/1:12:83:1,2,3,6 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 0/1:3,9:12:99:358,0,99:1,2,3,6 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 0/1:3,9:12:99:369,0,99:2,1,4,5 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 0/1:37:99:14,5,10,8 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 0/1:36,32:68:99:805,0,793:18,18,16,16 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 0/1:100,97:197:99:2595,0,2573:56,44,60,37 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 0/1:75,75:150:99:2210,0,2104:27,48,30,45 chr1 228112121 . A G 816.05 PASS AC=1;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 0/1:35,46:81:99:1190,0,818:15,20,17,29 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 1/1:0,9:9:27:243,27,0:0,0,5,4 chr1 228113163 . A G 927.74 PASS AC=1;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 0/1:45,51:96:99:1191,0,1075:18,27,23,28 chr1 228129197 . T C 718.53 PASS AC=1;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 0/1:23,41:64:99:988,0,523:12,11,20,21 chr1 228156143 . G C 247.99 PASS AC=1;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 0/1:10,9:19:99:239,0,307:6,4,3,6 chr1 228158981 . G T 144.93 PASS AC=1;AF=0.5;AN=2;DP=30;FractionInformativeReads=1;set=variant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:99:106,0,143:4,3,1,3 chr1 228247351 . T C 1129.74 PASS AC=1;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 0/1:48,48:96:99:1214,0,1210:28,20,23,25 chr1 228270268 . A G 286.34 PASS AC=1;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 0/1:4,10:14:99:333,0,120:3,1,8,2 chr1 228271153 . T A 349.11 PASS AC=1;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 0/1:13,12:25:99:344,0,388:2,11,2,10 chr1 228288896 . C T 1778.5 PASS AC=1;AF=0.5;AN=2;DP=279;FractionInformativeReads=1;MQ=60;set=variant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:60,69:129:99:1699,0,1506:38,22,41,28 chr1 228289843 . C T 485.42 PASS AC=1;AF=0.5;AN=2;DP=339;FractionInformativeReads=1;MQ=60;set=variant9-variant16-variant21-variant22-variant23-variant26-variant33-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,13:37:99:314,0,676:15,9,8,5 chr1 228294300 . T C 1597.9 PASS AC=1;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 0/1:26,24:50:99:681,0,813:21,5,19,5 chr1 228296745 . C T 4733.88 PASS AC=1;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 0/1:58,66:124:99:1871,0,1605:19,39,24,42 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 1/1:0,20:20:60:717,60,0:0,0,16,4 chr1 228334418 . GAT G 430.49 PASS AC=1;AF=0.65;AN=2;DP=372;MQ=60;set=variant5-variant8-variant9-variant13-variant16-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:306,0,447:8,2,7,1 chr1 228334436 . G A 417.53 PASS AC=1;AF=0.65;AN=2;DP=515;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant9-variant13-variant16-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:369,0,459:11,3,10,2 chr1 228346936 . G A 1214.89 PASS AC=1;AF=0.5;AN=2;DP=320;FractionInformativeReads=1;MQ=60;set=variant21-variant22-variant23-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,49:89:99:1299,0,1152:22,18,26,23 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 1/1:0,113:113:99:3528,339,0:0,0,51,62 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 1/1:0,80:80:99:2508,240,0:0,0,41,39 chr1 228353651 . G C 2279.35 PASS AC=1;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 0/1:78,69:147:99:1640,0,1976:49,29,38,31 chr1 228362682 . G A 1266.63 PASS AC=1;AF=0.643;AN=2;DP=3294;MQ=60;set=variant2-variant5-variant8-variant9-variant13-variant16-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:79,48:127:99:1159,0,1947:44,35,24,24 chr1 228364605 . T C 852.98 PASS AC=1;AF=0.611;AN=2;DP=1698;MQ=60;set=variant2-variant3-variant5-variant8-variant9-variant10-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,29:58:99:628,0,735:17,12,16,13 chr1 228366286 . CAAA C 205.68 PASS AC=2;AF=0.66;AN=2;DP=220;MQ=60;set=variant2-variant3-variant5-variant8-variant9-variant10-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:225,15,0:0,0,5,0 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 1/1:0,44:44:99:1344,131,0:0,0,26,18 chr1 228366791 . AT A,ATT 105.76 PASS AC=1,0;AF=0.417,0.083;AN=2;DP=516;MQ=60;set=filterInvariant3-filterInvariant9-filterInvariant10-filterInvariant11-variant13-variant23-filterInvariant24-filterInvariant25-filterInvariant29-filterInvariant32-variant34-filterInvariant40 GT:DP:GQ:SB 0/1:31:99:13,5,6,7 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 1/1:0,39:39:99:1336,119,0:0,0,20,19 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 1/1:0,74:74:99:2374,222,0:0,0,38,36 chr1 228368353 . GT G,GTT 119.76 PASS AC=1,0;AF=0.462,0.038;AN=2;DP=924;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant11-filterInvariant14-filterInvariant18-filterInvariant23-filterInvariant28-variant32-variant33-filterInvariant34-variant36-filterInvariant42 GT:DP:GQ:SB 0/1:58:81:19,29,4,6 chr1 228368862 . T C 631.74 PASS AC=1;AF=0.643;AN=2;DP=907;MQ=60;set=variant2-variant5-variant8-variant9-variant13-variant16-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,20:36:99:468,0,405:9,7,11,9 chr1 228369893 . CTTCA C 1594.14 PASS AC=1;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 0/1:45,54:99:99:2132,0,2406:21,24,23,31 chr1 228391382 . T TA 3438.33 PASS AC=1;AF=0.5;AN=2;DP=11456;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:58,122:180:99:2246,0,795:22,36,61,61 chr1 228391591 . G C 2767.82 PASS AC=1;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 0/1:109,95:204:99:2179,0,2975:54,55,46,49 chr1 228399482 . C G 3690.38 PASS AC=1;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 0/1:57,61:118:99:1605,0,1420:34,23,32,29 chr1 228399766 . T C 5142.97 PASS AC=1;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 0/1:113,82:195:99:1797,0,2485:54,59,40,42 chr1 228400646 . T C 2695.8 PASS AC=1;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 0/1:27,19:46:99:661,0,1222:9,18,3,16 chr1 228400653 . A T 2592.79 PASS AC=1;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 0/1:20,15:35:99:547,0,1152:6,14,2,13 chr1 228402047 . A G 13248.9 PASS AC=1;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 0/1:249,202:451:99:4532,0,5757:121,128,96,106 chr1 228402121 . A G 9366.56 PASS AC=1;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 0/1:162,135:297:99:3519,0,4010:71,91,51,84 chr1 228402508 . C T 842.97 PASS AC=1;AF=0.648;AN=2;DP=1292;MQ=60;set=variant3-variant5-variant8-variant9-variant10-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,17:41:99:388,0,723:17,7,11,6 chr1 228403897 . T C 113.92 PASS AC=1;AF=0.667;AN=2;DP=364;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant9-variant13-variant16-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:177,0,186:3,5,5,2 chr1 228404475 . C T 1077.73 PASS AC=1;AF=0.5;AN=2;DP=71;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.679;QD=15.18;ReadPosRankSum=-0.415;SOR=0.591;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:25,46:71:99:1106,0,572:9,16,18,28 chr1 228404668 . T C 1223.37 PASS AC=1;AF=0.648;AN=2;DP=2060;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant8-variant9-variant10-variant13-variant15-variant16-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,29:68:99:771,0,1136:26,13,21,8 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 1/1:0,14:14:45:420,45,0:0,0,2,12 chr1 228407010 . C T 5384.88 PASS AC=1;AF=0.66;AN=2;DP=8741;MQ=60;set=variant3-variant8-variant9-variant10-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:132,180:312:99:4526,0,3364:84,48,108,72 chr1 228407260 . G A 5531.69 PASS AC=1;AF=0.66;AN=2;DP=9643;MQ=60;set=variant3-variant8-variant9-variant10-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:160,139:299:99:3506,0,4229:57,103,46,93 chr1 228412106 . T C 1648.8 PASS AC=1;AF=0.667;AN=2;DP=2817;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant9-variant10-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,47:100:99:1245,0,1382:37,16,32,15 chr1 228412227 . T C 6630.66 PASS AC=1;AF=0.667;AN=2;DP=8907;set=variant3-variant8-variant9-variant10-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:140,141:281:99:5476,0,6537:85,55,91,50 chr1 228412228 . G A 6622.87 PASS AC=1;AF=0.66;AN=2;DP=8380;set=variant3-variant8-variant9-variant10-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:141,141:282:99:5476,0,6537:84,57,91,50 chr1 228412308 . G A 5308.01 PASS AC=1;AF=0.667;AN=2;DP=12266;set=variant3-variant8-variant9-variant10-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:196,182:378:99:4351,0,5032:104,92,93,89 chr1 228430697 . A G 192.83 PASS AC=1;AF=0.711;AN=2;DP=871;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:198,0,110:3,1,4,1 chr1 228431095 . A G 2354.3 PASS AC=1;AF=0.711;AN=2;DP=12543;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:147,168:315:99:3937,0,3462:67,80,72,96 chr1 228431235 . G A 510.42 PASS AC=1;AF=0.646;AN=2;DP=959;MQ=60;set=variant3-variant8-variant9-variant10-variant13-variant15-variant16-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,16:36:99:415,0,697:2,18,3,13 chr1 228431930 . C T 2946.94 PASS AC=1;AF=0.711;AN=2;DP=11792;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:155,118:273:99:2771,0,4042:89,66,65,53 chr1 228432987 . G C 1240.89 PASS AC=1;AF=0.66;AN=2;DP=2107;set=variant3-variant8-variant9-variant10-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,33:64:99:939,0,836:22,9,23,10 chr1 228433217 . A G 1506.39 PASS AC=1;AF=0.711;AN=2;DP=15378;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:201,189:390:99:4651,0,4957:113,88,100,89 chr1 228434395 . T C 3172.2 PASS AC=1;AF=0.711;AN=2;DP=22222;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:262,259:521:99:6203,0,6208:130,132,125,134 chr1 228434467 . T C 3110.34 PASS AC=1;AF=0.711;AN=2;DP=17037;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:217,220:437:99:5059,0,5263:99,118,95,125 chr1 228437603 . T C 3296.13 PASS AC=1;AF=0.711;AN=2;DP=13930;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:141,157:298:99:3971,0,3477:87,54,95,62 chr1 228444297 . T G 2366.7 PASS AC=1;AF=0.658;AN=2;DP=4825;set=variant8-variant9-variant13-variant16-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:77,121:198:99:3145,0,1648:44,33,74,47 chr1 228444318 . T G 2088.53 PASS AC=1;AF=0.711;AN=2;DP=11300;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,142:235:99:3755,0,2234:55,38,86,56 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 1/1:0,497:497:99:14831,1483,0:0,0,207,290 chr1 228444741 . C T 590.94 PASS AC=1;AF=0.711;AN=2;DP=2233;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,18:41:99:590,0,768:4,19,1,17 chr1 228447513 . T G 4484.61 PASS AC=1;AF=0.66;AN=2;DP=6111;set=variant3-variant8-variant9-variant10-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:93,105:198:99:3945,0,4300:24,69,42,63 chr1 228447519 . T A 4377.3 PASS AC=1;AF=0.66;AN=2;DP=5558;FractionInformativeReads=1;set=variant3-variant8-variant9-variant10-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,96:177:99:3799,0,4133:21,60,37,59 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 0/1:107,65:172:99:1557,0,2970:59,48,33,32 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 0/1:261,228:489:99:5483,0,6418:128,133,108,120 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 1/1:0,40:40:99:1351,123,0:0,0,19,21 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 0/1:115,87:202:99:2051,0,2723:64,51,47,40 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 0/1:131,100:231:99:2326,0,3240:67,64,54,46 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 0/1:98,121:219:99:3222,0,2784:41,57,69,52 chr1 228465346 . A G 9678.01 PASS AC=1;AF=0.661;AN=2;DP=5477;MQ=60;set=variant3-variant5-variant6-variant8-variant9-variant10-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:92,96:188:99:2263,0,2168:44,48,47,49 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 0/1:79,82:161:99:2101,0,2088:36,43,35,47 chr1 228465674 . C CAAG 73.17 PASS AC=1;AF=0.684;AN=2;DP=567;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:189,0,367:2,5,1,4 chr1 228466750 . T C 1733.35 PASS AC=1;AF=0.64;AN=2;DP=878;MQ=60;set=variant3-variant6-variant8-variant9-variant10-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,22:35:99:567,0,308:6,7,11,11 chr1 228469432 . C T 202.09 PASS AC=1;AF=0.5;AN=2;DP=74;FractionInformativeReads=1;MQ=60;set=variant17-variant21-variant23 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:148,0,143:4,2,4,1 chr1 228471046 . C T 904.57 PASS AC=1;AF=0.625;AN=2;DP=889;MQ=60;set=variant3-variant6-variant8-variant9-variant13-variant16-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant36-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,35:53:99:964,0,485:4,14,15,20 chr1 228471379 . G C 6605.71 PASS AC=1;AF=0.635;AN=2;DP=4783;MQ=60;set=variant3-variant6-variant8-variant9-variant10-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,90:160:99:2256,0,1900:32,38,43,47 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 0/1:89,93:182:99:2561,0,2511:51,38,50,43 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 0/1:70,65:135:99:1525,0,1871:46,24,37,28 chr1 228482010 . C T 2769.5 PASS AC=1;AF=0.571;AN=2;DP=11165;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:196,188:384:99:4700,0,4865:95,101,101,87 chr1 228482059 . G A 4305.62 PASS AC=1;AF=0.5;AN=2;DP=765;MQ=60;set=variant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:171,213:384:99:5292,0,4424:76,95,104,109 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 0/1:39,25:64:99:768,0,1228:14,25,11,14 chr1 228492044 . G A 1330.67 PASS AC=1;AF=0.571;AN=2;DP=6114;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:89,96:185:99:2448,0,2118:48,41,51,45 chr1 228494382 . T G,C 913.18 PASS AC=1,0;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 0/1:106:99:28,36,13,29 chr1 228494790 . G A 1560.63 PASS AC=1;AF=0.556;AN=2;DP=4121;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:64,56:120:99:1544,0,1580:24,40,29,27 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 0/1:15,13:28:99:402,0,415:12,3,10,3 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 0/1:44,36:80:99:896,0,1252:24,20,16,20 chr1 228497081 . G A 973.44 PASS AC=1;AF=0.5;AN=2;DP=92;FS=3.991;FractionInformativeReads=1;MQ=60;MQRankSum=0.274;QD=10.58;ReadPosRankSum=0.924;SOR=0.579;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:54,38:92:99:1002,0,1517:31,23,18,20 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 0/1:131,107:238:99:2394,0,3281:76,55,61,46 chr1 228504239 . G T 100.96 PASS AC=1;AF=0.589;AN=2;DP=387;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,12:20:99:376,0,213:6,2,9,3 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 0/1:73,55:128:99:1244,0,1867:39,34,28,27 chr1 228504670 . C T 190.31 PASS AC=1;AF=0.554;AN=2;DP=1265;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,29:61:99:760,0,766:12,20,8,21 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 0/1:17,11:28:99:411,0,1002:6,11,3,8 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 0/1:135,119:254:99:2794,0,3445:71,64,63,56 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 0/1:141,122:263:99:2855,0,3414:71,70,61,61 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 0/1:134,108:242:99:2822,0,3375:67,67,55,53 chr1 228520763 . G A 151.65 PASS AC=1;AF=0.558;AN=2;DP=609;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,11:19:99:391,0,269:0,8,1,10 chr1 228520880 . C T 341.95 PASS AC=1;AF=0.558;AN=2;DP=966;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,13:33:99:376,0,523:14,6,9,4 chr1 228520973 . C G 861.07 PASS AC=1;AF=0.558;AN=2;DP=2734;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:52,38:90:99:890,0,1290:32,20,19,19 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 0/1:9,9:18:99:309,0,309:6,3,7,2 chr1 228522047 . A T 209.08 PASS AC=1;AF=0.558;AN=2;DP=706;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:303,0,289:8,3,8,4 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 0/1:36,22:58:99:857,0,3170:23,13,13,9 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 0/1:36,24:60:99:899,0,3167:23,13,15,9 chr1 228523448 . G A 730.13 PASS AC=1;AF=0.558;AN=2;DP=2015;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,24:60:99:899,0,3167:23,13,15,9 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 0/1:36,25:61:99:659,0,955:13,23,12,13 chr1 228524919 . G A 1028.57 PASS AC=1;AF=0.54;AN=2;DP=3672;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:78,58:136:99:1374,0,2046:41,37,32,26 chr1 228524961 . C A 1160.9 PASS AC=1;AF=0.54;AN=2;DP=4551;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:98,78:176:99:1690,0,2333:46,52,38,40 chr1 228525627 . C A 245.78 PASS AC=1;AF=0.54;AN=2;DP=1977;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,23:71:99:425,0,1202:25,23,15,8 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 0/1:46,26:72:99:707,0,1348:26,20,17,9 chr1 228526486 . G A 368.08 PASS AC=1;AF=0.54;AN=2;DP=1608;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,40:71:99:1058,0,882:24,7,26,14 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 0/1:38,44:82:99:1127,0,995:15,23,18,26 chr1 228526742 . CCACA CCACACA,CCACACACACA,CCACACACA,CCA,C,CCACACACACACA 57.98 PASS AC=0,1,0,0,0,0;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 0/2:11:40:0,3,1,7 chr1 228528412 . G A 2131.91 PASS AC=1;AF=0.558;AN=2;DP=5547;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant12-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:92,103:195:99:2338,0,2345:45,47,50,53 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 0/1:82,58:140:99:1381,0,1962:34,48,22,36 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 0/1:12,15:27:99:592,0,802:0,12,1,14 chr1 228530025 . G T 650.43 PASS AC=1;AF=0.5;AN=2;DP=233;FractionInformativeReads=1;MQ=60;set=variant17-variant21-variant23 GT:AD:DP:GQ:PL:SB 0/1:53,38:91:99:895,0,1305:28,25,17,21 chr1 228539300 . G A 134.62 PASS AC=1;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 0/1:20,27:47:99:600,0,564:5,15,13,14 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 0/1:88,71:159:99:1943,0,2476:37,51,31,40 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 0/1:27,26:53:99:547,0,701:15,12,14,12 chr1 228559430 . G A 3296.36 PASS AC=1;AF=0.5;AN=2;DP=797;MQ=60;set=variant-variant17-variant23 GT:AD:DP:GQ:PL:SB 0/1:144,108:252:99:2448,0,3734:73,71,51,57 chr1 228559994 . C T 3026.26 PASS AC=1;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 0/1:140,103:243:99:2541,0,3595:67,73,55,48 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 1/1:0,112:112:99:4075,337,0:0,0,43,69 chr1 228560700 . T C 1357.63 PASS AC=1;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 0/1:65,53:118:99:1295,0,1854:33,32,26,27 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 0/1:44,53:97:99:1258,0,1260:24,20,28,25 chr1 228612444 . A G 896.49 PASS AC=2;AF=0.886;AN=2;DP=1483;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1345,126,0:0,0,27,15 chr1 228612838 . G T 2635.69 PASS AC=2;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 1/1:1,140:141:99:4583,411,0:1,0,76,64 chr1 228613052 . T C 2394.73 PASS AC=2;AF=0.886;AN=2;DP=5635;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,121:121:99:3807,363,0:0,0,49,72 chr1 228645063 . A G 4309.36 PASS AC=2;AF=0.841;AN=2;DP=5718;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3070,320,0:0,0,61,46 chr1 228646356 . CGTGT CGTGTGT,CGT,CGTGTGTGTGTGT,CGTGTGTGT,CGTGTGTGTGT,C 192.89 PASS AC=1,0,0,0,0,0;AF=0.179,0.205,0.038,0.115,0.051,0.013;AN=2;DP=4133;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-filterInvariant10-variant11-variant12-variant13-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:52:99:7,22,6,17 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 1/1:0,130:130:99:3891,390,0:0,0,62,68 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 1/1:0,53:53:99:1658,159,0:0,0,29,24 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 1/1:0,218:218:99:6576,653,0:0,0,114,104 chr1 228785805 . C T 877.56 PASS AC=1;AF=0.526;AN=2;DP=811;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant15-variant18-variant19-variant20-variant23-variant28-variant29-variant30-variant32-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,11:27:99:298,0,597:15,1,9,2 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 0/1:85,114:199:99:2620,0,2112:55,30,73,41 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 0/1:6,13:19:99:430,0,154:1,5,5,8 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 0/1:89,91:180:99:2094,0,2162:43,46,40,51 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 0/1:53,46:99:99:1268,0,1536:14,39,13,33 chr1 228880115 . G A 1229.76 PASS AC=1;AF=0.545;AN=2;DP=1158;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant11-variant16-variant18-variant19-variant23-variant40 GT:AD:DP:GQ:PL:SB 0/1:34,39:73:99:1213,0,1039:9,25,9,30 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 0/1:34,22:56:99:690,0,1119:9,25,6,16 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 0/1:16,14:30:99:365,0,488:9,7,6,8 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 0/1:37,18:55:99:480,0,1132:23,14,15,3 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 0/1:22,12:34:99:293,0,670:11,11,6,6 chr1 228881201 . A G 422.29 PASS AC=1;AF=0.545;AN=2;DP=393;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant11-variant16-variant18-variant19-variant23-variant40 GT:AD:DP:GQ:PL:SB 0/1:11,18:29:99:609,0,344:9,2,15,3 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 0/1:1,5:6:14:91,0,14:1,0,3,2 chr1 229385256 . G A 277.83 PASS AC=2;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 1/1:0,14:14:42:600,42,0:0,0,12,2 chr1 229385897 . C CGTGTGT,CGT,CGTGTGTGTGT,CGTGT,CGTGTGTGT 79.67 PASS AC=0,0,2,0,0;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 3/3:5:15:0,0,2,3 chr1 229386237 . T A 814.21 PASS AC=2;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 1/1:0,40:40:99:1382,120,0:0,0,22,18 chr1 229407233 . G C 318.41 PASS AC=2;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 1/1:0,27:27:80:815,80,0:0,0,10,17 chr1 229422193 . T C 2240.65 PASS AC=2;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 1/1:0,41:41:99:1364,123,0:0,0,27,14 chr1 229438828 . G A 507.1 PASS AC=2;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 1/1:0,18:18:54:636,54,0:0,0,4,14 chr1 229439639 . T A 5064.62 PASS AC=2;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 1/1:0,396:396:99:11605,1185,0:0,0,206,190 chr1 229440190 . C T 2279.87 PASS AC=2;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 1/1:0,117:117:99:3867,351,0:0,0,47,70 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 1/1:0,270:270:99:8380,806,0:0,0,131,139 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 0/1:47:99:6,5,22,14 chr1 229460246 . A T 1672.86 PASS AC=2;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 1/1:0,104:104:99:3478,312,0:0,0,67,37 chr1 229461024 . C T 2336.31 PASS AC=2;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 1/1:0,165:165:99:5307,494,0:0,0,57,108 chr1 229461202 . T C 361.19 PASS AC=1;AF=0.5;AN=2;DP=93;FractionInformativeReads=1;MQ=60;set=variant23-variant29 GT:AD:DP:GQ:PL:SB 0/1:34,17:51:99:389,0,882:15,19,7,10 chr1 229477767 . A G 1702.36 PASS AC=1;AF=0.528;AN=2;DP=2355;MQ=60;set=variant-variant6-variant7-variant8-variant10-variant13-variant14-variant15-variant16-variant18-variant23-variant26-variant29-variant30-variant33-variant34-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:78,63:141:99:1490,0,1832:45,33,38,25 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 1/1:0,16:16:48:580,48,0:0,0,3,13 chr1 229569803 . A G 1171.48 PASS AC=1;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 0/1:29,29:58:99:1090,0,1409:12,17,10,19 chr1 229569804 . G A 1171.48 PASS AC=1;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 0/1:28,29:57:99:1090,0,1409:12,16,10,19 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 1/1:0,64:64:99:2872,193,0:0,0,38,26 chr1 229729769 . C T 1322.83 PASS AC=1;AF=0.5;AN=2;DP=1351;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant17-variant18-variant19-variant23-variant24-variant31-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,34:83:99:1258,0,2301:23,26,16,18 chr1 229729777 . C T 1267.82 PASS AC=1;AF=0.5;AN=2;DP=1190;MQ=60;set=variant2-variant3-variant6-variant17-variant18-variant19-variant23-variant24-variant31-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,32:77:99:1228,0,2227:21,24,15,17 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 0/1:56,50:106:99:1155,0,1343:27,29,27,23 chr1 229735022 . G GT 2832.15 PASS AC=1;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 0/1:57,63:120:99:1324,0,1114:17,40,21,42 chr1 229737227 . G A 7026.46 PASS AC=1;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 0/1:107,102:209:99:2617,0,2765:40,67,38,64 chr1 229738170 . T G 3605.86 PASS AC=1;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 0/1:48,44:92:99:1098,0,1076:26,22,20,24 chr1 229738236 . G A 1369.73 PASS AC=1;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 0/1:43,33:76:99:900,0,1118:21,22,16,17 chr1 229746019 . C T 3088.17 PASS AC=1;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 0/1:37,42:79:99:981,0,956:10,27,17,25 chr1 229750343 . T G 580.7 PASS AC=1;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 0/1:50,43:93:99:994,0,1327:16,34,18,25 chr1 229762054 . T A 3191.04 PASS AC=1;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 0/1:66,55:121:99:1199,0,1565:32,34,29,26 chr1 229768297 . C T 398.91 PASS AC=1;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 0/1:19,12:31:99:354,0,590:4,15,2,10 chr1 229772693 . T G 3468.93 PASS AC=1;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 0/1:46,68:114:99:1844,0,1124:23,23,42,26 chr1 229781532 . T G 591.69 PASS AC=1;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 0/1:7,5:12:99:189,0,202:6,1,5,0 chr1 229781744 . T C 4710.12 PASS AC=1;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 0/1:97,105:202:99:2485,0,2350:45,52,47,58 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 1/1:0,82:82:99:3030,246,0:0,0,47,35 chr1 229783240 . T C 4417.22 PASS AC=1;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 0/1:47,36:83:99:942,0,1168:26,21,22,14 chr1 229790048 . A G 1783.76 PASS AC=1;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 0/1:76,36:112:99:792,0,1951:39,37,20,16 chr1 229795070 . T G 661.86 PASS AC=1;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 0/1:30,56:86:99:1498,0,692:14,16,22,34 chr1 229795330 . T C 939.01 PASS AC=1;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 0/1:34,26:60:99:744,0,855:21,13,15,11 chr1 229795683 . AT A 695.61 PASS AC=1;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 0/1:15,41:56:99:1039,0,268:9,6,29,12 chr1 229795714 . T C 1075.02 PASS AC=1;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 0/1:25,61:86:99:1828,0,638:16,9,43,18 chr1 229795966 . AT A 1223.67 PASS AC=1;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 0/1:39,39:78:99:1105,0,1047:9,30,8,31 chr1 230371883 . G A 735.85 PASS AC=1;AF=0.603;AN=2;DP=1914;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant11-variant13-variant14-variant15-variant17-variant19-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,37:62:99:1057,0,711:10,15,16,21 chr1 230384970 . G A 1758.6 PASS AC=1;AF=0.5;AN=2;DP=859;MQ=60;set=variant2-variant22-variant23-variant26-variant28-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:61,53:114:99:1140,0,1430:24,37,22,31 chr1 230386341 . T A 1785.88 PASS AC=1;AF=0.6;AN=2;DP=2989;set=variant-variant2-variant4-variant5-variant6-variant11-variant13-variant14-variant15-variant17-variant19-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,72:134:99:1737,0,1548:25,37,30,42 chr1 230415025 . A G 2412.05 PASS AC=1;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 0/1:88,81:169:99:1918,0,2084:48,40,47,34 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 0/1:43,31:74:99:934,0,1312:26,17,21,10 chr1 230415551 . C T 2872.04 PASS AC=1;AF=0.5;AN=2;DP=214;FS=0;FractionInformativeReads=0.991;MQ=60;MQRankSum=-1.367;QD=13.42;ReadPosRankSum=2.388;SOR=0.706;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:99,113:212:99:2900,0,2521:45,54,51,62 chr1 230416038 . G A 2611.75 PASS AC=1;AF=0.563;AN=2;DP=1476;MQ=60;set=variant7-variant9-variant14-variant22-variant23-variant29-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:80,98:178:99:2287,0,1756:45,35,53,45 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 0/1:8,13:21:99:418,0,176:4,4,5,8 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 0/1:9,9:18:99:280,0,224:5,4,6,3 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 0/1:37,52:89:99:1334,0,827:19,18,19,33 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 0/1:32,42:74:99:1030,0,729:16,16,21,21 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 0/1:57,51:108:99:1934,0,3492:35,22,32,19 chr1 230416953 . A G 1086.16 PASS AC=1;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 0/1:56,49:105:99:1878,0,3448:35,21,31,18 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 0/1:30,26:56:99:645,0,743:16,14,10,16 chr1 230417408 . T C 723.97 PASS AC=1;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 0/1:39,46:85:99:1062,0,968:21,18,24,22 chr1 230417557 . T C 1517.35 PASS AC=1;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 0/1:46,31:77:99:1149,0,2632:24,22,16,15 chr1 230417560 . A G 1517.35 PASS AC=1;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 0/1:46,32:78:99:1183,0,2629:25,21,17,15 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 0/1:60,79:139:99:1979,0,1601:32,28,48,31 chr1 230417916 . T G 454.6 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=165;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:41,18:59:99:255,0,1096:32,9,1,17 chr1 230417921 . T G 55.95 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=219;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:36,18:54:99:253,0,1059:28,8,0,18 chr1 230417999 . C T 334.39 PASS AC=1;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 0/1:23,10:33:99:245,0,705:5,18,2,8 chr1 230451517 . G GATGT 89.09 PASS AC=1;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 0/1:2,2:4:78:78,0,111:1,1,1,1 chr1 230451839 . CAT C 319.73 PASS AC=2;AF=0.7;AN=2;DP=46;MQ=60;set=variant23-variant28-variant29-variant36-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:357,24,0:0,0,8,0 chr1 230451864 . C CTATGTGTATACATACATATGTATATGTGTACACATATATG 156.44 PASS AC=1;AF=0.5;AN=2;DP=37;FS=0;set=variant7-variant11-variant20-variant23 GT:AD:DP:GQ:PL:SB 0/1:6,2:8:99:140,0,241:6,0,2,0 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 1/1:0,38:38:99:1710,114,0:0,0,22,16 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 1/1:0,44:44:99:1860,132,0:0,0,21,23 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 0/1:50,47:97:99:1214,0,1338:33,17,27,20 chr1 230459433 . GC G 650.31 PASS AC=1;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 0/1:25,24:49:99:600,0,621:5,20,7,17 chr1 230461079 . G A 1485.89 PASS AC=1;AF=0.5;AN=2;DP=1766;MQ=60;set=variant-variant7-variant9-variant11-variant14-variant20-variant23-variant24-variant27-variant30-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:76,59:135:99:1371,0,2002:41,35,33,26 chr1 230473103 . A C 377.27 PASS AC=1;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 0/1:18,7:25:99:185,0,454:6,12,2,5 chr1 230497940 . G T 1827.68 PASS AC=2;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 1/1:0,62:62:99:1868,185,0:0,0,40,22 chr1 230498232 . C T 1084.63 PASS AC=2;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 1/1:0,40:40:99:1428,120,0:0,0,9,31 chr1 230503684 . C T 1188.6 PASS AC=2;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 1/1:0,52:52:99:1715,156,0:0,0,38,14 chr1 230504070 . C G 235.14 PASS AC=2;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 1/1:0,4:4:12:167,12,0:0,0,1,3 chr1 230513128 . G A 2007.27 PASS AC=2;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 1/1:0,44:44:99:1487,132,0:0,0,24,20 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 1/1:0,17:17:51:541,51,0:0,0,3,14 chr1 230778491 . G C 4029.16 PASS AC=1;AF=0.793;AN=2;DP=5680;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-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-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,73:128:99:1845,0,1306:17,38,26,47 chr1 230795177 . T C 1396.63 PASS AC=1;AF=0.803;AN=2;DP=1647;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-variant29-variant30-variant32-variant34-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,16:27:99:434,0,247:6,5,11,5 chr1 230819155 . TAAAAA TAAAA,TAAA,TA,TAA,T 153.87 PASS AC=0,1,0,0,0;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 0/2:11:17:1,2,7,1 chr1 230819295 . ATTC A 1354.07 PASS AC=1;AF=0.536;AN=2;DP=1244;MQ=60;set=variant-variant2-variant6-variant11-variant12-variant14-variant16-variant23-variant26-variant29-variant34-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,63:100:99:2534,0,1550:21,16,36,27 chr1 230819479 . G GT,GTT 658.59 PASS AC=1,0;AF=0.714,0.129;AN=2;DP=1828;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-variant-variant30-variant31-variant32-variant33-variant34-variant41-variant42 GT:DP:GQ:SB 0/1:17:13:0,3,3,11 chr1 230820763 . C CACATT 3831.97 PASS AC=1;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 0/1:36,39:75:99:1596,0,2271:21,15,24,15 chr1 230822607 . G A 203.7 PASS AC=1;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 0/1:11,9:20:99:345,0,417:11,0,9,0 chr1 230825942 . A G 938.31 PASS AC=1;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 0/1:13,13:26:99:366,0,292:6,7,5,8 chr1 230828987 . C A 2067.53 PASS AC=1;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 0/1:22,10:32:99:253,0,537:11,11,8,2 chr1 230829139 . A G 1069.86 PASS AC=1;AF=0.536;AN=2;DP=1266;MQ=60;set=variant-variant2-variant6-variant11-variant12-variant14-variant16-variant23-variant26-variant29-variant34-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,24:54:99:622,0,842:18,12,15,9 chr1 230829727 . CA C 256.29 PASS AC=1;AF=0.5;AN=2;DP=137;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant11-variant12-variant23-variant26-variant40 GT:AD:DP:GQ:PL:SB 0/1:15,10:25:99:329,0,530:6,9,4,6 chr1 230840096 . T C 515.8 PASS AC=1;AF=0.5;AN=2;DP=281;MQ=60;set=variant-variant6-variant12-variant23-variant26-variant34-variant40 GT:AD:DP:GQ:PL:SB 0/1:17,22:39:99:624,0,410:6,11,9,13 chr1 230841687 . T C 1895.07 PASS AC=2;AF=0.92;AN=2;DP=4390;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2190,216,0:0,0,39,33 chr1 230845794 . A G 2012.81 PASS AC=1;AF=0.656;AN=2;DP=5298;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,69:135:99:1701,0,1523:41,25,42,27 chr1 230846336 . C A 2359.78 PASS AC=1;AF=0.5;AN=2;DP=203;FS=14.702;FractionInformativeReads=1;MQ=60;MQRankSum=-1.095;QD=11.62;ReadPosRankSum=-2.344;SOR=0.632;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:110,93:203:99:2388,0,2761:67,43,42,51 chr1 230846679 . T C 1073.5 PASS AC=1;AF=0.5;AN=2;DP=706;MQ=60;set=variant-variant6-variant12-variant23-variant26-variant34-variant40 GT:AD:DP:GQ:PL:SB 0/1:56,58:114:99:1421,0,1344:23,33,24,34 chr1 230849799 . A G 873.1 PASS AC=1;AF=0.652;AN=2;DP=999;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:146,0,216:7,1,4,3 chr1 230849872 . C T 1600.46 PASS AC=1;AF=0.652;AN=2;DP=1827;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,29:49:99:644,0,502:13,7,16,13 chr1 230883466 . C T 902.95 PASS AC=1;AF=0.567;AN=2;DP=2507;MQ=60;set=variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,52:90:99:1248,0,938:12,26,20,32 chr1 230883484 . T C 564.74 PASS AC=1;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 0/1:29,48:77:99:1191,0,737:8,21,18,30 chr1 230883499 . T C 446.73 PASS AC=1;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 0/1:22,35:57:99:995,0,607:7,15,9,26 chr1 230891248 . C T 574.61 PASS AC=1;AF=0.611;AN=2;DP=617;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant23-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:172,0,294:1,8,1,5 chr1 230895340 . C A 539.75 PASS AC=1;AF=0.5;AN=2;DP=424;FractionInformativeReads=1;MQ=60;set=variant12-variant20-variant22-variant23-variant25-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,26:53:99:603,0,709:10,17,11,15 chr1 230898231 . T A 589.48 PASS AC=1;AF=0.583;AN=2;DP=916;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant23-variant27-variant28-variant30-variant31-variant32-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,15:25:99:363,0,248:6,4,11,4 chr1 230898494 . C T 1742.51 PASS AC=1;AF=0.589;AN=2;DP=3123;MQ=60;set=variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,52:111:99:1323,0,1452:25,34,20,32 chr1 230898615 . G GA 195.92 PASS AC=1;AF=0.583;AN=2;DP=633;MQ=60;set=variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant23-variant27-variant28-variant30-variant31-variant32-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,10:19:99:246,0,222:2,7,4,6 chr1 230903234 . A G 484.52 PASS AC=2;AF=0.683;AN=2;DP=580;MQ=60;set=variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:605,54,0:0,0,14,4 chr1 230903350 . T C 1463.61 PASS AC=1;AF=0.542;AN=2;DP=2662;MQ=60;set=variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant23-variant27-variant28-variant30-variant31-variant32-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,50:102:99:1141,0,1173:30,22,28,22 chr1 230904911 . C T 710.02 PASS AC=1;AF=0.587;AN=2;DP=1625;MQ=60;set=variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant23-variant27-variant28-variant30-variant31-variant32-variant36-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,31:70:99:715,0,938:24,15,21,10 chr1 230914612 . A G 722.71 PASS AC=1;AF=0.587;AN=2;DP=1836;MQ=60;set=variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant23-variant27-variant28-variant30-variant31-variant32-variant36-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,32:62:99:782,0,781:15,15,17,15 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 0/1:37,38:75:99:796,0,875:17,20,19,19 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 0/1:6,8:14:99:237,0,210:5,1,6,2 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 0/1:6,8:14:99:176,0,110:1,5,4,4 chr1 230928351 . C T 1166.65 PASS AC=2;AF=0.667;AN=2;DP=981;MQ=60;set=variant5-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant27-variant28-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,28:29:76:1025,76,0:0,1,8,20 chr1 230928392 . G A 291.59 PASS AC=1;AF=0.5;AN=2;DP=51;FractionInformativeReads=1;MQ=60;set=variant23-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,10:21:99:320,0,391:3,8,3,7 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 0/1:62,48:110:99:1163,0,1521:39,23,31,17 chr1 230933898 . C T 841.76 PASS AC=1;AF=0.55;AN=2;DP=1787;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant23-variant27-variant28-variant30-variant31-variant32-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,34:80:99:757,0,1079:23,23,21,13 chr1 230974260 . TA T,TAA 106.53 PASS AC=1,0;AF=0.462,0.038;AN=2;DP=425;MQ=60;set=variant2-filterInvariant5-variant8-variant9-variant18-filterInvariant19-filterInvariant22-variant23-filterInvariant26-filterInvariant27-filterInvariant31-variant41-variant42 GT:DP:GQ:SB 0/1:26:99:9,8,5,4 chr1 230974609 . C T 1771.27 PASS AC=1;AF=0.5;AN=2;DP=1511;MQ=60;set=variant7-variant8-variant12-variant13-variant18-variant20-variant22-variant23-variant24-variant34-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,45:93:99:1229,0,1169:22,26,20,25 chr1 230974774 . T C 1428.04 PASS AC=1;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 0/1:49,49:98:99:1136,0,1172:26,23,23,26 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 1/1:0,116:116:99:3993,348,0:0,0,62,54 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 1/1:0,6:6:18:217,18,0:0,0,2,4 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 0/1:19,24:43:99:737,0,471:8,11,8,16 chr1 231042732 . T A 697.57 PASS AC=2;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 1/1:0,83:83:99:2386,248,0:0,0,37,46 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 1/1:0,24:24:72:1080,72,0:0,0,12,12 chr1 231047392 . G A 130.47 PASS AC=2;AF=0.857;AN=2;DP=143;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant17-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant31-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:184,15,0:0,0,1,4 chr1 231051876 . A G 954.23 PASS AC=1;AF=0.5;AN=2;DP=83;FS=3.05;FractionInformativeReads=1;MQ=60;MQRankSum=-0.069;QD=11.5;ReadPosRankSum=-1.141;SOR=1.112;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:46,37:83:99:982,0,1226:27,19,25,12 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 1/1:0,9:9:27:299,27,0:0,0,3,6 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 1/1:0,15:15:45:566,45,0:0,0,2,13 chr1 231060736 . T C 1004.97 PASS AC=2;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 1/1:2,82:84:99:2590,201,0:1,1,29,53 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 1/1:0,4:4:15:225,15,0:0,0,3,1 chr1 231064611 . G A 617.2 PASS AC=2;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 1/1:0,12:12:36:471,36,0:0,0,11,1 chr1 231067236 . C T 613.27 PASS AC=2;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 1/1:0,59:59:99:1880,176,0:0,0,24,35 chr1 231067318 . G T 264.07 PASS AC=2;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 1/1:0,25:25:75:852,75,0:0,0,9,16 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 1/1:0,28:28:84:925,84,0:0,0,7,21 chr1 231081304 . T G 274.65 PASS AC=2;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 1/1:0,18:18:54:739,54,0:0,0,1,17 chr1 231091972 . C T 250.87 PASS AC=2;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 1/1:0,20:20:60:626,60,0:0,0,14,6 chr1 231093785 . CT C 366.45 PASS AC=2;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 1/1:0,16:16:48:461,48,0:0,0,12,4 chr1 231094050 . GAA GA,GAAA,G 355.26 PASS AC=0,1,0;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 0/2:30:99:4,13,6,7 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 1/2:206:99:8,6,98,94 chr1 231155953 . T G 841.4 PASS AC=1;AF=0.5;AN=2;DP=368;FractionInformativeReads=1;MQ=60;set=variant6-variant12-variant23-variant28-variant32-variant33-variant40 GT:AD:DP:GQ:PL:SB 0/1:17,28:45:99:816,0,418:6,11,10,18 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 0/1:18:13:2,1,9,6 chr1 231175644 . C G 411.79 PASS AC=1;AF=0.536;AN=2;DP=251;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant9-variant12-variant14-variant15-variant16-variant22-variant23-variant25-variant27-variant33-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:9,5:14:89:89,0,166:5,4,3,2 chr1 231297984 . G T 99.32 PASS AC=1;AF=0.5;AN=2;DP=110;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant23-variant27-variant30 GT:AD:DP:GQ:PL:SB 0/1:11,13:24:99:255,0,342:6,5,7,6 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 1/1:0,25:25:75:1030,75,0:0,0,14,11 chr1 231298003 . G A 85.09 PASS AC=1;AF=0.5;AN=2;DP=119;FractionInformativeReads=1;MQ=60;set=variant3-variant23-variant27-variant30 GT:AD:DP:GQ:PL:SB 0/1:14,15:29:99:335,0,406:8,6,9,6 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 1/1:0,34:34:99:1559,108,0:0,0,19,15 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 1/1:0,37:37:99:1584,111,0:0,0,20,17 chr1 231298255 . T C 2641.53 PASS AC=1;AF=0.5;AN=2;DP=1287;MQ=60;set=variant3-variant4-variant23-variant24-variant27-variant30-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,80:161:99:1746,0,1565:38,43,43,37 chr1 231298611 . G A 1229.75 PASS AC=1;AF=0.5;AN=2;DP=191;MQ=60;set=variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:43,48:91:99:1258,0,1175:29,14,27,21 chr1 231298699 . T G 2921.38 PASS AC=1;AF=0.5;AN=2;DP=1472;MQ=60;set=variant3-variant4-variant23-variant24-variant27-variant30-variant44 GT:AD:DP:GQ:PL:SB 0/1:110,103:213:99:2530,0,2723:65,45,61,42 chr1 231298898 . C A 3306.94 PASS AC=1;AF=0.5;AN=2;DP=712;set=variant3-variant23-variant27-variant30 GT:AD:DP:GQ:PL:SB 0/1:81,58:139:99:1620,0,2300:26,55,20,38 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 1/1:0,5:5:15:176,15,0:0,0,4,1 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 0/1:31,27:58:99:734,0,850:22,9,15,12 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 0/1:77,60:137:99:1479,0,2194:31,46,27,33 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 0/1:33,32:65:99:925,0,719:17,16,16,16 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 0/1:34,31:65:99:885,0,712:17,17,16,15 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 0/1:37,27:64:99:973,0,2602:15,22,12,15 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 0/1:35,27:62:99:1007,0,2581:14,21,11,16 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 0/1:33,26:59:99:1010,0,2548:14,19,11,15 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 0/1:26,25:51:99:591,0,602:12,14,15,10 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 0/1:41,42:83:99:1597,0,2331:14,27,20,22 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 0/1:35,40:75:99:1563,0,2264:10,25,19,21 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 0/1:14,12:26:99:381,0,428:10,4,4,8 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 0/1:41,33:74:99:782,0,920:20,21,13,20 chr1 231377081 . C T 2116.78 PASS AC=2;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 1/1:0,83:83:99:2508,248,0:0,0,42,41 chr1 231401204 . T C 903.98 PASS AC=1;AF=0.567;AN=2;DP=900;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant11-variant14-variant17-variant18-variant23-variant26-variant27-variant28-variant29-variant30-variant33-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:18,21:39:99:568,0,429:6,12,6,15 chr1 231401596 . T C 2097.64 PASS AC=2;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 1/1:0,80:80:99:2494,239,0:0,0,26,54 chr1 231401902 . G A 4926.56 PASS AC=2;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 1/1:0,141:141:99:4276,422,0:0,0,77,64 chr1 231403775 . G A 326.84 PASS AC=1;AF=0.5;AN=2;DP=36;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant32 GT:AD:DP:GQ:PL:SB 0/1:6,13:19:99:355,0,167:1,5,3,10 chr1 231406295 . T C 694.22 PASS AC=2;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 1/1:0,11:11:33:407,33,0:0,0,9,2 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 0/1:44,37:81:99:983,0,1109:22,22,21,16 chr1 231468606 . A G 5952.04 PASS AC=1;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 0/1:168,174:342:99:4352,0,3870:96,72,91,83 chr1 231468953 . G A 3514.47 PASS AC=1;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 0/1:105,114:219:99:2925,0,2852:48,57,58,56 chr1 231470650 . T C 6602.35 PASS AC=1;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 0/1:197,159:356:99:3671,0,4807:90,107,70,89 chr1 231470772 . A G 1936.45 PASS AC=1;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 0/1:31,29:60:99:838,0,985:9,22,6,23 chr1 231480507 . A G 387.7 PASS AC=1;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 0/1:11,23:34:99:530,0,246:3,8,11,12 chr1 231486989 . A C 709.82 PASS AC=1;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 0/1:19,21:40:99:524,0,597:16,3,14,7 chr1 231487017 . T C 1080.6 PASS AC=1;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 0/1:26,32:58:99:975,0,725:19,7,22,10 chr1 231487993 . T C 3518.95 PASS AC=1;AF=0.55;AN=2;DP=3161;MQ=60;set=variant2-variant4-variant19-variant20-variant23-variant25-variant32-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:138,122:260:99:3012,0,3550:68,70,54,68 chr1 231488085 . G C 3002.92 PASS AC=1;AF=0.55;AN=2;DP=2577;MQ=60;set=variant2-variant4-variant19-variant20-variant23-variant25-variant32-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:120,84:204:99:1954,0,3152:52,68,37,47 chr1 231488524 . C T 1277.86 PASS AC=1;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 0/1:40,42:82:99:1168,0,1131:18,22,18,24 chr1 231489353 . G T 5356.22 PASS AC=1;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 0/1:175,138:313:99:3160,0,4298:74,101,56,82 chr1 231489539 . A G 550.91 PASS AC=1;AF=0.55;AN=2;DP=599;MQ=60;set=variant2-variant4-variant19-variant20-variant23-variant25-variant32-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,23:47:99:665,0,539:10,14,8,15 chr1 231490105 . C T 2466.59 PASS AC=1;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 0/1:89,80:169:99:1910,0,2204:39,50,35,45 chr1 231490819 . A AT 39.79 PASS AC=1;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 0/1:2,3:5:54:87,0,54:0,2,0,3 chr1 231500353 . A AT 6108.21 PASS AC=1;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 0/1:232,185:417:99:4356,0,5837:104,128,82,103 chr1 231501508 . CA C 1905.27 PASS AC=1;AF=0.55;AN=2;DP=1703;MQ=60;set=variant2-variant4-variant19-variant20-variant23-variant25-variant32-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:86,71:157:99:1656,0,2034:44,42,40,31 chr1 231502245 . T A 1174.94 PASS AC=1;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 0/1:92,71:163:99:1317,0,2374:30,62,27,44 chr1 231502310 . T C 1019.67 PASS AC=1;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 0/1:22,33:55:99:1152,0,697:2,20,5,28 chr1 231506557 . G A 734.14 PASS AC=1;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 0/1:17,22:39:99:542,0,441:6,11,8,14 chr1 231557255 . C G 1590.33 PASS AC=1;AF=0.55;AN=2;DP=972;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant12-variant14-variant18-variant23-variant27-variant28-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:66,44:110:99:1205,0,1652:22,44,11,33 chr1 231559226 . A G 3807.41 PASS AC=1;AF=0.531;AN=2;DP=3364;MQ=60;set=variant-variant4-variant6-variant7-variant12-variant14-variant17-variant18-variant20-variant23-variant24-variant27-variant28-variant29-variant30-variant42 GT:AD:DP:GQ:PL:SB 0/1:93,112:205:99:3111,0,2416:43,50,53,59 chr1 231559340 . A G 5536.48 PASS AC=1;AF=0.545;AN=2;DP=4005;MQ=60;set=variant4-variant9-variant19-variant20-variant23-variant25-variant30-variant32-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:183,147:330:99:3692,0,4683:106,77,75,72 chr1 231560220 . A G 1716.25 PASS AC=1;AF=0.531;AN=2;DP=1982;MQ=60;set=variant-variant4-variant6-variant7-variant12-variant14-variant17-variant18-variant20-variant23-variant24-variant27-variant28-variant29-variant30-variant42 GT:AD:DP:GQ:PL:SB 0/1:59,48:107:99:1162,0,2265:29,30,25,23 chr1 231560226 . A C 2625.12 PASS AC=1;AF=0.542;AN=2;DP=1478;FractionInformativeReads=1;MQ=60;set=variant4-variant8-variant9-variant19-variant20-variant23-variant25-variant30-variant32-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,56:102:99:2149,0,1763:23,23,27,29 chr1 231560233 . A G 2596.57 PASS AC=1;AF=0.542;AN=2;DP=1489;FractionInformativeReads=1;MQ=60;set=variant4-variant8-variant9-variant19-variant20-variant23-variant25-variant30-variant32-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,53:101:99:2126,0,1823:24,24,25,28 chr1 231560557 . G A 4271.02 PASS AC=1;AF=0.542;AN=2;DP=4208;MQ=60;set=variant4-variant8-variant9-variant19-variant20-variant23-variant25-variant30-variant32-variant36-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:150,197:347:99:4415,0,3297:77,73,103,94 chr1 231560775 . G GT 733.24 PASS AC=1;AF=0.538;AN=2;DP=771;MQ=60;set=variant4-variant8-variant9-variant19-variant20-variant23-variant25-variant30-variant32-variant36-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,24:52:99:589,0,719:6,22,8,16 chr1 231664753 . T A 882.8 PASS AC=1;AF=0.55;AN=2;DP=472;MQ=60;set=variant-variant12-variant14-variant18-variant23-variant27-variant28-variant29-variant30-variant41 GT:AD:DP:GQ:PL:SB 0/1:27,21:48:99:613,0,754:9,18,9,12 chr1 231697030 . G A 498.53 PASS AC=2;AF=0.712;AN=2;DP=401;MQ=60;set=variant-variant2-variant4-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant36-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:543,42,0:0,0,2,12 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 2/2:9:4:0,1,0,8 chr1 231747989 . G A 115.49 PASS AC=1;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 0/1:3,7:10:99:272,0,103:0,3,0,7 chr1 231752797 . A G 208.62 PASS AC=1;AF=0.5;AN=2;DP=39;FractionInformativeReads=1;MQ=60;set=variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:237,0,182:2,4,2,6 chr1 231762398 . C CTG,CTGTGTGTGTG,CTGTGTGTGTGTG 216.52 PASS AC=1,0,0;AF=0.417,0.125,0.021;AN=2;DP=594;set=variant-variant4-variant7-variant9-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant38-variant39-variant40-variant42 GT:DP:GQ:SB 0/1:25:99:9,6,9,1 chr1 231762413 . T TGTGTGCGC,TGTGTGTGTGC,TGTGTGTGTGTGC,TGTATGTCTGTGTGTGTGTGTGTGTGTGCGC,TGTATGTCTGTGTGTGTGTGTGTGTGTGTGC,TGTATGTCTGTGTGTGTGTGTGTGTGTGTGTGC 267.92 PASS AC=0,1,0,0,0,0;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 0/2:31:99:10,4,10,7 chr1 231830295 . G A 3253.46 PASS AC=1;AF=0.611;AN=2;DP=4822;MQ=60;set=variant-variant3-variant4-variant5-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:78,74:152:99:1894,0,1867:37,41,34,40 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 1/1:0,34:34:99:1038,102,0:0,0,21,13 chr1 231859181 . G A 1467.46 PASS AC=2;AF=0.645;AN=2;DP=2273;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1441,135,0:0,0,21,24 chr1 231859514 . G A 1096.88 PASS AC=1;AF=0.583;AN=2;DP=448;FractionInformativeReads=1;MQ=60;set=variant16-variant20-variant23-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,24:70:99:549,0,1425:18,28,13,11 chr1 231881422 . C T 235.7 PASS AC=1;AF=0.5;AN=2;DP=68;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant27-variant29 GT:AD:DP:GQ:PL:SB 0/1:14,9:23:99:264,0,433:3,11,1,8 chr1 231902850 . T C 1566.01 PASS AC=1;AF=0.5;AN=2;DP=229;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:56,64:120:99:1594,0,1304:33,23,38,26 chr1 231903010 . C T 1343.8 PASS AC=1;AF=0.5;AN=2;DP=393;FractionInformativeReads=1;MQ=60;set=variant23-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:68,59:127:99:1372,0,1728:28,40,25,34 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 0/1:46,56:102:99:1322,0,1094:26,20,35,21 chr1 231906847 . C T 268.61 PASS AC=1;AF=0.5;AN=2;DP=101;FractionInformativeReads=1;MQ=60;set=variant23-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,10:24:99:297,0,377:4,10,3,7 chr1 231931048 . T C 1311.67 PASS AC=2;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 1/1:0,56:56:99:1797,168,0:0,0,17,39 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 1/1:0,64:64:99:1941,191,0:0,0,21,43 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 0/1:23,19:42:99:544,0,636:17,6,14,5 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 0/1:35,32:67:99:844,0,990:14,21,16,16 chr1 231954872 . C T 577.04 PASS AC=1;AF=0.64;AN=2;DP=1283;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant20-variant21-variant22-variant23-variant28-variant32-variant36-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,18:41:99:522,0,596:7,16,4,14 chr1 231955906 . G A 124.68 PASS AC=2;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 1/1:0,2:2:6:90,6,0:0,0,2,0 chr1 231956086 . A T 1928.79 PASS AC=2;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 1/1:0,45:45:99:1304,134,0:0,0,23,22 chr1 232002392 . A G 1773.18 PASS AC=1;AF=0.625;AN=2;DP=3299;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant26-variant29-variant32-variant33-variant36-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,52:94:99:1353,0,1121:24,18,33,19 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 0/1:4,6:10:99:193,0,153:0,4,1,5 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 0/1:16,13:29:99:457,0,559:1,15,1,12 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 0/1:14,10:24:99:329,0,518:1,13,0,10 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 0/1:73,55:128:99:1305,0,1802:39,34,32,23 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 0/1:18,23:41:99:642,0,622:3,15,8,15 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 0/1:4,2:6:63:63,0,123:2,2,1,1 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 0/1:7:99:1,2,3,1 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 0/1:4,8:12:99:346,0,257:2,2,6,2 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 0/1:4,9:13:99:346,0,257:2,2,6,3 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 0/1:9,5:14:72:72,0,278:3,6,2,3 chr1 232173396 . G C 1794.73 PASS AC=1;AF=0.5;AN=2;DP=271;FractionInformativeReads=1;MQ=60;set=variant3-variant23 GT:AD:DP:GQ:PL:SB 0/1:54,41:95:99:959,0,1578:30,24,23,18 chr1 232173521 . C T 764.56 PASS AC=1;AF=0.587;AN=2;DP=3382;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant32-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,46:106:99:1057,0,1674:28,32,25,21 chr1 232173560 . G T 1926.28 PASS AC=1;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 0/1:45,47:92:99:1345,0,1388:26,19,21,26 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 0/1:63,59:122:99:2229,0,3185:29,34,30,29 chr1 232174173 . T C 3900.04 PASS AC=1;AF=0.625;AN=2;DP=3096;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant34-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,55:104:99:1365,0,1306:28,21,33,22 chr1 232174266 . G A 1920.38 PASS AC=1;AF=0.5;AN=2;DP=169;FS=1.213;FractionInformativeReads=1;MQ=60;MQRankSum=-1.258;QD=11.36;ReadPosRankSum=-2.153;SOR=0.571;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:94,75:169:99:1949,0,2528:52,42,39,36 chr1 232174775 . T C 573.94 PASS AC=1;AF=0.625;AN=2;DP=955;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant34-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,12:27:99:256,0,386:8,7,6,6 chr1 232175697 . G GCTGT 2572.16 PASS AC=1;AF=0.625;AN=2;DP=1793;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant34-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,27:53:99:1055,0,1307:9,17,4,23 chr1 232176195 . G T 512.51 PASS AC=1;AF=0.591;AN=2;DP=1597;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant32-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,18:60:99:367,0,1085:22,20,7,11 chr1 232176306 . G A 311.63 PASS AC=1;AF=0.58;AN=2;DP=943;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant32-variant34-variant36-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,14:35:99:397,0,632:9,12,9,5 chr1 232176987 . C T 8838.13 PASS AC=1;AF=0.62;AN=2;DP=8209;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:159,124:283:99:2998,0,3971:72,87,52,72 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 0/1:28,17:45:99:618,0,1054:27,1,17,0 chr1 232534303 . CT C,CTT 147.56 DRAGENHardINDEL AC=1,0;AF=0.483,0.017;AN=2;DP=17946;set=FilteredInAll GT:DP:GQ:SB 0/1:523:99:222,226,41,34 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 0/1:67,42:109:99:893,0,1690:31,36,19,23 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 1/1:0,63:63:99:1994,189,0:0,0,24,39 chr1 232551416 . G A 1653.26 PASS AC=1;AF=0.593;AN=2;DP=4600;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant16-variant17-variant20-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,90:166:99:2030,0,1920:34,42,44,46 chr1 232564096 . CTTTT CTTT,CTT,CTTTTT,C 95.49 PASS AC=0,1,0,0;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 0/2:23:99:8,6,5,4 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 1/1:0,63:63:99:2110,189,0:0,0,20,43 chr1 232579204 . A C 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=0.693;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:99:117,0,101:3,0,3,0 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 1/1:0,251:251:99:8084,752,0:0,0,124,127 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 0/1:121,70:191:99:1679,0,3284:58,63,31,39 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 0/1:20,19:39:99:532,0,443:8,12,7,12 chr1 232941153 . C T 793.97 PASS AC=1;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 0/1:37,50:87:99:1382,0,944:17,20,25,25 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 1/1:0,256:256:99:7760,767,0:0,0,115,141 chr1 233091463 . T A 1012.25 PASS AC=1;AF=0.5;AN=2;DP=1095;MQ=60;set=variant-variant2-variant7-variant11-variant14-variant15-variant16-variant20-variant23-variant25-variant27-variant29-variant33-variant37 GT:AD:DP:GQ:PL:SB 0/1:42,26:68:99:635,0,970:20,22,8,18 chr1 233105677 . G A 1633.9 PASS AC=1;AF=0.5;AN=2;DP=372;FractionInformativeReads=0.995;MQ=60;set=variant9-variant23 GT:AD:DP:GQ:PL:SB 0/1:105,83:188:99:1841,0,2511:55,50,42,41 chr1 233114608 . C T 667.97 PASS AC=1;AF=0.5;AN=2;DP=531;MQ=60;set=variant-variant2-variant7-variant10-variant11-variant14-variant15-variant16-variant20-variant23-variant25-variant27-variant29-variant33-variant37 GT:AD:DP:GQ:PL:SB 0/1:18,23:41:99:647,0,511:4,14,5,18 chr1 233119881 . T C 170.98 PASS AC=1;AF=0.545;AN=2;DP=436;set=variant3-variant7-variant10-variant11-variant12-variant14-variant15-variant23-variant24-variant29-variant38 GT:AD:DP:GQ:PL:SB 0/1:17,28:45:99:676,0,293:11,6,17,11 chr1 233137225 . CATAA C 52.73 PASS AC=2;AF=0.98;AN=2;DP=137;FS=0;MQ=60;MQRankSum=2.219;ReadPosRankSum=-0.361;set=variant-variant2-variant5-variant6-variant8-variant10-variant13-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant27-variant29-variant33-variant34-variant36-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:230,18,0:0,0,3,3 chr1 233160772 . T C 1365.16 PASS AC=1;AF=0.583;AN=2;DP=1913;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant10-variant11-variant12-variant14-variant19-variant21-variant22-variant23-variant24-variant29-variant30-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,51:89:99:1195,0,967:26,12,31,20 chr1 233193599 . C CA,CAA 1254.67 PASS AC=2,0;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 1/1:110:99:4,2,68,36 chr1 233296759 . A C 577.43 PASS AC=1;AF=0.5;AN=2;DP=78;FractionInformativeReads=1;MQ=60;set=variant3-variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:4,8:12:99:231,0,136:4,0,6,2 chr1 233395214 . T A 588.62 PASS AC=2;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 1/1:0,10:10:30:371,30,0:0,0,1,9 chr1 233397267 . G A 402.88 PASS AC=1;AF=0.5;AN=2;DP=354;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant10-variant17-variant18-variant23-variant31-variant32-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:336,0,361:1,10,3,9 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 0/1:76,59:135:99:1297,0,1969:47,29,31,28 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 0/1:4,15:19:99:511,0,126:4,0,13,2 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 0/1:15,20:35:99:591,0,398:11,4,15,5 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 0/1:12,12:24:99:447,0,692:3,9,3,9 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 0/1:11,11:22:99:447,0,692:3,8,2,9 chr1 233431241 . G A 1464.76 PASS AC=2;AF=0.563;AN=2;DP=941;MQ=60;set=variant7-variant8-variant23-variant24-variant29-variant34-variant36-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3179,316,0:0,0,51,56 chr1 233463785 . G C 541.55 PASS AC=1;AF=0.5;AN=2;DP=164;FractionInformativeReads=1;MQ=60;set=variant7-variant8-variant23 GT:AD:DP:GQ:PL:SB 0/1:36,27:63:99:740,0,1074:10,26,6,21 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 0/1:43,24:67:99:584,0,1166:23,20,14,10 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 0/1:45,31:76:99:745,0,1235:22,23,17,14 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 0/1:22,19:41:99:483,0,566:10,12,8,11 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 0/1:25,12:37:99:618,0,5280:19,6,9,3 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 0/1:28,17:45:99:567,0,5350:20,8,11,6 chr1 233512355 . C T 528.46 PASS AC=1;AF=0.5;AN=2;DP=62;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.036;QD=8.52;ReadPosRankSum=-0.686;SOR=0.826;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:38,24:62:99:557,0,1483:14,24,8,16 chr1 233512362 . A G 802.59 PASS AC=1;AF=0.583;AN=2;DP=1168;MQ=60;set=variant3-variant6-variant8-variant11-variant13-variant17-variant18-variant19-variant21-variant23-variant27-variant28-variant31-variant33-variant36-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,37:59:99:916,0,835:7,15,13,24 chr1 233514934 . G A 1849.24 PASS AC=1;AF=0.594;AN=2;DP=1943;MQ=60;set=variant3-variant6-variant8-variant11-variant13-variant17-variant18-variant21-variant23-variant27-variant28-variant31-variant33-variant36-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:58,56:114:99:1410,0,1450:29,29,28,28 chr1 233514975 . G T 1609.55 PASS AC=1;AF=0.594;AN=2;DP=1853;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant8-variant11-variant13-variant17-variant18-variant21-variant23-variant27-variant28-variant31-variant33-variant36-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:56,52:108:99:1428,0,1530:28,28,29,23 chr1 233515071 . C T 2575.47 PASS AC=1;AF=0.594;AN=2;DP=2654;MQ=60;set=variant3-variant6-variant8-variant11-variant13-variant17-variant18-variant21-variant23-variant27-variant28-variant31-variant33-variant36-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:102,90:192:99:2244,0,2592:58,44,54,36 chr1 233515102 . T G 2933.61 PASS AC=1;AF=0.594;AN=2;DP=3347;MQ=60;set=variant3-variant6-variant8-variant11-variant13-variant17-variant18-variant21-variant23-variant27-variant28-variant31-variant33-variant36-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:120,107:227:99:2629,0,2944:65,55,60,47 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 0/1:45,54:99:99:1414,0,1417:8,37,18,36 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 0/1:144,147:291:99:3686,0,3629:77,67,78,69 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 0/1:169,143:312:99:4368,0,5341:77,92,57,86 chr1 233749855 . A G 267.33 PASS AC=1;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 0/1:6,10:16:99:228,0,141:4,2,6,4 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 0/1:24,16:40:99:743,0,882:17,7,14,2 chr1 233785786 . A C 1088.44 PASS AC=1;AF=0.63;AN=2;DP=2374;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant36-variant37-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:53,49:102:99:1125,0,1246:21,32,19,30 chr1 233808313 . ATG A 210.36 PASS AC=1;AF=0.639;AN=2;DP=335;FS=0;set=variant5-variant6-variant7-variant11-variant12-variant14-variant17-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant31-variant32-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:99:130,0,279:0,8,0,4 chr1 234040742 . A C 2353.78 PASS AC=1;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 0/1:85,72:157:99:1556,0,1939:50,35,39,33 chr1 234041422 . G C 3261.85 PASS AC=1;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 0/1:159,164:323:99:4115,0,4042:86,73,82,82 chr1 234367549 . T C 934.26 PASS AC=1;AF=0.679;AN=2;DP=2330;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant29-variant30-variant31-variant33-variant34-variant36-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,34:67:99:1001,0,943:7,26,8,26 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 0/1:22,19:41:99:449,0,494:9,13,7,12 chr1 234444761 . TA T,TAAAAA,TAAAA,TAA 369.39 PASS AC=0,1,0,0;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 0/2:5:75:3,0,2,0 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 1/1:0,14:14:42:563,42,0:0,0,11,3 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 0/1:5,10:15:99:283,0,138:4,1,7,3 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 0/1:6,4:10:68:68,0,86:4,2,2,2 chr1 234563060 . T C 1364.44 PASS AC=1;AF=0.625;AN=2;DP=2407;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant10-variant15-variant17-variant21-variant22-variant23-variant24-variant25-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,27:69:99:632,0,1077:22,20,15,12 chr1 234573265 . C T 754.18 PASS AC=1;AF=0.5;AN=2;DP=285;FractionInformativeReads=1;MQ=60;set=variant22-variant23-variant30-variant38 GT:AD:DP:GQ:PL:SB 0/1:42,37:79:99:932,0,1188:13,29,15,22 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 0/1:17,21:38:99:602,0,492:5,12,7,14 chr1 234582457 . C T 313.43 PASS AC=2;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 1/1:0,8:8:24:316,24,0:0,0,6,2 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 0/1:5,6:11:99:153,0,148:4,1,5,1 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 0/1:75,66:141:99:1538,0,1818:33,42,30,36 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 0/1:105,72:177:99:1686,0,2514:61,44,42,30 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 0/1:10,9:19:99:310,0,383:0,10,0,9 chr1 234584446 . G A 364.71 PASS AC=1;AF=0.5;AN=2;DP=281;MQ=60;set=variant2-variant10-variant16-variant20-variant21-variant22-variant23-variant24-variant29-variant31-variant34-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:9,9:18:99:339,0,351:0,9,0,9 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 0/1:20,27:47:99:730,0,525:15,5,20,7 chr1 234596202 . T A 530.23 PASS AC=1;AF=0.558;AN=2;DP=857;MQ=60;set=variant2-variant5-variant7-variant10-variant11-variant12-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,14:30:99:478,0,541:3,13,2,12 chr1 234601586 . G A 523.58 PASS AC=1;AF=0.533;AN=2;DP=680;FractionInformativeReads=1;MQ=60;set=variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,33:52:99:748,0,390:7,12,16,17 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 1/1:0,16:16:47:529,47,0:0,0,14,2 chr1 234603386 . G T 473.72 PASS AC=1;AF=0.533;AN=2;DP=612;FractionInformativeReads=1;MQ=60;set=variant16-variant18-variant20-variant21-variant23-variant24-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,8:21:99:248,0,490:3,10,1,7 chr1 234606604 . C T 160.84 PASS AC=1;AF=0.5;AN=2;DP=56;set=variant-variant3-variant19-variant23-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,8:13:99:240,0,190:5,0,6,2 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 0/1:13,14:27:99:338,0,423:10,3,9,5 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 0/1:29,29:58:99:791,0,729:20,9,17,12 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 0/1:50,40:90:99:819,0,1205:24,26,19,21 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 0/1:14,14:28:99:466,0,481:6,8,5,9 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 0/1:9,7:16:99:259,0,272:2,7,0,7 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 0/1:7,4:11:99:144,0,236:1,6,0,4 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 1/1:4:12:0,0,0,4 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 0/1:24,14:38:99:332,0,586:11,13,7,7 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 0/1:126,109:235:99:2570,0,3232:70,56,65,44 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 0/1:213,161:374:99:6573,0,9370:113,100,86,75 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 0/1:33,51:84:99:1261,0,892:10,23,21,30 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 0/1:51,57:108:99:1332,0,1273:30,21,31,26 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 1/1:0,10:10:30:321,30,0:0,0,1,9 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 1/1:0,4:4:15:152,15,0:0,0,1,3 chr1 235273179 . G A 20791.4 PASS AC=2;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 1/1:2,370:372:99:11689,1093,0:1,1,190,180 chr1 235285740 . C T 176.57 PASS AC=2;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 1/1:0,28:28:83:752,83,0:0,0,14,14 chr1 235350207 . T C 46.72 PASS AC=2;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 1/1:0,3:3:9:94,9,0:0,0,2,1 chr1 235350358 . C T 348.84 PASS AC=1;AF=0.5;AN=2;DP=38;FractionInformativeReads=1;MQ=60;set=variant4-variant23-variant26-variant38 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:37:78,0,37:1,1,1,1 chr1 235357303 . A ATG 855.54 PASS AC=2;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 1/1:0,25:25:75:1125,75,0:0,0,17,8 chr1 235357314 . AT A 417.38 PASS AC=2;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 1/1:0,28:28:84:1045,84,0:0,0,20,8 chr1 235357543 . A G 226.33 PASS AC=2;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 1/1:0,12:12:36:425,36,0:0,0,3,9 chr1 235383188 . A G 3509.65 PASS AC=2;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 1/1:2,64:66:99:1895,147,0:1,1,21,43 chr1 235392546 . T C 1212.75 PASS AC=2;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 1/1:0,47:47:99:1574,141,0:0,0,33,14 chr1 235394541 . A C 589.24 PASS AC=2;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 1/1:0,10:10:30:299,30,0:0,0,3,7 chr1 235397937 . GCA G 392.31 PASS AC=2;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 1/1:0,7:7:21:274,21,0:0,0,2,5 chr1 235490391 . CA C 374.91 PASS AC=2;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 1/1:0,29:29:87:1066,87,0:0,0,12,17 chr1 235491075 . T C 347.47 PASS AC=1;AF=0.5;AN=2;DP=24;FS=1.569;FractionInformativeReads=1;MQ=60;MQRankSum=-0.927;QD=14.48;ReadPosRankSum=-0.695;SOR=0.412;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:11,13:24:99:376,0,285:7,4,7,6 chr1 235492546 . T G 1337.18 PASS AC=2;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 1/1:0,51:51:99:1623,153,0:0,0,20,31 chr1 235492948 . TA T 769.25 PASS AC=1;AF=0.556;AN=2;DP=261;MQ=60;set=variant3-variant4-variant12-variant23-variant26-variant29-variant31-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:1,11:12:5:420,0,5:0,1,4,7 chr1 235492972 . T G 337.25 PASS AC=2;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 1/1:0,12:12:35:492,35,0:0,0,5,7 chr1 235505313 . A AT 244.12 PASS AC=2;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 1/1:0,20:20:60:609,60,0:0,0,12,8 chr1 235506853 . G A 46.68 PASS AC=2;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 1/1:0,16:16:48:519,48,0:0,0,9,7 chr1 235506865 . C CA 89.83 PASS AC=2;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 1/1:0,15:15:45:428,45,0:0,0,8,7 chr1 235506918 . G C 362.91 PASS AC=2;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 1/1:0,17:17:51:556,51,0:0,0,8,9 chr1 235507466 . CAA CA,CAAAA,C,CAAA 223.45 PASS AC=1,0,0,0;AF=0.397,0.052,0.034,0.017;AN=2;DP=1090;set=variant2-variant4-variant7-variant8-variant9-variant11-variant12-variant13-variant15-filterInvariant16-variant17-variant19-variant22-variant23-filterInvariant24-variant25-variant26-variant29-variant30-filterInvariant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant42-variant44 GT:DP:GQ:SB 0/1:25:99:9,3,10,3 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 0/2:28:99:15,5,7,1 chr1 235543476 . TTGTGTGTGTGTGTGTGTGTGTG T,TTGTGTGTG,TTGTGTG,TTGTGTGTGTGTGTGTGTGTG,TTGTGTGTGTGTGTGTGTG,TTGTG,TTGTGTGTGTG,TTGTGTGTGTGTG,TTGTGTGTGTGTGTGTG,TTGTGTGTGTGTGTG 1103.38 PASS AC=0,0,0,0,0,0,0,0,1,0;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 0/9:37:99:4,13,7,13 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 1/1:0,46:46:99:1383,138,0:0,0,25,21 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 1/1:0,28:28:84:1076,84,0:0,0,24,4 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 1/1:0,89:89:99:2678,267,0:0,0,53,36 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 1/1:0,69:69:99:2280,206,0:0,0,20,49 chr1 235714862 . A C 325.04 PASS AC=1;AF=0.625;AN=2;DP=797;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant19-variant20-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,14:19:99:427,0,161:5,0,10,4 chr1 235715064 . A T 2292.06 PASS AC=1;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 0/1:40,40:80:99:791,0,932:16,24,17,23 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 0/1:76,63:139:99:1420,0,1889:29,47,28,35 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 0/1:46,40:86:99:1082,0,1292:11,35,13,27 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 0/1:16,20:36:99:586,0,521:2,14,6,14 chr1 235747005 . C T 509.59 PASS AC=1;AF=0.614;AN=2;DP=807;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant12-variant13-variant15-variant17-variant19-variant22-variant23-variant28-variant29-variant30-variant31-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,18:41:99:458,0,664:16,7,12,6 chr1 235747154 . A G 968.12 PASS AC=1;AF=0.614;AN=2;DP=2436;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant12-variant13-variant15-variant17-variant19-variant22-variant23-variant28-variant29-variant30-variant31-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,53:101:99:1332,0,1174:24,24,25,28 chr1 235758570 . G A 150.44 PASS AC=1;AF=0.614;AN=2;DP=606;MQ=60;set=variant-variant3-variant6-variant7-variant9-variant12-variant13-variant15-variant17-variant19-variant22-variant23-variant28-filterInvariant29-variant30-variant31-variant34-variant36-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,14:32:99:291,0,475:12,6,8,6 chr1 235758911 . A G 193.54 PASS AC=1;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 0/1:6,4:10:99:109,0,189:1,5,1,3 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 0/1:9,17:26:99:341,0,160:2,7,4,13 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 0/1:3,7:10:99:273,0,107:0,3,0,7 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 0/1:6,11:17:99:434,0,223:6,0,10,1 chr1 235840495 . G T 1105.77 PASS AC=1;AF=0.5;AN=2;DP=103;FS=2.58;FractionInformativeReads=1;MQ=60;MQRankSum=-0.709;QD=10.74;ReadPosRankSum=-1.336;SOR=1.012;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:53,50:103:99:1134,0,1137:25,28,20,30 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 0/1:18,15:33:99:439,0,539:4,14,3,12 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 0/1:45,37:82:99:874,0,1140:21,24,20,17 chr1 235887276 . G T 461.76 PASS AC=1;AF=0.667;AN=2;DP=839;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,9:23:99:319,0,479:12,2,9,0 chr1 235896726 . C T 507.04 PASS AC=1;AF=0.656;AN=2;DP=723;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,12:28:99:268,0,429:11,5,9,3 chr1 235910392 . A G 753.76 PASS AC=1;AF=0.656;AN=2;DP=2340;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,29:56:99:872,0,808:20,7,20,9 chr1 235910542 . C T 1411.91 PASS AC=1;AF=0.656;AN=2;DP=4230;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,61:123:99:1453,0,1473:26,36,26,35 chr1 235918688 . CAAAAGAAAAG CAAAAG,CAAAAGAAAAGAAAAG,CAAAAGAAAAGAAAAGAAAAG,C 627.4 PASS AC=1,1,0,0;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 1/2:9:84:0,0,7,2 chr1 235922228 . T C 527.48 PASS AC=1;AF=0.543;AN=2;DP=767;MQ=60;set=variant6-variant8-variant11-variant13-variant15-variant16-variant17-variant18-variant21-variant23-variant26-variant28-variant30-variant31-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,17:31:99:539,0,417:11,3,14,3 chr1 235940450 . C T 1473.36 PASS AC=1;AF=0.656;AN=2;DP=4255;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,66:117:99:1584,0,1182:31,20,35,31 chr1 235945294 . T C 1884.63 PASS AC=1;AF=0.656;AN=2;DP=4946;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,83:162:99:1968,0,1844:39,40,41,42 chr1 235972435 . T C 1810.27 PASS AC=1;AF=0.656;AN=2;DP=4047;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,63:120:99:1589,0,1343:28,29,34,29 chr1 235972867 . T C 1050.33 PASS AC=1;AF=0.656;AN=2;DP=3014;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,30:82:99:662,0,1345:23,29,17,13 chr1 236030045 . A T 62.99 PASS AC=1;AF=0.69;AN=2;DP=302;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant11-variant12-variant13-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:66:198,0,66:2,2,3,4 chr1 236139141 . A T 1110.25 PASS AC=1;AF=0.556;AN=2;DP=1377;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant19-variant23-variant25-variant28-variant30-variant34-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,29:69:99:607,0,935:24,16,16,13 chr1 236139817 . C T 6180.51 PASS AC=1;AF=0.556;AN=2;DP=6337;MQ=60;set=variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant19-variant23-variant25-variant28-variant30-variant34-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:177,154:331:99:4043,0,4703:84,93,77,77 chr1 236139894 . T G 5152.14 PASS AC=1;AF=0.556;AN=2;DP=5703;MQ=60;set=variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant19-variant23-variant25-variant28-variant30-variant34-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:146,158:304:99:3932,0,3637:70,76,72,86 chr1 236140266 . A C 1847.22 PASS AC=1;AF=0.553;AN=2;DP=2543;set=variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant19-variant23-variant25-variant28-variant30-variant34-variant36-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,59:132:99:1542,0,1937:36,37,32,27 chr1 236140739 . G A 1622.86 PASS AC=1;AF=0.556;AN=2;DP=1645;MQ=60;set=variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant19-variant23-variant25-variant28-variant30-variant34-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,51:82:99:1479,0,815:14,17,20,31 chr1 236141174 . T C 1647.19 PASS AC=1;AF=0.556;AN=2;DP=1861;MQ=60;set=variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant19-variant23-variant25-variant28-variant30-variant34-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,37:85:99:821,0,1195:29,19,19,18 chr1 236142253 . T G 1207.21 PASS AC=1;AF=0.556;AN=2;DP=1234;MQ=60;set=variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant19-variant23-variant25-variant28-variant30-variant34-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,33:56:99:924,0,563:13,10,21,12 chr1 236142565 . T C 351.5 PASS AC=2;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 1/1:0,35:35:99:1401,105,0:0,0,5,30 chr1 236142570 . C G 479.96 PASS AC=1;AF=0.556;AN=2;DP=493;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant19-variant23-variant25-variant28-variant30-variant34-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,14:31:99:483,0,573:2,15,1,13 chr1 236143302 . C CA 1553.64 PASS AC=1;AF=0.556;AN=2;DP=2030;MQ=60;set=variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant19-variant23-variant25-variant28-variant30-variant34-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,36:82:99:794,0,1122:16,30,13,23 chr1 236144951 . A G 1850.28 PASS AC=1;AF=0.559;AN=2;DP=1745;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant9-variant10-variant11-variant12-variant19-variant23-variant25-variant28-variant30-variant34-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,21:57:99:446,0,963:21,15,12,9 chr1 236145145 . T C 823.58 PASS AC=1;AF=0.559;AN=2;DP=916;MQ=60;set=variant3-variant7-variant9-variant10-variant11-variant12-variant19-variant23-variant25-variant28-variant30-variant34-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,21:56:99:455,0,927:12,23,8,13 chr1 236154057 . AGGACTACAT A 476.13 PASS AC=1;AF=0.583;AN=2;DP=602;MQ=60;set=variant7-variant10-variant11-variant12-variant23-variant25-variant28-variant34-variant36-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,23:41:99:912,0,675:13,5,14,9 chr1 236154365 . G T 331.73 PASS AC=1;AF=0.563;AN=2;DP=456;MQ=60;set=variant3-variant7-variant9-variant10-variant11-variant12-variant19-variant23-variant25-variant28-variant30-variant34-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,15:27:99:502,0,348:3,9,4,11 chr1 236175153 . T C 68.44 PASS AC=1;AF=0.545;AN=2;DP=327;FractionInformativeReads=1;set=variant2-variant6-variant8-variant9-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant27-variant28-variant29-variant30-variant31-variant32-variant36-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:79:79,0,116:3,0,1,2 chr1 236175327 . C A 1421.69 PASS AC=1;AF=0.5;AN=2;DP=819;MQ=60;set=variant-variant4-variant5-variant11-variant23-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,42:87:99:957,0,1154:29,16,22,20 chr1 236175339 . T C 1734.52 PASS AC=2;AF=0.586;AN=2;DP=4423;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,87:87:99:2647,260,0:0,0,50,37 chr1 236176990 . T C 153.11 PASS AC=1;AF=0.537;AN=2;DP=976;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant7-variant8-variant9-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant27-variant28-variant29-variant30-variant31-variant32-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,10:24:99:224,0,417:3,11,3,7 chr1 236180580 . C G 1015.84 PASS AC=1;AF=0.5;AN=2;DP=630;FractionInformativeReads=1;set=variant-variant4-variant5-variant10-variant11-variant18-variant23-variant34-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,34:67:99:1113,0,936:10,23,5,29 chr1 236187365 . T C 882.47 PASS AC=1;AF=0.5;AN=2;DP=664;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant11-variant23-variant39 GT:AD:DP:GQ:PL:SB 0/1:45,43:88:99:1278,0,1137:25,20,26,17 chr1 236193145 . G C 625.9 PASS AC=1;AF=0.55;AN=2;DP=1517;MQ=60;set=variant2-variant6-variant8-variant9-variant10-variant11-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,16:47:99:349,0,803:11,20,6,10 chr1 236201609 . T G 394.98 PASS AC=1;AF=0.5;AN=2;DP=660;MQ=60;set=variant2-variant6-variant8-variant9-variant11-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant37-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,9:21:99:247,0,300:4,8,2,7 chr1 236205090 . C T 239.06 PASS AC=1;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 0/1:7,6:13:99:181,0,220:6,1,5,1 chr1 236205121 . T C 1329.7 PASS AC=1;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 0/1:15,17:32:99:579,0,479:13,2,15,2 chr1 236208688 . A G 871.77 PASS AC=1;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 0/1:13,6:19:99:213,0,731:11,2,6,0 chr1 236208689 . T A 871.77 PASS AC=1;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 0/1:13,6:19:99:213,0,731:11,2,6,0 chr1 236208773 . C T 2041.02 PASS AC=1;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 0/1:50,50:100:99:1180,0,1228:32,18,31,19 chr1 236209024 . C G 1189.07 PASS AC=1;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 0/1:24,16:40:99:398,0,676:8,16,4,12 chr1 236209081 . G A 248.05 PASS AC=1;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 0/1:13,6:19:99:166,0,399:3,10,1,5 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 1/1:8:25:0,0,8,0 chr1 236305885 . G A 1234.11 PASS AC=1;AF=0.559;AN=2;DP=1456;MQ=60;set=variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant19-variant22-variant23-variant25-variant27-variant34-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,48:83:99:1077,0,807:22,13,26,22 chr1 236368391 . C CT 1092.61 PASS AC=1;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 0/1:36,33:69:99:1005,0,1126:25,11,19,14 chr1 236368708 . T C 76.67 PASS AC=1;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 0/1:3,3:6:76:76,0,77:1,2,1,2 chr1 236379034 . TG T 7386.88 PASS AC=1;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 0/1:136,159:295:99:5469,0,4579:81,55,81,78 chr1 236379149 . A C 5169.3 PASS AC=1;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 0/1:164,149:313:99:3793,0,4238:79,85,65,84 chr1 236379221 . TACAG T 5670.76 PASS AC=1;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 0/1:141,110:251:99:4155,0,7153:58,83,49,61 chr1 236379623 . G A 4163.01 PASS AC=1;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 0/1:184,151:335:99:3485,0,4712:99,85,74,77 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 0/1:86,96:182:99:2423,0,2185:39,47,43,53 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 1/1:0,107:107:99:3540,321,0:0,0,37,70 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 1/1:0,30:30:95:1327,95,0:0,0,10,20 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 1/1:0,33:33:99:1046,99,0:0,0,13,20 chr1 236380913 . T C 199.29 PASS AC=1;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 0/1:1,9:10:12:245,0,12:0,1,3,6 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 1/1:0,87:87:99:2621,260,0:0,0,34,53 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 1/1:0,38:38:99:1159,114,0:0,0,16,22 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 1/1:0,18:18:54:590,54,0:0,0,5,13 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 1/1:0,11:11:33:370,33,0:0,0,3,8 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 1/1:0,2:2:6:90,6,0:0,0,0,2 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 1/1:0,2:2:6:90,6,0:0,0,0,2 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 1/1:0,52:52:99:1923,156,0:0,0,43,9 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 1/1:0,291:291:99:8746,872,0:0,0,137,154 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 1/1:0,251:251:99:7690,753,0:0,0,111,140 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 1/1:0,224:224:99:6475,670,0:0,0,130,94 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 1/1:0,241:241:99:7015,721,0:0,0,136,105 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 1/1:0,209:209:99:8918,626,0:0,0,96,113 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 1/1:0,33:33:99:1055,99,0:0,0,11,22 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 1/1:0,17:17:51:656,51,0:0,0,16,1 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 1/1:0,49:49:99:1532,147,0:0,0,32,17 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 1/1:0,58:58:99:1830,174,0:0,0,20,38 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 1/1:0,42:42:99:1420,126,0:0,0,10,32 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 1/1:0,24:24:72:870,72,0:0,0,5,19 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 1/1:0,32:32:96:1047,96,0:0,0,23,9 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 1/1:0,69:69:99:2070,207,0:0,0,26,43 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 1/1:0,17:17:50:532,50,0:0,0,5,12 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 1/1:0,12:12:36:412,36,0:0,0,4,8 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 1/1:0,63:63:99:1905,189,0:0,0,25,38 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 1/1:0,16:16:47:555,47,0:0,0,2,14 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 1/1:0,11:11:33:391,33,0:0,0,3,8 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 1/1:0,54:54:99:2180,163,0:0,0,28,26 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 1/1:0,26:26:87:1194,87,0:0,0,17,9 chr1 236444973 . C T 532.06 PASS AC=1;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 0/1:21,28:49:99:636,0,533:10,11,14,14 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 1/1:0,55:55:99:1679,165,0:0,0,24,31 chr1 236557771 . G A 1444.61 PASS AC=2;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 1/1:0,110:110:99:3326,330,0:0,0,54,56 chr1 236557928 . G A 121.25 PASS AC=2;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 1/1:0,16:16:48:634,48,0:0,0,1,15 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 0/1:10:64:5,0,4,1 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 0/1:88,73:161:99:1784,0,2345:45,43,44,29 chr1 236647156 . T C 1225.2 PASS AC=1;AF=0.5;AN=2;DP=90;FS=3.955;FractionInformativeReads=1;MQ=60;MQRankSum=-0.11;QD=13.61;ReadPosRankSum=1.693;SOR=0.547;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:40,50:90:99:1253,0,914:23,17,24,26 chr1 236647511 . T C 1024.11 PASS AC=1;AF=0.667;AN=2;DP=1644;MQ=60;set=variant7-variant12-variant13-variant14-variant18-variant19-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,25:67:99:548,0,1151:23,19,15,10 chr1 236647550 . C G,A 1179.77 PASS AC=0,1;AF=0.452,0.214;AN=2;DP=1855;MQ=60;set=variant7-variant12-variant13-variant14-variant18-variant19-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant38-variant41-variant43 GT:DP:GQ:SB 0/2:76:99:25,23,18,10 chr1 236648008 . GAA G,GA 130.55 PASS AC=0,1;AF=0.191,0.382;AN=2;DP=779;set=variant-variant2-variant3-variant4-filterInvariant5-variant6-variant7-variant8-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:19:69:3,3,5,8 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 0/1:18,19:37:99:460,0,375:9,9,11,8 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 1/1:0,37:37:99:1043,111,0:0,0,17,20 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 1/1:0,9:9:27:321,27,0:0,0,7,2 chr1 236687145 . C T 2112.82 PASS AC=1;AF=0.764;AN=2;DP=2534;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,36:72:99:1015,0,962:15,21,21,15 chr1 236688177 . G T 156.15 PASS AC=1;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 0/1:1,4:5:12:124,0,12:0,1,1,3 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 0/1:30,26:56:99:635,0,725:19,11,18,8 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 0/1:35,29:64:99:689,0,859:21,14,18,11 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 0/1:38,38:76:99:900,0,848:21,17,21,17 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 0/1:23,28:51:99:688,0,563:9,14,10,18 chr1 236702153 . G A 319.19 PASS AC=1;AF=0.759;AN=2;DP=189;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant13-variant15-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:31:86,0,31:1,0,3,1 chr1 236702209 . C T 836.28 PASS AC=1;AF=0.688;AN=2;DP=453;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:273,0,277:4,3,5,2 chr1 236702210 . A G 836.28 PASS AC=1;AF=0.806;AN=2;DP=526;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:273,0,277:4,3,5,2 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 0/1:38:99:7,6,12,13 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 0/1:12,15:27:99:594,0,459:3,9,5,10 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 0/1:12,15:27:99:594,0,459:3,9,5,10 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 0/1:10,9:19:99:247,0,265:3,7,3,6 chr1 236702497 . AGTTT A 527.5 PASS AC=1;AF=0.625;AN=2;DP=363;MQ=60;set=variant-variant2-variant4-variant8-variant10-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant27-variant28-variant29-variant33-variant34-variant37-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:270,0,315:2,6,2,5 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 0/1:6,7:13:99:180,0,147:2,4,2,5 chr1 236703734 . T C 336.22 PASS AC=1;AF=0.823;AN=2;DP=178;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:15:79,0,15:1,0,2,1 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 0/1:3,4:7:73:156,0,73:2,1,3,1 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 0/1:37:99:13,6,12,6 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 0/1:1,3:4:99:123,0,166:1,0,2,1 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 0/1:1,3:4:99:123,0,166:1,0,2,1 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 0/1:1,3:4:99:123,0,166:1,0,2,1 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 0/1:21,17:38:99:393,0,504:8,13,6,11 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 0/1:14,14:28:99:343,0,367:4,10,5,9 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 0/1:3,5:8:67:152,0,67:1,2,1,4 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 0/1:7,12:19:99:419,0,250:7,0,12,0 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 0/1:63,49:112:99:1356,0,1522:42,21,31,18 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 0/1:119,90:209:99:2057,0,2980:59,60,44,46 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 0/1:46,34:80:99:770,0,1235:15,31,12,22 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 0/1:31,26:57:99:957,0,1764:8,23,6,20 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 0/1:27,23:50:99:884,0,1625:8,19,6,17 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 0/1:39:99:7,3,20,9 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 0/1:43,43:86:99:1113,0,995:17,26,15,28 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 0/1:12,15:27:99:428,0,377:2,10,4,11 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 0/1:5,4:9:99:153,0,269:1,4,0,4 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 0/1:9,4:13:99:100,0,234:6,3,3,1 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 0/1:11,7:18:99:180,0,279:8,3,4,3 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 0/1:55,54:109:99:1470,0,1493:33,22,29,25 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 0/1:54,53:107:99:1348,0,1360:23,31,22,31 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 0/1:28,22:50:99:801,0,1173:11,17,9,13 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 0/1:28,19:47:99:771,0,1143:11,17,8,11 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 0/1:20,33:53:99:1344,0,776:11,9,16,17 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 0/1:21,34:55:99:1344,0,776:11,10,16,18 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 0/1:22,32:54:99:820,0,564:12,10,15,17 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 0/1:13,27:40:99:1095,0,659:6,7,11,16 chr1 236712785 . T A 1426.79 PASS AC=1;AF=0.5;AN=2;DP=144;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.831;QD=9.91;ReadPosRankSum=0.604;SOR=0.708;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:89,55:144:99:1455,0,2423:44,45,28,27 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 0/1:94,70:164:99:1587,0,2356:44,50,33,37 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 0/1:20,15:35:99:453,0,461:12,8,9,6 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 0/1:157,196:353:99:5169,0,3589:91,66,112,84 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 0/1:93,134:227:99:3422,0,2261:43,50,69,65 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 0/1:9,10:19:99:385,0,332:1,8,4,6 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 0/1:6,11:17:99:356,0,164:4,2,5,6 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 0/1:30,32:62:99:1102,0,1018:21,9,23,9 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 0/1:43,39:82:99:988,0,1158:29,14,25,14 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 0/1:139,137:276:99:3195,0,3379:74,65,76,61 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 0/1:158,177:335:99:4318,0,3927:82,76,104,73 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 0/1:32,65:97:99:1853,0,873:9,23,18,47 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 0/1:9,5:14:99:163,0,208:4,5,1,4 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 0/1:10,4:14:99:109,0,288:5,5,1,3 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 0/1:12,3:15:87:87,0,385:2,10,0,3 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 0/1:7,8:15:99:226,0,191:4,3,6,2 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 0/1:19,14:33:99:436,0,486:11,8,11,3 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 0/1:58,73:131:99:1723,0,1386:25,33,33,40 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 0/1:18,16:34:99:446,0,435:6,12,4,12 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 0/1:35,28:63:99:725,0,887:21,14,16,12 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 0/1:8,7:15:99:235,0,227:6,2,6,1 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 0/1:15,14:29:99:342,0,427:12,3,9,5 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 0/1:39,42:81:99:1108,0,992:23,16,25,17 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 0/1:46,39:85:99:914,0,1153:26,20,26,13 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 0/1:62,56:118:99:1340,0,1539:36,26,29,27 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 0/1:56,47:103:99:1160,0,1308:26,30,21,26 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 0/1:8,10:18:99:315,0,163:3,5,2,8 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 0/1:32,37:69:99:899,0,812:14,18,15,22 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 0/1:18,18:36:99:536,0,600:3,15,7,11 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 0/1:31,29:60:99:704,0,796:20,11,18,11 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 0/1:48,42:90:99:995,0,1083:27,21,22,20 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 1/1:0,109:109:99:3298,326,0:0,0,53,56 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 1/1:0,37:37:99:1160,111,0:0,0,24,13 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 0/1:28,31:59:99:1208,0,1686:11,17,9,22 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 0/1:28,30:58:99:1208,0,1686:11,17,9,21 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 0/1:25,24:49:99:666,0,629:15,10,16,8 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 0/1:54,34:88:99:818,0,1420:28,26,14,20 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 0/1:25,12:37:99:404,0,633:9,16,0,12 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 0/1:16,4:20:99:107,0,510:3,13,0,4 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 0/1:29,24:53:99:533,0,695:17,12,14,10 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 0/1:37,39:76:99:845,0,1051:20,17,19,20 chr1 236732198 . C A 170.14 PASS AC=1;AF=0.75;AN=2;DP=241;set=variant-variant4-variant5-variant6-variant8-variant11-variant14-variant15-variant17-variant19-variant21-variant22-variant23-variant25-variant28-variant29-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:94:94,0,183:5,0,3,0 chr1 236732199 . A AC,AAC 161.1 PASS AC=1,0;AF=0.684,0.079;AN=2;DP=219;set=variant-variant4-variant5-variant6-variant8-variant11-variant14-variant15-variant19-variant22-variant23-variant25-variant28-variant29-variant37-variant38-variant40-variant43-variant44 GT:DP:GQ:SB 0/1:8:94:5,0,3,0 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 0/1:47,51:98:99:1534,0,1201:27,20,28,23 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 0/1:28,30:58:99:787,0,769:21,7,21,9 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 0/1:26,18:44:99:457,0,672:17,9,11,7 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 0/1:6,11:17:99:260,0,121:4,2,8,3 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 0/1:5,5:10:99:145,0,125:1,4,1,4 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 0/1:30,40:70:99:1045,0,734:12,18,18,22 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 0/1:23,29:52:99:815,0,518:11,12,17,12 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 0/1:66,92:158:99:2076,0,1322:28,38,43,49 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 0/1:41,23:64:99:683,0,1154:11,30,4,19 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 0/1:7,6:13:99:219,0,289:1,6,0,6 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 0/1:7,6:13:99:222,0,256:1,6,0,6 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 0/1:8,3:11:99:102,0,492:6,2,3,0 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 0/1:8,3:11:59:59,0,518:6,2,3,0 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 0/1:7,9:16:99:316,0,212:1,6,1,8 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 0/1:2,5:7:99:204,0,145:1,1,4,1 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 0/1:34,43:77:99:1076,0,688:18,16,21,22 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 0/1:16,16:32:99:380,0,375:8,8,6,10 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 0/1:9,10:19:99:348,0,306:2,7,2,8 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 0/1:14,21:35:99:540,0,444:12,2,15,6 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 0/1:23,17:40:99:488,0,571:8,15,3,14 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 0/1:1,3:4:34:114,0,34:1,0,3,0 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 0/1:26,13:39:99:483,0,1466:17,9,9,4 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 0/1:32,13:45:99:426,0,1590:20,12,8,5 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 0/1:15,12:27:99:258,0,335:6,9,3,9 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 0/1:19,9:28:99:225,0,632:16,3,7,2 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 0/1:28,17:45:99:365,0,844:21,7,11,6 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 0/1:6,4:10:99:143,0,221:0,6,0,4 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 0/1:30,61:91:99:1416,0,624:15,15,29,32 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 0/1:8,12:20:99:407,0,195:2,6,9,3 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 0/1:6,9:15:99:267,0,187:1,5,2,7 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 0/1:26,13:39:99:518,0,1519:17,9,10,3 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 0/1:29,16:45:99:515,0,1547:20,9,12,4 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 0/1:56,40:96:99:891,0,1330:26,30,17,23 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 0/1:22,23:45:99:591,0,533:8,14,8,15 chr1 236881403 . C T 406.52 PASS AC=1;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 0/1:6,6:12:99:135,0,192:1,5,2,4 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 1/1:0,90:90:99:2768,270,0:0,0,57,33 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 1/1:0,67:67:99:2268,201,0:0,0,20,47 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 1/1:0,13:13:39:496,39,0:0,0,11,2 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 1/1:0,66:66:99:1860,197,0:0,0,39,27 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 1/1:0,110:110:99:3393,329,0:0,0,49,61 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 1/1:0,25:25:75:915,75,0:0,0,5,20 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 1/1:0,18:18:54:670,54,0:0,0,13,5 chr1 236894647 . G A 1666.77 PASS AC=1;AF=0.596;AN=2;DP=3301;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant21-variant22-variant23-variant31-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,62:115:99:1564,0,1304:21,32,26,36 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 1/1:0,52:52:99:1545,154,0:0,0,36,16 chr1 236899042 . G A 3229.74 PASS AC=1;AF=0.571;AN=2;DP=4139;MQ=60;set=variant-variant6-variant7-variant9-variant11-variant15-variant22-variant23-variant24-variant31-variant32-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:130,110:240:99:2485,0,3435:56,74,53,57 chr1 236899899 . TC T 2870.98 PASS AC=1;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 0/1:42,50:92:99:1324,0,1091:16,26,19,31 chr1 236900018 . G A 702.27 PASS AC=1;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 0/1:7,10:17:99:308,0,214:1,6,2,8 chr1 236900598 . C T 139.61 PASS AC=1;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 0/1:9,5:14:99:149,0,236:3,6,0,5 chr1 236902560 . C T,G 2293.48 PASS AC=1,0;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 0/1:60:99:15,9,21,15 chr1 236902594 . C G 4104.2 PASS AC=1;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 0/1:31,54:85:99:1348,0,758:18,13,30,24 chr1 236902865 . A C 3858.13 PASS AC=1;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 0/1:85,69:154:99:1606,0,2176:41,44,33,36 chr1 236902955 . T C 3131.02 PASS AC=1;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 0/1:67,45:112:99:1115,0,1668:28,39,20,25 chr1 236910863 . T C 56.41 PASS AC=1;AF=0.65;AN=2;DP=176;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant15-variant20-variant22-variant23-variant24-variant25-variant31-variant32-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:99:151,0,112:3,0,2,2 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 1/1:0,10:10:30:442,30,0:0,0,10,0 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 1/1:0,15:15:45:570,45,0:0,0,13,2 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 1/1:2,69:71:99:2191,164,0:1,1,32,37 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 3/3:5:15:0,0,1,4 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 1/1:0,5:5:15:187,15,0:0,0,1,4 chr1 236925844 . G A 2136.61 PASS AC=1;AF=0.538;AN=2;DP=2294;MQ=60;set=variant3-variant5-variant6-variant10-variant12-variant16-variant20-variant22-variant23-variant25-variant33-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:70,65:135:99:1604,0,1695:35,35,34,31 chr1 236926030 . A G 1320.86 PASS AC=1;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 0/1:54,58:112:99:1603,0,1377:29,25,32,26 chr1 236926366 . C G 3893.62 PASS AC=1;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 0/1:177,125:302:99:3253,0,4575:90,87,61,64 chr1 236926445 . T C 4008.94 PASS AC=1;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 0/1:181,137:318:99:3475,0,4553:84,97,69,68 chr1 236926643 . G C 1502.17 PASS AC=1;AF=0.538;AN=2;DP=1097;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant10-variant12-variant16-variant20-variant22-variant23-variant25-variant33-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:44,51:95:99:1473,0,1318:10,34,16,35 chr1 236926667 . A G 721.39 PASS AC=1;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 0/1:39,29:68:99:887,0,1211:13,26,4,25 chr1 236958532 . G T 347.39 PASS AC=1;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 0/1:21,22:43:99:508,0,601:13,8,14,8 chr1 236978992 . T TTCTG 580.66 PASS AC=1;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 0/1:23,12:35:99:435,0,1357:5,18,4,8 chr1 236987790 . G T 185.88 PASS AC=1;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 0/1:6,14:20:99:405,0,151:1,5,5,9 chr1 236988593 . A AT 359.72 PASS AC=1;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 0/1:18,29:47:99:833,0,418:10,8,21,8 chr1 237001926 . A G 503.99 PASS AC=1;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 0/1:35,27:62:99:652,0,819:15,20,9,18 chr1 237002032 . A C 105.22 PASS AC=1;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 0/1:5,7:12:99:200,0,151:1,4,1,6 chr1 237013550 . AT A 40.69 PASS AC=1;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 0/1:1,3:4:96:120,0,96:1,0,2,1 chr1 237013553 . T A 49.73 PASS AC=1;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 0/1:2,3:5:96:120,0,96:2,0,2,1 chr1 237023333 . T C 139.14 PASS AC=1;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 0/1:9,5:14:99:180,0,310:2,7,0,5 chr1 237037998 . CTTT CTT,CT,C 143.27 PASS AC=1,0,0;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 0/1:21:99:6,2,8,5 chr1 237038008 . T A 211.25 PASS AC=1;AF=0.5;AN=2;DP=323;MQ=60;set=variant5-variant7-variant9-variant11-filterInvariant13-variant15-variant18-variant19-variant2-variant23 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:218,0,440:9,3,7,5 chr1 237038161 . T C 4306.15 PASS AC=1;AF=0.661;AN=2;DP=4069;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant27-variant30-variant31-variant32-variant34-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,72:153:99:1684,0,1721:39,42,33,39 chr1 237048562 . G A 186.13 PASS AC=1;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 0/1:19,16:35:99:420,0,508:6,13,5,11 chr1 237049879 . C T 722.7 PASS AC=1;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 0/1:24,19:43:99:470,0,652:8,16,6,13 chr1 237054569 . A G 1106.71 PASS AC=1;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 0/1:51,32:83:99:738,0,1166:25,26,14,18 chr1 237057608 . G A 465.02 PASS AC=1;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 0/1:34,33:67:99:837,0,832:22,12,22,11 chr1 237058622 . G A 1270.37 PASS AC=1;AF=0.5;AN=2;DP=217;FractionInformativeReads=1;MQ=60;set=variant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:41,59:100:99:1476,0,965:24,17,36,23 chr1 237058744 . C A 2037.59 PASS AC=1;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 0/1:92,89:181:99:1961,0,2327:43,49,42,47 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 0/1:56,65:121:99:1661,0,1485:25,31,30,35 chr1 237058996 . C CTATT 508.33 PASS AC=1;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 0/1:23,18:41:99:684,0,1329:8,15,6,12 chr1 237060433 . G T 1046.6 PASS AC=1;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 0/1:46,63:109:99:1505,0,1154:13,33,27,36 chr1 237061056 . A C 574.95 PASS AC=1;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 0/1:36,32:68:99:938,0,1061:16,20,12,20 chr1 237062198 . A C 314.8 PASS AC=1;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 0/1:16,15:31:99:422,0,485:11,5,10,5 chr1 237062305 . A G 1903.77 PASS AC=1;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 0/1:72,87:159:99:1982,0,1803:45,27,52,35 chr1 237063335 . G C 3318.72 PASS AC=1;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 0/1:123,118:241:99:2955,0,3173:62,61,56,62 chr1 237063504 . A G 2950.44 PASS AC=1;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 0/1:111,141:252:99:3418,0,3005:58,53,77,64 chr1 237063709 . T TA,TAA 1238.61 PASS AC=1,0;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 0/1:125:99:24,41,25,35 chr1 237063717 . AAG A 4575.3 PASS AC=1;AF=0.661;AN=2;DP=3670;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant25-variant27-variant30-variant31-variant32-variant34-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,67:128:99:2573,0,2353:25,36,25,42 chr1 237064626 . T G 583.29 PASS AC=1;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 0/1:7,10:17:99:269,0,162:3,4,6,4 chr1 237065326 . C T 682.02 PASS AC=1;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 0/1:51,37:88:99:789,0,1333:26,25,21,16 chr1 237065583 . G T 906.82 PASS AC=1;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 0/1:33,23:56:99:673,0,930:9,24,7,16 chr1 237433524 . C T 772.66 PASS AC=1;AF=0.5;AN=2;DP=524;FractionInformativeReads=1;MQ=60;set=variant3-variant12-variant15-variant19-variant23-variant26-variant31-variant39 GT:AD:DP:GQ:PL:SB 0/1:25,30:55:99:685,0,638:16,9,15,15 chr1 237433625 . C T 769.9 PASS AC=2;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 1/1:0,51:51:99:1595,152,0:0,0,23,28 chr1 237504818 . A G 1496.67 PASS AC=1;AF=0.5;AN=2;DP=120;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.773;QD=12.47;ReadPosRankSum=0.983;SOR=0.734;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:57,63:120:99:1525,0,1415:32,25,36,27 chr1 237516046 . G A 674.81 PASS AC=1;AF=0.5;AN=2;DP=49;FS=6.054;FractionInformativeReads=1;MQ=60;MQRankSum=-0.231;QD=13.77;ReadPosRankSum=0.492;SOR=0.229;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:22,27:49:99:703,0,569:16,6,15,12 chr1 237527551 . A G 741.26 PASS AC=1;AF=0.5;AN=2;DP=182;MQ=60;set=variant10-variant16-variant23-variant31 GT:AD:DP:GQ:PL:SB 0/1:22,27:49:99:626,0,520:13,9,16,11 chr1 237551241 . G GTC 688.29 PASS AC=1;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 0/1:20,18:38:99:683,0,733:14,6,12,6 chr1 237551376 . T A 1216.98 PASS AC=1;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 0/1:41,60:101:99:1504,0,953:19,22,31,29 chr1 237580606 . G T 376.77 PASS AC=1;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 0/1:1,4:5:76:156,0,76:0,1,0,4 chr1 237580612 . G C 376.77 PASS AC=1;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 0/1:1,2:3:80:123,0,80:0,1,0,2 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 0/1:33,40:73:99:935,0,784:19,14,24,16 chr1 237619875 . AT ATT,A,ATTT 538.87 PASS AC=1,0,0;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 0/1:109:99:33,16,36,24 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 0/1:70,51:121:99:1299,0,1934:23,47,19,32 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 0/1:6,9:15:99:319,0,198:6,0,9,0 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 0/1:6,4:10:99:150,0,251:0,6,0,4 chr1 237634229 . A G 286.83 PASS AC=1;AF=0.611;AN=2;DP=819;MQ=60;set=variant-variant4-variant5-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant23-variant24-variant28-variant32-variant33-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,13:34:99:261,0,651:17,4,8,5 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 1/1:0,21:21:63:773,63,0:0,0,17,4 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 1/1:13:45:0,0,13,0 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 1/1:0,16:16:48:694,48,0:0,0,15,1 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 1/1:1,123:124:99:3685,331,0:1,0,64,59 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 1/1:0,56:56:99:2268,168,0:0,0,5,51 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 1/1:0,28:28:84:1152,84,0:0,0,1,27 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 1/1:0,26:26:78:1050,78,0:0,0,23,3 chr1 237796850 . A G 589.81 PASS AC=1;AF=0.5;AN=2;DP=203;FractionInformativeReads=1;MQ=60;set=variant23-variant29-variant39 GT:AD:DP:GQ:PL:SB 0/1:32,27:59:99:618,0,919:20,12,14,13 chr1 237798414 . G A 526.57 PASS AC=1;AF=0.5;AN=2;DP=42;FS=5.887;FractionInformativeReads=1;MQ=60;MQRankSum=0.597;QD=12.54;ReadPosRankSum=3.215;SOR=1.994;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:24,18:42:99:555,0,632:7,17,2,16 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 1/1:0,161:161:99:4919,482,0:0,0,62,99 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 1/1:0,60:60:99:1820,180,0:0,0,24,36 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 0/1:7,2:9:63:63,0,211:6,1,2,0 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 0/1:39,24:63:99:575,0,1171:15,24,9,15 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 0/1:7,4:11:99:125,0,256:0,7,0,4 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 0/1:44,38:82:99:798,0,899:23,21,21,17 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 1/1:0,8:8:24:276,24,0:0,0,2,6 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 1/1:0,15:15:45:461,45,0:0,0,10,5 chr1 237850643 . G GT 101.33 PASS AC=1;AF=0.5;AN=2;DP=12;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.378;QD=8.44;ReadPosRankSum=1.813;SOR=0.693;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:139,0,205:4,2,4,2 chr1 237850666 . C CT,CTT 594.53 PASS AC=0,1;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 0/2:18:99:5,5,4,4 chr1 237862164 . G C 1577.79 PASS AC=1;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 0/1:22,18:40:99:422,0,610:16,6,11,7 chr1 237863439 . G A 1416.83 PASS AC=1;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 0/1:11,11:22:99:305,0,269:9,2,8,3 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 1/1:0,74:74:99:2397,222,0:0,0,30,44 chr1 237863790 . G GT 42.47 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=95;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:30,7:37:67:67,0,674:10,20,1,6 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 1/1:0,53:53:99:1790,159,0:0,0,39,14 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 1/1:1,17:18:43:410,43,0:1,0,14,3 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 1/1:0,89:89:99:2463,266,0:0,0,43,46 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 1/1:0,183:183:99:5453,548,0:0,0,89,94 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 1/1:0,44:44:99:1212,131,0:0,0,21,23 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 0/1:8,8:16:99:146,0,173:5,3,6,2 chr1 237905571 . T C 37.14 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=19;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.898;QD=1.95;ReadPosRankSum=-1.25;SOR=0.495;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:14,5:19:65:65,0,326:9,5,3,2 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 2/1:25:99:0,1,4,20 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 0/1:19,12:31:99:401,0,709:5,14,2,10 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 0/1:19,11:30:99:401,0,709:5,14,2,9 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 0/1:10:99:1,3,0,6 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 0/1:9,13:22:99:351,0,222:7,2,9,4 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 0/1:12,17:29:99:423,0,304:8,4,11,6 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 0/1:29,31:60:99:769,0,705:13,16,16,15 chr1 237958750 . A AT 64.96 PASS AC=1;AF=0.727;AN=2;DP=545;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant14-variant17-variant18-filterInvariant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,5:6:9:106,0,9:0,1,1,4 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 0/1:4,6:10:99:199,0,153:3,1,4,2 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 0/1:39,18:57:99:618,0,1611:20,19,11,7 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 0/1:43,20:63:99:688,0,1688:21,22,12,8 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 0/1:46,30:76:99:730,0,1075:23,23,17,13 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 0/1:35,34:69:99:869,0,883:15,20,20,14 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 0/1:61:99:17,18,14,12 chr1 237993724 . C T 710.87 PASS AC=1;AF=0.618;AN=2;DP=271;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant11-variant13-variant16-variant17-variant22-variant23-variant24-variant25-variant27-variant28-variant32-variant36-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:189,0,229:6,0,5,0 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 0/1:33:7:0,4,12,17 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 0/1:10,7:17:99:101,0,165:4,6,1,6 chr1 237996734 . C A 247.85 PASS AC=1;AF=0.5;AN=2;DP=53;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant39 GT:AD:DP:GQ:PL:SB 0/1:16,9:25:99:276,0,507:11,5,7,2 chr1 237996834 . G GAAAC 3913.8 PASS AC=1;AF=0.579;AN=2;DP=1972;MQ=60;set=variant7-variant8-variant10-variant12-variant15-variant17-variant18-variant20-variant21-variant23-variant27-variant29-variant31-variant32-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,55:102:99:2167,0,2575:31,16,29,26 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 0/1:192,149:341:99:3516,0,5142:101,91,83,66 chr1 238048325 . A G 1300.54 PASS AC=2;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 1/1:0,42:42:99:1181,125,0:0,0,23,19 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 0/1:24,12:36:99:117,0,659:2,22,12,0 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 0/1:24,9:33:99:117,0,659:2,22,9,0 chr1 238107361 . C T 54.21 PASS AC=2;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 1/1:0,9:9:27:280,27,0:0,0,5,4 chr1 238108482 . C T 3102.8 PASS AC=2;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 1/1:0,194:194:99:5742,580,0:0,0,114,80 chr1 240072721 . G GAA,GAAA 4067.09 PASS AC=0,2;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 2/2:33:97:0,0,12,21 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 0/1:83,90:173:99:2176,0,2140:39,44,39,51 chr1 240073619 . G A 1014.68 PASS AC=1;AF=0.625;AN=2;DP=600;MQ=60;set=variant3-variant4-variant7-variant9-variant10-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:361,0,321:3,9,2,10 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 0/1:58:99:17,14,13,14 chr1 240075424 . ATC A 30.45 PASS AC=1;AF=0.5;AN=2;DP=563;MQ=60;set=filterInvariant-variant7-filterInvariant11-filterInvariant18-filterInvariant23-filterInvariant24-filterInvariant31-filterInvariant34 GT:AD:DP:GQ:PL:SB 0/1:34,5:39:72:72,0,1147:9,25,2,3 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 0/1:18,13:31:99:388,0,432:8,10,5,8 chr1 240255568 . GGGC G 1502.47 PASS AC=1;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 0/1:36,14:50:99:126,0,1359:22,14,10,4 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 0/1:59,62:121:99:1734,0,1558:20,39,19,43 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 0/1:103,85:188:99:1999,0,2760:43,60,41,44 chr1 240371075 . C T 121.08 PASS AC=1;AF=0.5;AN=2;DP=116;set=variant-variant2-variant11-variant13-variant18-variant23-variant32-filterInvariant33-variant36 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:99:108,0,278:1,4,0,3 chr1 240371085 . A T 165.27 PASS AC=1;AF=0.563;AN=2;DP=83;set=variant-variant2-variant11-variant13-variant18-variant23-variant30-variant32 GT:AD:DP:GQ:PL:SB 0/1:5,2:7:69:69,0,281:1,4,0,2 chr1 240408572 . C G 698.13 PASS AC=1;AF=0.673;AN=2;DP=537;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant13-variant16-variant19-variant21-variant23-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,18:29:99:491,0,299:9,2,11,7 chr1 240408789 . G A 1060.21 PASS AC=1;AF=0.563;AN=2;DP=602;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant23-variant25-variant30-variant38-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,32:64:99:779,0,802:17,15,18,14 chr1 240421383 . G A 1612.52 PASS AC=2;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 1/1:0,37:37:99:1286,110,0:0,0,8,29 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 0/1:3,10:13:86:332,0,86:0,3,1,9 chr1 240448434 . G T 831.22 PASS AC=1;AF=0.5;AN=2;DP=701;MQ=60;set=variant-variant6-variant23-variant25-variant28-variant34-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,37:76:99:813,0,1089:25,14,23,14 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 1/1:0,66:66:99:2404,198,0:0,0,23,43 chr1 240492734 . G A 2008.37 PASS AC=2;AF=0.625;AN=2;DP=3865;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-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,124:124:99:3585,369,0:0,0,64,60 chr1 240492952 . G C 281.81 PASS AC=2;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 1/1:0,14:14:42:427,42,0:0,0,5,9 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 1/1:0,52:52:99:1550,156,0:0,0,30,22 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 0/1:3,10:13:69:327,0,69:0,3,3,7 chr1 240519251 . CAAAAAAAAAAAAAAAAAAAAA CA,CAA,C,CAAA 360.19 PASS AC=0,1,0,0;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 0/2:19:99:2,4,2,11 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 1/1:0,19:19:57:675,57,0:0,0,15,4 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 1/1:0,9:9:27:316,27,0:0,0,7,2 chr1 240635747 . T G 294.84 PASS AC=1;AF=0.5;AN=2;DP=103;FractionInformativeReads=1;MQ=60;set=variant17-variant23-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,26:33:96:678,0,96:3,4,9,17 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 0/1:19,20:39:99:687,0,548:15,4,18,2 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 0/1:27,33:60:99:816,0,608:10,17,15,18 chr1 240655330 . G A 901.88 PASS AC=1;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 0/1:20,29:49:99:870,0,470:11,9,15,14 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 0/1:25,29:54:99:689,0,684:12,13,14,15 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 0/1:21,31:52:99:971,0,848:8,13,10,21 chr1 240656841 . A T 609.41 PASS AC=1;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 0/1:21,27:48:99:1020,0,847:8,13,10,17 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 1/1:0,32:32:96:919,96,0:0,0,20,12 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 0/1:43,29:72:99:666,0,1069:27,16,16,13 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 0/1:22,10:32:99:256,0,691:4,18,2,8 chr1 240977964 . G T 1021.91 PASS AC=1;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 0/1:11,12:23:99:304,0,266:7,4,9,3 chr1 240979803 . G A 151.77 PASS AC=1;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 0/1:1,4:5:21:165,0,21:0,1,0,4 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 0/1:1,6:7:21:188,0,21:1,0,1,5 chr1 241146322 . A G 1639.37 PASS AC=1;AF=0.635;AN=2;DP=1321;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant28-variant30-variant31-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,19:41:99:422,0,502:11,11,11,8 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 1/1:0,66:66:99:1981,197,0:0,0,30,36 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 1/1:0,65:65:99:1856,194,0:0,0,38,27 chr1 241663902 . TGAGA TGAGAGA,TGAGAGAGA,TGAGAGAGAGA,TGA,TGAGAGAGAGAGAGAGAGA,TGAGAGAGAGAGA,TGAGAGAGAGAGAGAGA,TGAGAGAGAGAGAGA,T 991.71 PASS AC=0,0,1,0,0,0,0,0,0;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 0/3:50:99:7,19,8,16 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 0/1:17,12:29:99:328,0,518:14,3,9,3 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 1/1:0,37:37:99:1189,110,0:0,0,29,8 chr1 241667523 . C T 483.96 PASS AC=1;AF=0.5;AN=2;DP=171;MQ=60;set=variant15-variant16-variant23-variant24 GT:AD:DP:GQ:PL:SB 0/1:20,18:38:99:457,0,573:5,15,6,12 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 0/1:10,3:13:93:93,0,320:8,2,3,0 chr1 241676758 . C T 688.9 PASS AC=2;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 1/1:0,56:56:99:1711,168,0:0,0,36,20 chr1 241677035 . T A 695.6 PASS AC=1;AF=0.5;AN=2;DP=225;FractionInformativeReads=1;MQ=60;set=variant15-variant16-variant23-variant24 GT:AD:DP:GQ:PL:SB 0/1:22,28:50:99:837,0,600:7,15,7,21 chr1 241695792 . T C 1155.11 PASS AC=1;AF=0.5;AN=2;DP=321;FractionInformativeReads=1;MQ=60;set=variant15-variant16-variant23-variant24 GT:AD:DP:GQ:PL:SB 0/1:28,21:49:99:474,0,809:7,21,9,12 chr1 241695845 . C G 709.9 PASS AC=1;AF=0.5;AN=2;DP=158;FractionInformativeReads=1;MQ=60;set=variant15-variant16-variant23-variant24 GT:AD:DP:GQ:PL:SB 0/1:9,13:22:99:335,0,295:1,8,4,9 chr1 241712134 . C T 1201.5 PASS AC=1;AF=0.62;AN=2;DP=1305;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant12-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant30-variant31-variant33-variant34-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,34:58:99:696,0,659:15,9,18,16 chr1 241728198 . A G 1221.18 PASS AC=1;AF=0.5;AN=2;DP=910;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant8-variant13-variant16-variant19-variant20-variant21-variant22-variant23-variant29-variant36 GT:AD:DP:GQ:PL:SB 0/1:36,35:71:99:943,0,787:23,13,24,11 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 1/1:0,6:6:18:264,18,0:0,0,5,1 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 1/1:0,11:11:33:406,33,0:0,0,2,9 chr1 241755567 . T C 2919.78 PASS AC=1;AF=0.5;AN=2;DP=3015;MQ=60;set=variant5-variant7-variant8-variant16-variant19-variant20-variant21-variant22-variant23-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:125,113:238:99:2828,0,3073:64,61,62,51 chr1 241757409 . T TA 5442.47 PASS AC=1;AF=0.533;AN=2;DP=4509;MQ=60;set=variant-variant2-variant4-variant10-variant14-variant15-variant22-variant23-variant24-variant26-variant31-variant33-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:122,138:260:99:4307,0,3741:51,71,57,81 chr1 241758566 . G C 837.23 PASS AC=1;AF=0.5;AN=2;DP=793;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant8-variant16-variant19-variant20-variant21-variant22-variant23-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:43,28:71:99:1026,0,2137:20,23,11,17 chr1 241758568 . A G 997.63 PASS AC=1;AF=0.5;AN=2;DP=67;FS=3.4;FractionInformativeReads=1;MQ=60;MQRankSum=-0.134;QD=14.89;ReadPosRankSum=-2.346;SOR=1.167;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:40,27:67:99:1026,0,2137:19,21,10,17 chr1 241758631 . A G 1420.98 PASS AC=1;AF=0.528;AN=2;DP=1823;MQ=60;set=variant4-variant5-variant7-variant8-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant36-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:61,41:102:99:1150,0,1716:38,23,29,12 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 1/1:0,86:86:99:2611,258,0:0,0,37,49 chr1 241792562 . A G 4475.23 PASS AC=1;AF=0.5;AN=2;DP=4360;MQ=60;set=variant2-variant11-variant13-variant15-variant16-variant18-variant23-variant28-variant31-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:197,183:380:99:4467,0,4900:95,102,85,98 chr1 241793326 . A G 9112.89 PASS AC=1;AF=0.577;AN=2;DP=3772;MQ=60;set=variant4-variant5-variant10-variant14-variant15-variant16-variant19-variant21-variant22-variant23-variant31-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:111,117:228:99:3233,0,2846:47,64,57,60 chr1 241794056 . C A 4423.55 PASS AC=1;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 0/1:110,113:223:99:2972,0,2997:53,57,45,68 chr1 241794231 . C T 2863.38 PASS AC=1;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 0/1:148,77:225:99:1805,0,3962:73,75,40,37 chr1 241795123 . G A 573.22 PASS AC=1;AF=0.5;AN=2;DP=689;MQ=60;set=variant2-variant11-variant13-variant15-variant16-variant18-variant23-variant28-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:30,31:61:99:852,0,836:18,12,17,14 chr1 241795972 . C T 2374.03 PASS AC=1;AF=0.5;AN=2;DP=1684;MQ=60;set=variant11-variant13-variant16-variant18-variant23-variant28-variant31-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:96,78:174:99:2102,0,2564:49,47,39,39 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 1/1:0,118:118:99:3858,354,0:0,0,60,58 chr1 241796443 . T C 4618.69 PASS AC=1;AF=0.607;AN=2;DP=6016;MQ=60;set=variant2-variant4-variant5-variant10-variant14-variant15-variant16-variant19-variant21-variant22-variant23-variant31-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:180,171:351:99:3898,0,4284:92,88,87,84 chr1 241798631 . C T 2095.45 PASS AC=2;AF=0.684;AN=2;DP=3739;MQ=60;set=variant2-variant4-variant5-variant10-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant28-variant31-variant36-variant37-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,176:176:99:5555,528,0:0,0,95,81 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 1/1:0,18:18:54:694,54,0:0,0,10,8 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 1/1:0,20:20:60:842,60,0:0,0,10,10 chr1 241803672 . G A 477.26 PASS AC=1;AF=0.5;AN=2;DP=251;FractionInformativeReads=1;MQ=60;set=variant11-variant13-variant16-variant23-variant28-variant31-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,6:18:99:147,0,299:6,6,3,3 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 1/1:0,19:19:57:605,57,0:0,0,6,13 chr1 241838057 . C T 3417.3 PASS AC=1;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 0/1:24,24:48:99:908,0,1197:10,14,7,17 chr1 241838065 . T C 3334.16 PASS AC=1;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 0/1:20,23:43:99:895,0,1070:8,12,7,16 chr1 241847018 . C T,G 121.7 PASS AC=1,0;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 0/1:13:99:0,6,1,6 chr1 241850657 . T C 594.21 PASS AC=1;AF=0.583;AN=2;DP=125;FractionInformativeReads=1;MQ=60;set=variant15-variant23-variant28-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,10:15:99:383,0,177:5,0,10,0 chr1 241850713 . T C 416.71 PASS AC=1;AF=0.5;AN=2;DP=276;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant13-variant23-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:30,18:48:99:412,0,751:19,11,12,6 chr1 241875326 . T C 450.02 PASS AC=1;AF=0.545;AN=2;DP=757;MQ=60;set=variant2-variant5-variant6-variant7-variant9-variant10-variant12-variant15-variant16-variant20-variant21-variant22-variant23-variant26-variant27-variant30-variant31-variant32-variant34-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,17:38:99:407,0,658:5,16,6,11 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 0/1:32,35:67:99:939,0,789:17,15,19,16 chr1 241907948 . T C 134.64 PASS AC=1;AF=0.542;AN=2;DP=262;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant9-variant10-variant12-variant15-variant16-variant21-variant23-variant31-variant34-variant36 GT:AD:DP:GQ:PL:SB 0/1:17,14:31:99:428,0,462:5,12,2,12 chr1 241920562 . C T 553.09 PASS AC=1;AF=0.542;AN=2;DP=574;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant9-variant10-variant12-variant15-variant16-variant21-variant23-variant31-variant34-variant36 GT:AD:DP:GQ:PL:SB 0/1:23,16:39:99:389,0,610:16,7,10,6 chr1 241929542 . G A 976.5 PASS AC=1;AF=0.583;AN=2;DP=1550;MQ=60;set=variant6-variant7-variant9-variant10-variant12-variant15-variant16-variant21-variant23-variant31-variant34-variant36 GT:AD:DP:GQ:PL:SB 0/1:52,66:118:99:1433,0,1168:29,23,33,33 chr1 241935987 . AC A 424.37 PASS AC=1;AF=0.583;AN=2;DP=448;set=variant-variant2-variant3-variant8-variant12-variant15-variant17-variant19-variant23-variant24-variant28-variant29-variant30-variant32-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,13:24:99:454,0,372:10,1,12,1 chr1 241936055 . A G 955.09 PASS AC=1;AF=0.583;AN=2;DP=1035;set=variant6-variant7-variant9-variant10-variant12-variant15-variant16-variant21-variant23-variant31-variant34-variant36 GT:AD:DP:GQ:PL:SB 0/1:55,38:93:99:1018,0,1376:32,23,26,12 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 0/1:38,33:71:99:753,0,1138:10,28,10,23 chr1 241951034 . C T 140.9 PASS AC=2;AF=0.654;AN=2;DP=516;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant19-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:50:519,50,0:0,0,13,4 chr1 241951106 . A G 1323.61 PASS AC=2;AF=0.648;AN=2;DP=2314;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant19-variant21-variant23-variant24-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:2017,174,0:0,0,43,15 chr1 241951329 . C T 534.97 PASS AC=1;AF=0.583;AN=2;DP=547;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant9-variant10-variant12-variant15-variant16-variant21-variant23-variant31-variant34-variant36 GT:AD:DP:GQ:PL:SB 0/1:18,15:33:99:438,0,615:2,16,5,10 chr1 241958401 . C CTTGT 1214.25 PASS AC=1;AF=0.583;AN=2;DP=695;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant8-variant12-variant15-variant17-variant19-variant23-variant24-variant28-variant29-variant30-variant32-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,19:33:99:756,0,1320:12,2,16,3 chr1 241958409 . C T 1324.15 PASS AC=1;AF=0.583;AN=2;DP=841;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant8-variant12-variant15-variant17-variant19-variant23-variant24-variant28-variant29-variant30-variant32-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,23:42:99:847,0,1435:14,5,18,5 chr1 242011406 . T C 106.77 PASS AC=2;AF=0.797;AN=2;DP=537;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:472,45,0:0,0,9,6 chr1 242011534 . A G 654.11 PASS AC=2;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 1/1:0,52:52:99:1583,156,0:0,0,29,23 chr1 242012033 . G A 652.91 PASS AC=2;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 1/1:0,46:46:99:1525,138,0:0,0,34,12 chr1 242012149 . C T 2955.56 PASS AC=1;AF=0.633;AN=2;DP=5639;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:90,88:178:99:2152,0,2267:56,34,51,37 chr1 242012554 . C T 85.66 PASS AC=2;AF=0.661;AN=2;DP=613;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:602,57,0:0,0,6,13 chr1 242013592 . A AC 314.93 PASS AC=2;AF=0.661;AN=2;DP=1464;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1590,136,0:0,0,34,10 chr1 242015820 . A G 115.66 PASS AC=2;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 1/1:0,15:15:45:513,45,0:0,0,4,11 chr1 242016838 . T C 543.3 PASS AC=1;AF=0.5;AN=2;DP=184;FractionInformativeReads=1;MQ=60;set=variant23-variant26-variant31-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,22:38:99:572,0,374:7,9,10,12 chr1 242020495 . C T 689.09 PASS AC=2;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 1/1:0,29:29:87:1023,87,0:0,0,22,7 chr1 242030151 . A G 1117.66 PASS AC=2;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 1/1:0,88:88:99:2901,264,0:0,0,55,33 chr1 242030483 . A G 169.17 PASS AC=1;AF=0.5;AN=2;DP=41;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant26-variant31-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:99:197,0,107:0,3,2,5 chr1 242035673 . A G 163.22 PASS AC=1;AF=0.5;AN=2;DP=79;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant15-variant17-variant23-variant24-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:213,0,267:2,7,2,6 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 0/1:54,47:101:99:1313,0,1367:27,27,24,23 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 0/1:48,41:89:99:951,0,1085:26,22,23,18 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 0/1:20,15:35:99:373,0,522:7,13,4,11 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 1/1:0,116:116:99:3418,347,0:0,0,57,59 chr1 242048514 . G GTAAA,GTAAATAAA,GTAAATAAATAAA 148.84 PASS AC=1,0,0;AF=0.362,0.534,0.052;AN=2;DP=124;FS=0;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:4:23:1,0,2,1 chr1 242048945 . C T 71.28 PASS AC=1;AF=0.75;AN=2;DP=118;FractionInformativeReads=1;set=variant-variant6-variant7-variant10-variant12-variant13-variant14-variant16-variant17-variant19-variant21-variant23-variant24-variant25-variant27-variant28-variant30-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:77:183,0,77:1,2,0,5 chr1 242053042 . A G 6341.63 PASS AC=2;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 1/1:0,157:157:99:4772,470,0:0,0,73,84 chr1 242120914 . G A 285.1 PASS AC=2;AF=0.703;AN=2;DP=732;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:788,57,0:0,0,18,1 chr1 242121377 . T G 3235.72 PASS AC=1;AF=0.55;AN=2;DP=2750;MQ=60;set=variant2-variant5-variant7-variant15-variant17-variant23-variant30-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:120,126:246:99:2985,0,2786:69,51,68,58 chr1 242159220 . CA CAA,C 388.17 PASS AC=1,0;AF=0.556,0.028;AN=2;DP=895;MQ=60;set=variant-filterInvariant2-variant5-variant9-variant12-variant14-variant15-variant18-variant23-variant25-variant26-variant27-variant28-variant36-variant37-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:32:99:10,6,11,5 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 1/1:0,6:6:18:214,18,0:0,0,5,1 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 1/1:0,20:20:60:613,60,0:0,0,13,7 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 1/1:0,42:42:99:1189,126,0:0,0,25,17 chr1 242162525 . G A 447.91 PASS AC=1;AF=0.717;AN=2;DP=341;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:67:67,0,182:2,4,1,2 chr1 242252961 . A G 4186.88 PASS AC=1;AF=0.545;AN=2;DP=2837;MQ=60;set=variant-variant6-variant12-variant13-variant16-variant19-variant23-variant31-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:116,162:278:99:3647,0,2406:62,54,80,82 chr1 242383170 . T TAC 581.64 PASS AC=1;AF=0.528;AN=2;DP=877;MQ=60;set=variant4-variant6-variant8-variant13-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant26-variant29-variant32-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,28:54:99:1077,0,994:16,10,18,10 chr1 242383201 . T G 631.09 PASS AC=1;AF=0.528;AN=2;DP=1322;MQ=60;set=variant4-variant6-variant8-variant13-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant26-variant29-variant32-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,39:73:99:1012,0,840:20,14,24,15 chr1 242383510 . T C 602.23 PASS AC=1;AF=0.528;AN=2;DP=455;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant8-variant13-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant26-variant29-variant32-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,14:21:99:447,0,168:1,6,2,12 chr1 242511556 . AACAAAG A 2961.67 PASS AC=2;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 1/1:0,77:77:99:3402,232,0:0,0,25,52 chr1 242612420 . G A 298.83 PASS AC=1;AF=0.639;AN=2;DP=230;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant9-variant10-variant20-variant22-variant23-variant25-variant28-variant29-variant32-variant33-variant36-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:216,0,223:6,0,6,1 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 0/1:78,76:154:99:1791,0,1883:45,33,47,29 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 0/1:9,5:14:99:139,0,265:4,5,2,3 chr1 243217374 . A G 147.54 PASS AC=2;AF=0.895;AN=2;DP=135;FractionInformativeReads=1;set=variant-variant3-filterInvariant4-filterInvariant6-variant8-variant10-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant32-variant36-variant37-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:15:217,15,0:0,0,3,0 chr1 243217395 . A G 227.21 PASS AC=2;AF=0.808;AN=2;DP=380;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant8-variant10-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant27-variant28-filterInvariant29-variant31-variant32-variant36-variant37-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:18:254,18,0:0,0,4,1 chr1 243218685 . T G 362.17 PASS AC=1;AF=0.648;AN=2;DP=572;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant14-variant16-variant18-variant20-variant21-variant23-variant25-variant26-variant28-variant29-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:286,0,261:7,5,6,5 chr1 243218882 . G A 113.43 PASS AC=1;AF=0.55;AN=2;DP=188;FractionInformativeReads=1;set=variant6-variant9-variant10-variant11-variant15-variant17-variant23-variant24-variant27-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:215,0,356:3,10,4,5 chr1 243219400 . T C 251.83 PASS AC=2;AF=0.768;AN=2;DP=342;FractionInformativeReads=1;set=variant-variant3-variant4-filterInvariant6-variant7-variant8-variant9-filterInvariant11-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-filterInvariant24-variant25-variant26-variant29-variant31-filterInvariant32-variant33-variant36-filterInvariant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:348,30,0:0,0,8,2 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 0/1:52,10:62:61:61,0,1562:23,29,5,5 chr1 243291379 . T G 164.17 PASS AC=1;AF=0.538;AN=2;DP=136;FractionInformativeReads=1;set=variant6-variant9-variant10-variant11-variant15-variant17-variant19-variant23-variant24-variant25-variant27-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:216,0,174:5,3,6,1 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 0/1:161,51:212:99:719,0,4562:86,75,23,28 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 0/1:172,36:208:99:337,0,4602:93,79,16,20 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 0/1:5,6:11:99:232,0,177:4,1,5,1 chr1 243362331 . C T 1630.25 PASS AC=1;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 0/1:30,9:39:99:235,0,751:17,13,8,1 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 0/1:26,23:49:99:636,0,722:19,7,18,5 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 0/1:10,8:18:99:262,0,303:1,9,3,5 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 0/1:36,26:62:99:593,0,961:18,18,15,11 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 0/1:23,8:31:99:206,0,752:3,20,0,8 chr1 243578812 . G A 538.6 PASS AC=1;AF=0.688;AN=2;DP=273;FractionInformativeReads=1;MQ=60;set=variant6-variant9-variant15-variant22-variant23-variant24-variant27-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,14:26:99:406,0,345:9,3,11,3 chr1 243668090 . T C 3123.7 PASS AC=1;AF=0.538;AN=2;DP=3084;MQ=60;set=variant-variant3-variant8-variant9-variant10-variant14-variant23-variant26-variant28-variant31-variant33-variant34-variant40 GT:AD:DP:GQ:PL:SB 0/1:105,96:201:99:2221,0,2509:67,38,57,39 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 1/1:0,53:53:99:1658,159,0:0,0,16,37 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 1/1:0,26:26:77:689,77,0:0,0,12,14 chr1 244527857 . T C 752.86 PASS AC=1;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 0/1:18,16:34:99:404,0,536:14,4,11,5 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 1/1:0,40:40:99:1243,120,0:0,0,13,27 chr1 244572581 . T C 1082.37 PASS AC=1;AF=0.571;AN=2;DP=793;MQ=60;set=variant2-variant9-variant14-variant19-variant20-variant21-variant22-variant23-variant28-variant30-variant31-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,18:36:99:543,0,447:10,8,12,6 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 1/1:0,59:59:99:1608,179,0:0,0,32,27 chr1 244579519 . T C 121.48 PASS AC=1;AF=0.559;AN=2;DP=287;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant9-variant14-variant19-variant20-variant21-variant22-variant23-variant28-variant30-variant31-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,10:14:99:344,0,141:0,4,2,8 chr1 244587469 . T C 434.98 PASS AC=1;AF=0.5;AN=2;DP=135;FractionInformativeReads=1;MQ=60;set=variant8-variant13-variant18-variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:15,15:30:99:344,0,410:6,9,8,7 chr1 244601152 . C T 2227.05 PASS AC=1;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 0/1:31,20:51:99:458,0,668:15,16,11,9 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 0/1:23,25:48:99:715,0,606:16,7,19,6 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 0/1:63,41:104:99:1088,0,1534:26,37,14,27 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 0/1:3,4:7:38:78,0,38:3,0,3,1 chr1 244653781 . AT A 1478.57 PASS AC=1;AF=0.5;AN=2;DP=746;MQ=60;set=variant2-variant8-variant9-variant15-variant18-variant22-variant23-variant29-variant30-variant34-variant36 GT:AD:DP:GQ:PL:SB 0/1:24,28:52:99:733,0,576:11,13,14,14 chr1 244773514 . C T 1277.09 PASS AC=1;AF=0.5;AN=2;DP=1306;MQ=60;set=variant3-variant5-variant7-variant9-variant11-variant15-variant17-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant34-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,28:71:99:691,0,1180:30,13,19,9 chr1 244773784 . T C 1170.1 PASS AC=1;AF=0.795;AN=2;DP=1081;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:8,15:23:99:532,0,533:1,7,4,11 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 0/1:8,10:18:99:418,0,545:1,7,3,7 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 1/2:66:99:1,1,39,25 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 0/1:110,96:206:99:3740,0,4899:54,56,44,52 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 1/1:0,16:16:48:498,48,0:0,0,3,13 chr1 244816153 . G GA 96.1 PASS AC=2;AF=0.645;AN=2;DP=494;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant32-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:275,21,0:0,0,4,3 chr1 244869578 . TTTGTTAAAGTTG T 1159.2 PASS AC=1;AF=0.5;AN=2;DP=217;MQ=60;set=variant2-variant14-variant23 GT:AD:DP:GQ:PL:SB 0/1:33,30:63:99:1139,0,1550:16,17,17,13 chr1 244869642 . GCCCTGAGGGCTTGGAA G 1124.3 PASS AC=1;AF=0.5;AN=2;DP=233;MQ=60;set=variant2-variant14-variant23 GT:AD:DP:GQ:PL:SB 0/1:36,30:66:99:1153,0,1653:19,17,18,12 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 0/1:32:55:7,1,18,6 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 0/1:42,46:88:99:1080,0,987:17,25,22,24 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 1/1:0,67:67:99:2544,201,0:0,0,29,38 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 0/1:29,26:55:99:895,0,1037:16,13,10,16 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 0/1:41,34:75:99:1556,0,1539:19,22,12,22 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 0/1:43,64:107:99:1714,0,919:18,25,29,35 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 0/1:33:99:9,4,12,8 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 0/1:24,17:41:99:635,0,1199:8,16,4,13 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 0/1:17,15:32:99:579,0,983:4,13,3,12 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 1/1:0,22:22:66:753,66,0:0,0,16,6 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 1/1:0,81:81:99:2394,243,0:0,0,34,47 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 0/1:51,39:90:99:1356,0,2331:22,29,17,22 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 0/1:41,33:74:99:1235,0,2099:16,25,11,22 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 0/1:105,96:201:99:2572,0,2708:36,69,28,68 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 0/1:6,10:16:99:266,0,143:2,4,3,7 chr1 245286390 . A T 3053.09 PASS AC=1;AF=0.5;AN=2;DP=2208;MQ=60;set=variant3-variant9-variant10-variant13-variant15-variant16-variant17-variant20-variant23-variant27-variant30-variant32-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,52:127:99:1249,0,1777:41,34,33,19 chr1 245287474 . C G 361.23 PASS AC=1;AF=0.5;AN=2;DP=351;MQ=60;set=variant10-variant13-variant16-variant20-variant23-variant30-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:18,11:29:99:263,0,496:10,8,6,5 chr1 245287508 . G A 280.05 PASS AC=1;AF=0.5;AN=2;DP=371;MQ=60;set=variant10-variant13-variant16-variant20-variant23-variant30-variant36-variant37 GT:AD:DP:GQ:PL:SB 0/1:15,17:32:99:429,0,449:7,8,11,6 chr1 245287592 . A G 1025.26 PASS AC=1;AF=0.5;AN=2;DP=1287;MQ=60;set=variant3-variant5-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant23-variant27-variant30-variant32-variant36-variant37-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,33:53:99:769,0,490:11,9,16,17 chr1 245288239 . G A 1589.1 PASS AC=1;AF=0.5;AN=2;DP=947;MQ=60;set=variant3-variant9-variant10-variant13-variant15-variant16-variant17-variant20-variant23-variant27-variant30-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,29:43:99:785,0,264:9,5,17,12 chr1 245288493 . A G 1755.57 PASS AC=1;AF=0.5;AN=2;DP=1911;MQ=60;set=variant3-variant5-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant23-variant27-variant30-variant32-variant36-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,30:67:99:866,0,1095:15,22,14,16 chr1 245290111 . G A 1072.39 PASS AC=1;AF=0.5;AN=2;DP=805;MQ=60;set=variant3-variant9-variant10-variant13-variant15-variant16-variant17-variant20-variant23-variant27-variant29-variant30-variant32-variant36-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,23:42:99:584,0,515:12,7,13,10 chr1 245290227 . G A 2074.3 PASS AC=1;AF=0.5;AN=2;DP=2162;MQ=60;set=variant3-variant5-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant23-variant27-variant29-variant30-variant32-variant36-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,52:104:99:1294,0,1292:30,22,32,20 chr1 245290345 . C T 1342.97 PASS AC=1;AF=0.5;AN=2;DP=1523;MQ=60;set=variant10-variant13-variant16-variant20-variant23-variant29-variant30-variant32-variant36 GT:AD:DP:GQ:PL:SB 0/1:65,96:161:99:2436,0,1467:28,37,46,50 chr1 245290423 . GA G 900.16 PASS AC=1;AF=0.5;AN=2;DP=1400;MQ=60;set=variant3-variant9-variant10-variant13-variant15-variant16-variant17-variant20-variant23-variant27-variant29-variant30-variant32-variant36-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,33:47:99:760,0,218:7,7,8,25 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 1/1:0,53:53:99:1882,159,0:0,0,30,23 chr1 245318688 . C T 1364.82 PASS AC=1;AF=0.63;AN=2;DP=4284;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant11-variant12-variant15-variant16-variant17-variant20-variant21-variant23-variant26-variant27-variant28-variant29-variant31-variant33-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:90,65:155:99:1602,0,2219:50,40,36,29 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 0/1:14,14:28:99:418,0,423:9,5,10,4 chr1 245703990 . G T 3246.65 PASS AC=2;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 1/1:0,129:129:99:4038,385,0:0,0,67,62 chr1 245765800 . T A 778.3 PASS AC=1;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 0/1:17,17:34:99:466,0,458:12,5,12,5 chr1 245772529 . A G 919.26 PASS AC=2;AF=0.563;AN=2;DP=778;FractionInformativeReads=1;MQ=60;set=variant6-variant15-variant17-variant23-variant36-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:3101,276,0:0,0,56,36 chr1 245775356 . TTGTGTGTGTGTGTGTGTGTG TTGTGTGTGTG,TTGTGTGTGTGTG,TTGTGTGTGTGTGTGTGTG,TTGTGTGTGTGTGTGTG,TTGTGTGTGTGTGTGTGTGTGTG,TTGTGTGTGTGTGTG,T,TTGTGTG 173.6 PASS AC=0,1,0,0,0,0,0,0;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 0/2:12:43:0,3,1,8 chr1 245775407 . T A 139.37 PASS AC=1;AF=0.571;AN=2;DP=249;set=variant6-variant12-variant14-variant17-variant19-variant20-variant21-variant23-variant25-variant26-variant31-variant33-variant5-variant40 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:187,0,138:1,4,1,6 chr1 245809125 . T A 133.35 PASS AC=1;AF=0.5;AN=2;DP=19;FractionInformativeReads=1;MQ=60;set=variant23-variant40 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:99:162,0,106:3,0,4,2 chr1 245850095 . C T 4614.63 PASS AC=1;AF=0.587;AN=2;DP=10927;MQ=60;set=variant2-variant4-variant6-variant9-variant11-variant13-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:228,193:421:99:4662,0,5889:92,136,80,113 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 1/1:0,169:169:99:5190,506,0:0,0,75,94 chr1 245852208 . G A 810.23 PASS AC=1;AF=0.5;AN=2;DP=53;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.11;QD=15.29;ReadPosRankSum=-1.309;SOR=0.64;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:22,31:53:99:838,0,614:6,16,9,22 chr1 245861571 . C T 616.14 PASS AC=2;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 1/1:2,39:41:73:1193,73,0:1,1,12,27 chr1 245871108 . G A 555.63 PASS AC=1;AF=0.526;AN=2;DP=711;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant9-variant13-variant15-variant16-variant19-variant20-variant22-variant23-variant28-variant29-variant31-variant34-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,18:36:99:559,0,524:11,7,10,8 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 0/1:127,129:256:99:3169,0,3470:56,71,57,72 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 1/1:0,103:103:99:2967,309,0:0,0,47,56 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 1/1:0,39:39:99:1143,116,0:0,0,15,24 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 1/1:0,8:8:24:238,24,0:0,0,3,5 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 1/1:0,64:64:99:2995,202,0:0,0,44,20 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 1/1:0,67:67:99:3060,205,0:0,0,45,22 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 1/1:0,75:75:99:3253,226,0:0,0,49,26 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 1/1:0,39:39:99:1355,117,0:0,0,10,29 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 1/1:0,11:11:33:475,33,0:0,0,2,9 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 1/1:0,9:9:33:475,33,0:0,0,1,8 chr1 246093465 . GA G 750.08 PASS AC=2;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 1/1:2,47:49:89:1036,89,0:0,2,22,25 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 1/1:0,92:92:99:2936,276,0:0,0,60,32 chr1 246489196 . C T 9274.84 PASS AC=2;AF=0.83;AN=2;DP=12755;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,274:274:99:9885,825,0:0,0,137,137 chr1 246489201 . G A 3575.06 PASS AC=1;AF=0.5;AN=2;DP=1043;FractionInformativeReads=1;MQ=60;set=variant22-variant23-variant33-variant36 GT:AD:DP:GQ:PL:SB 0/1:153,124:277:99:2741,0,3684:74,79,61,63 chr1 246489706 . GA G 1771.89 PASS AC=2;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 1/1:0,62:62:99:1752,186,0:0,0,25,37 chr1 246490438 . T C 1591.77 PASS AC=2;AF=0.83;AN=2;DP=2820;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,55:55:99:2498,169,0:0,0,35,20 chr1 246490442 . A G 1793.26 PASS AC=2;AF=0.83;AN=2;DP=3015;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:2548,175,0:0,0,35,21 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 0/1:29,43:72:99:1147,0,704:17,12,28,15 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 0/1:15,13:28:99:338,0,428:3,12,3,10 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 0/1:13,9:22:99:244,0,361:7,6,5,4 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 0/1:12,11:23:99:293,0,270:5,7,6,5 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 1/1:0,34:34:99:1485,104,0:0,0,26,8 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 0/1:29,9:38:99:130,0,762:22,7,6,3 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 0/1:14,21:35:99:431,0,220:11,3,14,7 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 1/1:0,70:70:99:2304,209,0:0,0,38,32 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 1/1:0,415:415:99:11653,1242,0:0,0,207,208 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 1/1:0,92:92:99:4061,277,0:0,0,33,59 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 0/1:10,5:15:99:180,0,294:7,3,5,0 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 0/1:15,16:31:99:407,0,394:13,2,11,5 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 1/1:0,16:16:48:662,48,0:0,0,2,14 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 0/1:29,20:49:99:385,0,712:13,16,9,11 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 0/1:22,12:34:99:438,0,1304:9,13,5,7 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 0/1:21,12:33:99:438,0,1304:8,13,5,7 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 0/1:18,12:30:99:441,0,1282:6,12,5,7 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 1/1:0,6:6:18:256,18,0:0,0,1,5 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 1/1:0,40:40:99:1185,120,0:0,0,20,20 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 1/1:0,25:25:75:818,75,0:0,0,17,8 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 0/1:71,60:131:99:1350,0,1612:32,39,26,34 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 1/1:0,40:40:99:1414,120,0:0,0,10,30 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 0/1:80,98:178:99:2674,0,2070:55,25,65,33 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 1/1:0,90:90:99:2739,269,0:0,0,41,49 chr1 246805433 . TG T 123.5 PASS AC=1;AF=0.5;AN=2;DP=31;MQ=60;set=variant6-variant23-variant24 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:64:117,0,64:1,2,0,4 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 0/1:11,8:19:99:219,0,263:5,6,4,4 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 0/1:8,7:15:99:189,0,237:3,5,2,5 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 0/1:9,5:14:99:163,0,244:6,3,5,0 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 0/1:194,148:342:99:3662,0,5058:91,103,66,82 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 0/1:126,109:235:99:2817,0,3519:67,59,64,45 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 0/1:17,16:33:99:348,0,499:6,11,7,9 chr1 246930564 . G C 1691.45 PASS AC=1;AF=0.5;AN=2;DP=1481;FractionInformativeReads=1;MQ=60;set=variant-variant14-variant16-variant23-variant26-variant28-variant30-variant33-variant34 GT:AD:DP:GQ:PL:SB 0/1:66,85:151:99:2041,0,1615:39,27,47,38 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 0/1:63,61:124:99:1709,0,1829:43,20,41,20 chr1 246939513 . G A 1626.7 PASS AC=1;AF=0.553;AN=2;DP=1068;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant12-variant14-variant16-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,18:43:99:512,0,786:17,8,12,6 chr1 246940790 . TAAAGA T 303.11 PASS AC=1;AF=0.556;AN=2;DP=183;MQ=60;set=variant-variant5-variant12-variant14-variant16-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:99:246,0,121:0,2,1,5 chr1 246942159 . G A 4520.88 PASS AC=1;AF=0.553;AN=2;DP=3225;MQ=60;set=variant-variant5-variant12-variant14-variant16-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:87,81:168:99:1970,0,2147:53,34,46,35 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 0/1:10,13:23:99:354,0,262:7,3,9,4 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 0/1:19,20:39:99:499,0,493:5,14,7,13 chr1 247013445 . C T 1821.5 PASS AC=1;AF=0.5;AN=2;DP=330;FractionInformativeReads=1;set=variant23-variant29 GT:AD:DP:GQ:PL:SB 0/1:83,75:158:99:1850,0,2232:46,37,38,37 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 0/1:23,19:42:99:526,0,687:7,16,5,14 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 1/1:5:15:0,0,1,4 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 0/1:7,13:20:99:345,0,134:3,4,4,9 chr1 247031204 . CACACA CCACA,C,CCA 268.01 PASS AC=1,0,0;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 0/1:17:99:1,7,1,8 chr1 247031206 . CACA C 267.97 PASS AC=1;AF=0.563;AN=2;DP=133;set=variant-variant3-variant21-variant23-variant27-variant33-variant35-variant39 GT:AD:DP:GQ:PL:SB 0/1:8,9:17:99:300,0,511:1,7,1,8 chr1 247031237 . C G 587.07 PASS AC=1;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 0/1:5,7:12:99:276,0,179:0,5,0,7 chr1 247048834 . T C 172 PASS AC=1;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 0/1:9,4:13:99:101,0,256:7,2,2,2 chr1 247054530 . T C 34.26 PASS AC=1;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 0/1:4,5:9:99:148,0,120:0,4,1,4 chr1 247067139 . CAA CA,CAAA,C 285.51 PASS AC=1,0,0;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 0/1:28:99:13,6,9,0 chr1 247067492 . AG A 172.1 PASS AC=1;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 0/1:7,5:12:99:166,0,247:0,7,0,5 chr1 247091604 . CAAA CAA,CA,C 78.77 PASS AC=0,1,0;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 0/2:18:99:2,6,6,4 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 0/1:19,20:39:99:542,0,450:12,7,14,6 chr1 247109168 . G A 1921.13 PASS AC=1;AF=0.652;AN=2;DP=3580;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant9-variant11-variant12-variant14-variant16-variant19-variant21-variant22-variant23-variant24-variant30-variant31-variant33-variant34-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,57:122:99:1414,0,1757:37,28,30,27 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 0/1:54,50:104:99:1809,0,3929:21,33,22,28 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 0/1:39,42:81:99:1724,0,3551:13,26,16,26 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 0/1:38,40:78:99:1607,0,3475:13,25,14,26 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 0/1:2,4:6:69:140,0,69:2,0,4,0 chr1 247143092 . T A 115.49 PASS AC=2;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 1/1:0,3:3:9:94,9,0:0,0,2,1 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 0/1:1,4:5:30:84,0,30:1,0,2,2 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 0/1:90,81:171:99:2000,0,2197:54,36,55,26 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 0/1:47,71:118:99:2914,0,2339:19,28,29,42 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 0/1:85,83:168:99:2144,0,2141:40,45,42,41 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 0/1:59,80:139:99:2145,0,1484:24,35,33,47 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 0/1:36,36:72:99:1015,0,936:16,20,17,19 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 0/1:20,22:42:99:653,0,563:4,16,4,18 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 1/1:1,318:319:99:9239,944,0:0,1,141,177 chr1 247200173 . TAC TACACACACACACAC,TACACACACAC,TACACACACACACACAC,TACACACACACAC,TACACAC,TACACACAC,TACACACACACACACACAC,TACAC,TACACACACACACACACACAC,T,TAGAC 773.12 PASS AC=1,0,0,1,0,0,0,0,0,0,0;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 4/1:19:99:0,0,15,4 chr1 247200207 . T C 1022.91 PASS AC=2;AF=0.525;AN=2;DP=947;set=variant4-variant7-variant8-variant9-variant12-variant16-variant18-variant19-variant21-variant23-variant24-variant28-variant29-variant31-variant32-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1788,134,0:0,0,33,12 chr1 247200639 . T C 3135.16 PASS AC=1;AF=0.5;AN=2;DP=4228;MQ=60;set=variant4-variant7-variant8-variant9-variant12-variant16-variant18-variant19-variant23-variant24-variant28-variant29-variant31-variant32-variant36-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:108,83:191:99:2114,0,2677:53,55,36,47 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 0/1:3,7:10:65:184,0,65:2,1,5,2 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 0/1:35,43:78:99:983,0,1056:26,9,27,16 chr1 247241850 . G C 2519.77 PASS AC=1;AF=0.543;AN=2;DP=4394;MQ=60;set=variant4-variant5-variant7-variant8-variant9-variant12-variant13-variant16-variant18-variant19-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant34-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:84,94:178:99:2383,0,1985:46,38,57,37 chr1 247242032 . C T 1472.54 PASS AC=1;AF=0.5;AN=2;DP=2642;MQ=60;set=variant4-variant7-variant8-variant9-variant12-variant16-variant18-variant19-variant23-variant24-variant28-variant31-variant32-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:45,66:111:99:1597,0,1153:18,27,24,42 chr1 247267274 . C A 623.05 PASS AC=1;AF=0.543;AN=2;DP=1410;MQ=60;set=variant4-variant7-variant8-variant9-variant12-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant28-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,21:39:99:562,0,492:10,8,12,9 chr1 247267668 . G T 1810.85 PASS AC=1;AF=0.63;AN=2;DP=2845;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant28-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:55,32:87:99:780,0,1560:16,39,10,22 chr1 247274899 . A G 327.42 PASS AC=1;AF=0.7;AN=2;DP=534;MQ=60;set=variant4-variant6-variant7-variant9-variant10-variant12-variant15-variant16-variant17-variant18-variant23-variant24-variant28-variant31-variant32-variant36-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:10,15:25:99:461,0,196:5,5,9,6 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 0/1:30,50:80:99:1538,0,922:27,3,40,10 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 0/1:255,205:460:99:4942,0,6149:128,127,97,108 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 0/1:23,37:60:99:1036,0,489:10,13,14,23 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 0/1:40,24:64:99:600,0,1045:16,24,7,17 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 0/1:51,10:61:99:128,0,2292:19,32,2,8 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 0/1:28,32:60:99:1020,0,554:13,15,6,26 chr1 247287297 . A ATTTTTTTTT,ATTTTTT,ATTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTT,ATTTTTTT,ATTTTTTTTTTTTTT 70.4 PASS AC=0,0,0,1,0,0,0;AF=0.125,0.063,0.063,0.063,0.063,0.063,0.063;AN=2;DP=299;set=filterInvariant9-filterInvariant10-variant17-filterInvariant23-filterInvariant24-filterInvariant32-filterInvariant37-variant40 GT:DP:GQ:SB 0/4:28:99:5,18,1,4 chr1 247319489 . G A 5225.68 PASS AC=1;AF=0.553;AN=2;DP=8449;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant16-variant17-variant18-variant23-variant24-variant31-variant32-variant33-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:232,199:431:99:5069,0,6023:125,107,118,81 chr1 247321252 . TAA TA,T 49.18 PASS AC=1,0;AF=0.524,0.024;AN=2;DP=361;set=variant-variant4-variant5-variant6-variant7-variant9-variant16-variant18-variant21-variant22-variant23-variant24-variant25-variant31-variant32-variant33-variant36-variant37-variant39-variant40-variant42 GT:DP:GQ:SB 0/1:9:47:0,3,1,5 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 0/1:20,10:30:99:198,0,548:9,11,4,6 chr1 247322967 . G C 1275.18 PASS AC=1;AF=0.553;AN=2;DP=1825;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant16-variant17-variant18-variant23-variant24-variant31-variant32-variant33-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:50,36:86:99:846,0,1433:32,18,20,16 chr1 247323260 . C A 1200.73 PASS AC=1;AF=0.68;AN=2;DP=1015;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant16-variant17-variant18-variant21-variant23-variant24-variant26-variant28-variant31-variant32-variant33-variant34-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:10,24:34:99:763,0,308:1,9,6,18 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 0/1:59,37:96:99:811,0,1485:33,26,19,18 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 1/1:0,113:113:99:3328,339,0:0,0,68,45 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 1/1:0,105:105:99:3306,313,0:0,0,48,57 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 1/1:0,9:9:27:361,27,0:0,0,8,1 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 0/1:16,11:27:99:252,0,445:11,5,6,5 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 1/1:0,39:39:99:1314,117,0:0,0,25,14 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 1/1:0,37:37:99:1265,111,0:0,0,14,23 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 0/1:1,10:11:13:402,0,13:0,1,0,10 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 1/1:0,43:43:99:1315,129,0:0,0,28,15 chr1 247486213 . G A 1178.29 PASS AC=2;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 1/1:0,28:28:84:870,84,0:0,0,10,18 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 1/1:0,22:22:65:749,65,0:0,0,17,5 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 1/1:0,4:4:12:139,12,0:0,0,1,3 chr1 247582461 . TATA T,TTA 165.87 PASS AC=1,0;AF=0.705,0.023;AN=2;DP=211;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant16-variant20-variant21-variant23-variant27-variant28-variant30-variant32-variant34-variant38-variant40-variant43-variant44 GT:DP:GQ:SB 0/1:8:11:0,1,1,6 chr1 247582466 . A T 174.95 PASS AC=1;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 0/1:1,6:7:11:193,0,11:0,1,0,6 chr1 247587477 . G A 1152.99 PASS AC=1;AF=0.676;AN=2;DP=6330;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant34-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,75:149:99:1941,0,2028:30,44,37,38 chr1 247587531 . A G 3041.45 PASS AC=2;AF=0.943;AN=2;DP=7491;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,127:127:99:3858,380,0:0,0,56,71 chr1 247597329 . C T 55.3 PASS AC=2;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 1/1:0,8:8:24:276,24,0:0,0,7,1 chr1 247597364 . G GAT 451.16 PASS AC=1;AF=0.767;AN=2;DP=468;set=variant-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant34-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,10:18:99:578,0,298:7,1,7,3 chr1 247597365 . G A,GTGTTCTGAGGCCTTCTCTATTCCAGAGCTCTCTGGTCAGA 983.6 PASS AC=1,1;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 1/2:18:99:0,0,14,4 chr1 247597656 . TG T 299.71 PASS AC=2;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 1/1:0,53:53:99:1774,159,0:0,0,10,43 chr1 247599232 . G A 318.63 PASS AC=1;AF=0.706;AN=2;DP=685;MQ=60;set=variant-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-variant31-variant32-variant34-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:231,0,212:6,2,6,2 chr1 247607642 . C T 373.26 PASS AC=2;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 1/1:0,31:31:93:1042,93,0:0,0,8,23 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 0/1:25:45:2,2,12,9 chr1 247612151 . C CT 5709.29 PASS AC=2;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 1/1:0,165:165:99:5144,498,0:0,0,72,93 chr1 247612295 . C T 1632.69 PASS AC=2;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 1/1:0,46:46:99:1437,138,0:0,0,19,27 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 0/1:15,12:27:99:271,0,370:7,8,5,7 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 0/1:42,37:79:99:872,0,1054:24,18,22,15 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 0/1:44,46:90:99:1003,0,1049:24,20,24,22 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 0/1:46,43:89:99:1149,0,1283:25,21,23,20 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 1/1:0,114:114:99:3672,341,0:0,0,52,62 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 0/1:52,33:85:99:873,0,1269:26,26,16,17 chr1 247615261 . GA G 1789.9 PASS AC=1;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 0/1:64,49:113:99:1486,0,2047:25,39,23,26 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 1/1:0,12:12:36:441,36,0:0,0,4,8 chr1 247654993 . T C 2451.88 PASS AC=1;AF=0.54;AN=2;DP=4412;MQ=60;set=variant3-variant5-variant7-variant9-variant11-variant12-variant13-variant17-variant18-variant19-variant21-variant22-variant23-variant26-variant29-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:84,62:146:99:1548,0,2262:40,44,27,35 chr1 247655275 . T C 1972.7 PASS AC=1;AF=0.54;AN=2;DP=3364;MQ=60;set=variant3-variant5-variant7-variant9-variant11-variant12-variant13-variant17-variant18-variant19-variant21-variant22-variant23-variant26-variant29-variant32-variant33-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,37:107:99:922,0,1784:36,34,15,22 chr1 247655516 . C T 216.31 PASS AC=1;AF=0.542;AN=2;DP=471;MQ=60;set=variant3-variant5-variant7-variant9-variant11-variant12-variant13-variant17-variant18-variant19-variant21-variant22-variant23-variant26-variant29-variant32-variant33-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,7:19:99:174,0,351:3,9,2,5 chr1 247690104 . G T 1853.34 PASS AC=1;AF=0.5;AN=2;DP=166;FS=1.995;FractionInformativeReads=1;MQ=60;MQRankSum=-1.223;QD=11.16;ReadPosRankSum=1.901;SOR=0.523;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:84,82:166:99:1882,0,2145:54,30,49,33 chr1 247690320 . C T 3847.79 PASS AC=1;AF=0.545;AN=2;DP=3896;MQ=60;set=variant3-variant5-variant7-variant9-variant11-variant12-variant17-variant18-variant19-variant21-variant22-variant23-variant26-variant29-variant32-variant33-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,73:156:99:1767,0,2184:39,44,32,41 chr1 247690417 . T G 1261.51 PASS AC=1;AF=0.567;AN=2;DP=1905;MQ=60;set=variant6-variant7-variant8-variant11-variant12-variant19-variant20-variant23-variant25-variant27-variant28-variant33-variant34-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:47,74:121:99:1920,0,1188:18,29,28,46 chr1 247693340 . GGT GGTGT,G 129.51 PASS AC=1,0;AF=0.5,0.038;AN=2;DP=205;MQ=60;set=variant6-variant8-variant12-variant19-filterInvariant21-variant23-variant25-variant27-variant28-variant33-variant37-variant38-variant43 GT:DP:GQ:SB 0/1:13:99:4,1,6,2 chr1 247693819 . T TCCCC,TC,TCCC,TCC 226.68 PASS AC=0,0,1,0;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 0/3:37:99:8,16,3,10 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 1/1:0,47:47:99:1607,141,0:0,0,33,14 chr1 247694106 . C CTCCGTGGCCTAAACGGGCAGCCGAGCCCG,CTCCGTGGCCTAAATGGGCAGCCGAGCCCG 1817.27 PASS AC=1,0;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 0/1:94:99:22,32,19,21 chr1 247694550 . C G 2753.15 PASS AC=2;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 1/1:0,174:174:99:5179,521,0:0,0,95,79 chr1 247695446 . C T 1471.04 PASS AC=1;AF=0.5;AN=2;DP=91;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.238;QD=16.17;ReadPosRankSum=0.739;SOR=0.643;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:37,54:91:99:1499,0,932:19,18,27,27 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 1/1:0,109:109:99:3429,327,0:0,0,56,53 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 1/1:1,111:112:99:3423,289,0:0,1,54,57 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 1/1:0,10:10:30:366,30,0:0,0,2,8 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 1/1:0,71:71:99:2378,212,0:0,0,50,21 chr1 247702118 . C T 1755.71 PASS AC=1;AF=0.524;AN=2;DP=2277;MQ=60;set=variant3-variant4-variant5-variant7-variant9-variant11-variant12-variant17-variant19-variant21-variant22-variant23-variant26-variant29-variant32-variant33-variant36-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,45:96:99:1180,0,1372:27,24,29,16 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 1/1:0,117:117:99:5265,352,0:0,0,64,53 chr1 247737928 . A T 4631.9 PASS AC=1;AF=0.5;AN=2;DP=4899;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant14-variant20-variant22-variant23-variant25-variant28-variant33-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:145,138:283:99:3049,0,3264:79,66,70,68 chr1 247739213 . A G 5621.83 PASS AC=1;AF=0.5;AN=2;DP=5441;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant14-variant20-variant22-variant23-variant25-variant28-variant32-variant33-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:120,153:273:99:3646,0,2818:53,67,68,85 chr1 247740764 . C A 2959.28 PASS AC=1;AF=0.5;AN=2;DP=3045;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant11-variant12-variant14-variant20-variant22-variant23-variant25-variant28-variant32-variant33-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:74,75:149:99:1994,0,1903:32,42,37,38 chr1 247751731 . C G 1211.53 PASS AC=1;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 0/1:43,55:98:99:1463,0,1030:21,22,28,27 chr1 247752161 . T C 1407.31 PASS AC=1;AF=0.645;AN=2;DP=5391;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:64,65:129:99:1683,0,1457:30,34,29,36 chr1 247752367 . A G 3915.18 PASS AC=1;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 0/1:44,72:116:99:1944,0,999:20,24,39,33 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 1/1:0,37:37:99:1131,111,0:0,0,25,12 chr1 247835674 . G A 1239.59 PASS AC=2;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 1/1:0,128:128:99:4125,384,0:0,0,63,65 chr1 247835908 . T A 910.31 PASS AC=2;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 1/1:0,97:97:99:3161,290,0:0,0,41,56 chr1 247836008 . G A 964.76 PASS AC=2;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 1/1:0,78:78:99:2594,234,0:0,0,39,39 chr1 247836207 . T A 1493 PASS AC=2;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 1/1:0,93:93:99:3055,279,0:0,0,50,43 chr1 247921100 . T G 2540.34 PASS AC=2;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 1/1:2,88:90:99:2852,235,0:1,1,38,50 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 1/1:0,66:66:99:2207,198,0:0,0,36,30 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 1/1:0,53:53:99:1676,159,0:0,0,19,34 chr1 247921789 . AGT AGTGT,AGTGTGT,A,AGTGTGTGT 198.31 PASS AC=1,0,0,0;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 0/1:15:19:0,2,5,8 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 1/1:0,12:12:36:366,36,0:0,0,6,6 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 1/1:0,37:37:99:1087,111,0:0,0,23,14 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 1/1:0,104:104:99:3196,311,0:0,0,52,52 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 1/1:0,149:149:99:6633,449,0:0,0,72,77 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 1/1:0,40:40:99:1331,120,0:0,0,17,23 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 1/1:0,106:106:99:3431,318,0:0,0,55,51 chr1 248004687 . C G 2723.26 PASS AC=2;AF=0.875;AN=2;DP=6328;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:3518,350,0:0,0,60,57 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 1/1:0,88:88:99:2909,264,0:0,0,39,49 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 1/1:0,86:86:99:2836,257,0:0,0,43,43 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 1/1:0,91:91:99:4054,277,0:0,0,47,44 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 1/1:0,92:92:99:4108,280,0:0,0,48,44 chr1 248005213 . G C 3151.61 PASS AC=2;AF=0.875;AN=2;DP=4870;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2650,269,0:0,0,37,53 chr1 248020448 . G A 1000.87 PASS AC=1;AF=0.816;AN=2;DP=1058;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,11:19:99:273,0,183:3,5,4,7 chr1 248020556 . G C 3414.59 PASS AC=1;AF=0.795;AN=2;DP=4129;MQ=60;set=variant2-variant3-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-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,40:66:99:938,0,853:22,4,24,16 chr1 248023966 . C T 1518.37 PASS AC=1;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 0/1:29,21:50:99:500,0,727:13,16,10,11 chr1 248024073 . A C 548.79 PASS AC=1;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 0/1:9,12:21:99:372,0,303:2,7,3,9 chr1 248028219 . G A 599 PASS AC=1;AF=0.636;AN=2;DP=1304;MQ=60;set=variant2-variant3-variant5-variant6-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,19:33:99:460,0,344:4,10,8,11 chr1 248039451 . C T 2463.04 PASS AC=1;AF=0.63;AN=2;DP=2925;MQ=60;set=variant3-variant5-variant8-variant10-variant11-variant14-variant15-variant16-variant19-variant20-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,66:125:99:1647,0,1433:24,35,29,37 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 1/1:0,82:82:99:2588,246,0:0,0,40,42 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 1/1:0,79:79:99:2801,237,0:0,0,28,51 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 1/1:0,21:21:63:657,63,0:0,0,8,13 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 1/1:0,6:6:18:270,18,0:0,0,6,0 chr1 248058761 . G C 106.77 PASS AC=2;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 1/1:0,7:7:21:307,21,0:0,0,7,0 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 1/1:0,20:20:60:686,60,0:0,0,16,4 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 1/1:0,46:46:99:1514,138,0:0,0,31,15 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 1/1:0,81:81:99:2584,243,0:0,0,53,28 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 0/1:116,77:193:99:1759,0,3008:58,58,40,37 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 0/1:83,118:201:99:3128,0,1892:43,40,62,56 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 1/1:0,219:219:99:6951,656,0:0,0,114,105 chr1 248059703 . T A 7532.24 PASS AC=2;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 1/1:0,185:185:99:8064,559,0:0,0,79,106 chr1 248059712 . T C 7372.47 PASS AC=2;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 1/1:0,172:172:99:7836,533,0:0,0,71,101 chr1 248059856 . T C 2717.97 PASS AC=2;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 1/1:0,98:98:99:3023,294,0:0,0,41,57 chr1 248060029 . A G 975.82 PASS AC=2;AF=0.966;AN=2;DP=1166;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:511,39,0:0,0,2,11 chr1 248084222 . T C 1151.32 PASS AC=1;AF=0.536;AN=2;DP=366;MQ=60;set=variant-variant5-filterInvariant6-variant7-variant19-variant20-variant23-variant25-variant28-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:248,0,274:8,3,6,1 chr1 248084434 . G A 2804.28 PASS AC=1;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 0/1:27,30:57:99:750,0,671:9,18,13,17 chr1 248084464 . T C 1698.6 PASS AC=2;AF=0.955;AN=2;DP=2892;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1171,110,0:0,0,10,27 chr1 248084524 . G A 111.78 PASS AC=1;AF=0.5;AN=2;DP=26;FS=0;FractionInformativeReads=1;set=variant23-variant28 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:99:140,0,283:1,7,0,4 chr1 248084825 . C T 313.46 PASS AC=1;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 0/1:28,8:36:90:90,0,595:16,12,4,4 chr1 248085011 . C G 805.8 PASS AC=1;AF=0.545;AN=2;DP=210;set=variant-variant5-variant6-variant7-variant19-variant20-variant23-variant25-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:2,15:17:36:488,0,36:2,0,11,4 chr1 248085108 . C T 1861.97 PASS AC=1;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 0/1:50,38:88:99:1099,0,1241:30,20,30,8 chr1 248085124 . G A 3141.35 PASS AC=1;AF=0.545;AN=2;DP=1133;FractionInformativeReads=1;set=variant-variant5-variant6-variant7-variant19-variant20-variant23-variant25-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:44,58:102:99:1516,0,1058:30,14,36,22 chr1 248085341 . T A 2175.71 PASS AC=1;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 0/1:35,25:60:99:738,0,988:8,27,5,20 chr1 248097461 . C T 2429.61 PASS AC=1;AF=0.5;AN=2;DP=808;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant23-variant26-variant36 GT:AD:DP:GQ:PL:SB 0/1:70,80:150:99:2116,0,1843:30,40,40,40 chr1 248112627 . T C 7445.38 PASS AC=1;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 0/1:226,126:352:99:2987,0,5948:115,111,49,77 chr1 248112738 . C A 4299.22 PASS AC=1;AF=0.5;AN=2;DP=511;FractionInformativeReads=1;set=variant23-variant28 GT:AD:DP:GQ:PL:SB 0/1:127,159:286:99:4327,0,3703:56,71,72,87 chr1 248112745 . G T 6451.64 PASS AC=1;AF=0.818;AN=2;DP=9677;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:34,252:286:99:10246,0,640:8,26,120,132 chr1 248112754 . T C 453.92 PASS AC=1;AF=0.5;AN=2;DP=3560;set=variant6-variant8-filterInvariant9-variant12-variant13-filterInvariant15-variant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant29-variant34-filterInvariant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:253,33:286:99:253,0,10552:119,134,7,26 chr1 248112762 . T C 8478.52 PASS AC=1;AF=0.807;AN=2;DP=9516;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:186,87:273:99:3058,0,7627:77,109,46,41 chr1 248112763 . G A 8523.52 PASS AC=1;AF=0.807;AN=2;DP=9533;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:187,86:273:99:3122,0,7621:77,110,46,40 chr1 248112771 . C T 8422.94 PASS AC=1;AF=0.807;AN=2;DP=9818;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:184,90:274:99:3102,0,7505:75,109,48,42 chr1 248112809 . A G 6821.24 PASS AC=1;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 0/1:157,121:278:99:2815,0,4342:72,85,66,55 chr1 248112836 . A G 6809.8 PASS AC=1;AF=0.966;AN=2;DP=12077;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:152,137:289:99:3341,0,4213:75,77,72,65 chr1 248113026 . T A 3810.96 PASS AC=1;AF=0.966;AN=2;DP=7734;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:84,79:163:99:1862,0,2339:27,57,32,47 chr1 248113040 . A G 3959.03 PASS AC=2;AF=1;AN=2;DP=7366;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,156:156:99:5176,468,0:0,0,59,97 chr1 248113061 . C A 1529.7 PASS AC=1;AF=0.5;AN=2;DP=263;FractionInformativeReads=1;set=variant23-variant28 GT:AD:DP:GQ:PL:SB 0/1:86,65:151:99:1558,0,2212:35,51,27,38 chr1 248113206 . C G 552.37 PASS AC=1;AF=0.966;AN=2;DP=1508;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:12,27:39:99:759,0,306:4,8,8,19 chr1 248128722 . T C 2412.2 PASS AC=1;AF=0.5;AN=2;DP=172;FS=0.563;FractionInformativeReads=1;MQ=60;MQRankSum=-1.423;QD=14.02;ReadPosRankSum=-0.567;SOR=0.764;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:77,95:172:99:2440,0,1973:37,40,44,51 chr1 248128929 . G A 4730.35 PASS AC=1;AF=0.595;AN=2;DP=2671;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant9-variant13-variant15-variant19-variant20-variant23-variant25-variant29-variant30-variant31-variant34-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:60,48:108:99:1365,0,1634:32,28,24,24 chr1 248129240 . G A 3577.73 PASS AC=1;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 0/1:60,61:121:99:1503,0,1530:24,36,26,35 chr1 248129486 . C T 1130.92 PASS AC=1;AF=0.5;AN=2;DP=141;FS=1.367;FractionInformativeReads=0.993;MQ=60;MQRankSum=0.649;QD=8.02;ReadPosRankSum=1.342;SOR=0.867;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:84,56:140:99:1159,0,2452:43,41,31,25 chr1 248154224 . C T 4208.17 PASS AC=1;AF=0.5;AN=2;DP=1849;MQ=60;set=variant6-variant8-variant15-variant23-variant44 GT:AD:DP:GQ:PL:SB 0/1:144,145:289:99:3641,0,3727:70,74,75,70 chr1 248185883 . G A 6352.12 PASS AC=1;AF=0.5;AN=2;DP=2475;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant15-variant23-variant44 GT:AD:DP:GQ:PL:SB 0/1:220,231:451:99:5548,0,5331:112,108,120,111 chr1 248202344 . G C 5988.13 PASS AC=1;AF=0.588;AN=2;DP=7556;set=variant6-variant8-variant9-variant12-variant13-variant15-variant20-variant21-variant23-variant25-variant28-variant29-variant34-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:223,203:426:99:5014,0,5907:108,115,104,99 chr1 248224099 . T C 1977.85 PASS AC=1;AF=0.563;AN=2;DP=2142;FractionInformativeReads=1;set=variant6-variant8-variant9-variant12-variant13-variant15-variant20-variant21-variant22-variant23-variant29-variant34-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,59:120:99:1692,0,1626:33,28,29,30 chr1 248224216 . C T 3230.38 PASS AC=1;AF=0.563;AN=2;DP=3844;FractionInformativeReads=1;set=variant6-variant8-variant9-variant12-variant13-variant15-variant20-variant21-variant22-variant23-variant29-variant34-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:112,106:218:99:2648,0,3045:64,48,61,45 chr1 248224294 . C T 3566.33 PASS AC=1;AF=0.588;AN=2;DP=5857;set=variant6-variant8-variant9-variant12-variant13-variant15-variant20-variant21-variant22-variant23-variant29-variant34-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:163,126:289:99:2739,0,4044:83,80,61,65 chr1 248224398 . A G 1797.92 PASS AC=1;AF=0.563;AN=2;DP=3957;set=variant6-variant8-variant9-variant12-variant13-variant15-variant20-filterInvariant21-variant22-variant23-variant29-variant34-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:176,47:223:99:954,0,5176:79,97,10,37 chr1 248224746 . G T 3481.29 PASS AC=1;AF=0.571;AN=2;DP=2006;set=variant5-variant14-variant19-variant23-variant25-variant26-variant36 GT:AD:DP:GQ:PL:SB 0/1:106,96:202:99:2612,0,4118:55,51,47,49 chr1 248224754 . T C 3457.18 PASS AC=1;AF=0.588;AN=2;DP=4295;set=variant6-variant8-variant9-variant12-variant13-variant15-variant20-variant21-variant22-variant23-variant29-variant34-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:100,109:209:99:2762,0,3747:51,49,55,54 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 0/1:117,30:147:99:354,0,2931:65,52,19,11 chr1 248247363 . C T 836.9 PASS AC=1;AF=0.5;AN=2;DP=1425;set=variant-filterInvariant5-filterInvariant20-filterInvariant23-filterInvariant38-variant39-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:179,26:205:66:66,0,4196:93,86,18,8 chr1 248247463 . C T 1247.56 PASS AC=1;AF=0.5;AN=2;DP=1677;set=variant-variant5-variant6-variant7-variant19-variant20-variant23-variant25-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:89,40:129:99:677,0,2388:34,55,17,23 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 0/1:10,16:26:99:639,0,503:4,6,10,6 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 0/1:19,8:27:99:117,0,728:10,9,4,4 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 0/1:11,16:27:99:639,0,503:4,7,10,6 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 0/1:11,16:27:99:639,0,503:4,7,10,6 chr1 248247706 . G A 562.94 PASS AC=1;AF=0.5;AN=2;DP=1331;set=variant6-variant8-variant12-variant13-variant14-variant15-variant17-variant21-variant22-variant23-variant25-variant29-variant34-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,27:53:99:771,0,804:14,12,14,13 chr1 248264018 . C T 9491.88 PASS AC=1;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 0/1:145,148:293:99:3556,0,3270:74,71,79,69 chr1 248285441 . G T 1642.03 PASS AC=1;AF=0.5;AN=2;DP=1297;MQ=60;set=variant6-variant8-variant13-variant15-variant17-variant22-variant23-variant29-variant34-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,53:92:99:1589,0,1073:16,23,25,28 chr1 248285487 . A G 2392.55 PASS AC=1;AF=0.5;AN=2;DP=1999;set=variant6-variant8-variant13-variant15-variant17-variant22-variant23-variant29-variant34-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,74:135:99:2129,0,1492:31,30,47,27 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 1/1:1,164:165:99:5232,482,0:0,1,93,71 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 1/1:0,177:177:99:5696,530,0:0,0,88,89 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 1/1:0,142:142:99:4673,425,0:0,0,67,75 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 1/1:0,9:9:27:405,27,0:0,0,0,9 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 1/1:3,382:385:99:11177,1087,0:2,1,217,165 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 1/1:0,39:39:99:1326,117,0:0,0,9,30 chr1 248402758 . C T 1201.62 PASS AC=1;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 0/1:54,58:112:99:1529,0,1289:21,33,25,33 chr1 248436611 . G A 1195.57 PASS AC=1;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 0/1:71,38:109:99:1370,0,3648:38,33,28,10 chr1 248436616 . A G 1251.01 PASS AC=1;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 0/1:73,37:110:99:1334,0,3706:39,34,28,9 chr1 248436805 . T G 554.62 PASS AC=1;AF=0.739;AN=2;DP=4729;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:50,49:99:99:1506,0,1098:26,24,23,26 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 0/1:78,21:99:99:582,0,3871:39,39,9,12 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 0/1:79,21:100:99:582,0,3871:40,39,9,12 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 0/1:77,19:96:99:244,0,2235:49,28,7,12 chr1 248437247 . GCCCTAA G 1042.35 PASS AC=1;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 0/1:13,14:27:99:549,0,984:3,10,5,9 chr1 248457979 . C A 3426.87 PASS AC=1;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 0/1:173,135:308:99:2967,0,4188:80,93,63,72 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 0/1:11,3:14:76:76,0,324:10,1,3,0 chr1 248458676 . T C 628.02 PASS AC=1;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 0/1:35,33:68:99:925,0,984:25,10,26,7 chr1 248458689 . A G 749.11 PASS AC=1;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 0/1:41,36:77:99:949,0,1091:27,14,26,10 chr1 248458717 . C G 987.51 PASS AC=1;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 0/1:57,53:110:99:1246,0,1486:32,25,32,21 chr1 248458974 . T A 374.48 PASS AC=1;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 0/1:26,24:50:99:638,0,688:8,18,8,16 chr1 248486895 . G T 1268.48 PASS AC=1;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 0/1:82,64:146:99:1686,0,2097:54,28,42,22 chr1 248486913 . A G 1859.91 PASS AC=1;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 0/1:98,77:175:99:1868,0,2419:60,38,47,30 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 0/1:140,152:292:99:4143,0,3552:73,67,78,74 chr1 248487338 . C A 4676.93 PASS AC=1;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 0/1:133,152:285:99:4330,0,3406:71,62,82,70 chr1 248487638 . A G 2425 PASS AC=1;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 0/1:70,79:149:99:2103,0,2033:28,42,38,41 chr1 248487768 . A G 4116.89 PASS AC=1;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 0/1:136,163:299:99:4219,0,3592:77,59,96,67 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 0/1:35,22:57:99:495,0,976:23,12,14,8 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 0/1:44,30:74:99:638,0,1200:26,18,17,13 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 0/1:61,63:124:99:1606,0,1763:27,34,27,36 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 0/1:39,39:78:99:902,0,1044:16,23,19,20 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 0/1:37,34:71:99:900,0,1009:17,20,17,17 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 0/1:96,64:160:99:1360,0,2410:45,51,27,37 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 0/1:54,30:84:99:740,0,1578:19,35,9,21 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 0/1:118,109:227:99:3720,0,4060:53,65,51,58 chr1 248550976 . T G 1616.15 PASS AC=1;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 0/1:75,63:138:99:1568,0,1911:43,32,39,24 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 0/1:27,30:57:99:762,0,781:21,6,18,12 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 0/1:69,83:152:99:2022,0,1587:36,33,48,35 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 1/1:0,75:75:99:2215,225,0:0,0,32,43 chr1 248570551 . A AGAGT 481.3 PASS AC=2;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 1/1:0,27:27:81:1118,81,0:0,0,8,19 chr1 248570553 . A AT 481.3 PASS AC=2;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 1/1:0,22:22:81:1118,81,0:0,0,7,15 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 0/1:18,10:28:99:236,0,428:10,8,7,3 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 0/1:22,9:31:99:178,0,538:12,10,6,3 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 1/1:0,11:11:33:482,33,0:0,0,0,11 chr1 248604610 . G GT 161.26 PASS AC=1;AF=0.5;AN=2;DP=21;FS=0;FractionInformativeReads=1;MQ=31.4;MQRankSum=-2.872;QD=7.68;ReadPosRankSum=0.41;SOR=0.446;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:14,7:21:99:199,0,499:5,9,3,4 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 0/1:16,5:21:81:81,0,518:6,10,2,3 chr1 248604765 . T A 923.37 PASS AC=2;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 1/1:0,28:28:84:721,84,0:0,0,14,14 chr1 248605436 . C G 2239.47 PASS AC=2;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 1/1:0,47:47:99:2054,141,0:0,0,14,33 chr1 248605442 . G T 598.84 PASS AC=2;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 1/1:0,45:45:99:2005,135,0:0,0,11,34 chr1 248636641 . C CTG 43.7 PASS AC=2;AF=0.9;AN=2;DP=112;set=variant2-variant5-filterInvariant9-variant19-variant23-variant24-variant26-variant27-variant29-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:225,15,0:0,0,0,5 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 1/1:0,2:2:6:66,6,0:0,0,1,1 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 1/1:0,162:162:99:4892,485,0:0,0,74,88 chr1 248685719 . A T 1888.1 PASS AC=1;AF=0.55;AN=2;DP=1371;MQ=60;set=variant7-variant8-variant14-variant16-variant22-variant23-variant34-variant36-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:61,61:122:99:1468,0,1575:33,28,29,32 chr1 248722722 . T C 654.17 PASS AC=2;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 1/1:0,13:13:39:426,39,0:0,0,13,0 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 1/1:0,34:34:99:1351,102,0:0,0,34,0 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 0/1:56,11:67:99:208,0,1736:13,43,1,10 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 1/1:1,132:133:99:4157,389,0:1,0,79,53 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 1/1:0,185:185:99:6040,554,0:0,0,112,73 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 1/1:0,158:158:99:4823,472,0:0,0,81,77 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 1/1:0,24:24:81:1215,81,0:0,0,17,7 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 1/1:0,36:36:99:1665,111,0:0,0,26,10 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 1/1:0,39:39:99:1755,117,0:0,0,27,12 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 1/1:0,45:45:99:2025,135,0:0,0,32,13 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 1/1:0,49:49:99:2250,151,0:0,0,34,15 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 1/1:0,55:55:99:2610,175,0:0,0,38,17 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 1/1:0,64:64:99:2880,193,0:0,0,42,22 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 1/1:0,65:65:99:2925,196,0:0,0,40,25 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 1/1:0,66:66:99:3049,207,0:0,0,39,27 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 1/1:0,67:67:99:3049,207,0:0,0,39,28 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 1/1:0,70:70:99:3023,213,0:0,0,37,33 chr1 248801778 . A T 201.26 PASS AC=2;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 1/1:0,15:15:45:496,45,0:0,0,9,6 chr1 248801944 . TCAGCACG T 2326.05 PASS AC=2;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 1/1:0,199:199:99:8804,600,0:0,0,90,109 chr1 248802615 . G A 54.02 DRAGENHardSNP AC=2;AF=0.75;AN=2;DP=13;FS=0;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:67,6,0:0,0,2,0 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 1/1:0,16:16:48:628,48,0:0,0,14,2 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 1/1:0,2:2:6:78,6,0:0,0,0,2 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 0/1:58,11:69:99:146,0,1712:32,26,8,3 chr1 248814054 . G GA 673.81 PASS AC=1;AF=0.5;AN=2;DP=76;FS=0;FractionInformativeReads=0.987;MQ=32.88;MQRankSum=0.373;QD=8.87;ReadPosRankSum=-0.236;SOR=0.637;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:52,23:75:99:711,0,1764:30,22,13,10 chr1 248814080 . A C 1679.89 PASS AC=2;AF=0.989;AN=2;DP=5461;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:2531,291,0:0,0,52,45 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 0/1:84,38:122:99:609,0,1760:40,44,18,20 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 1/1:0,223:223:99:6693,668,0:0,0,106,117 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 1/1:0,138:138:99:4696,414,0:0,0,69,69 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 1/1:0,120:120:99:3833,358,0:0,0,57,63 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 1/1:0,130:130:99:4243,390,0:0,0,64,66 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 1/1:0,137:137:99:4159,409,0:0,0,64,73 chr1 249105926 . G C 1376.12 PASS AC=1;AF=0.5;AN=2;DP=727;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant11-variant14-variant17-variant22-variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:41,37:78:99:958,0,1027:18,23,16,21 chr1 249110906 . G C 670.23 PASS AC=2;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 1/1:0,54:54:99:1829,162,0:0,0,29,25 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 0/1:11,8:19:99:230,0,873:2,9,8,0 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 0/1:11,8:19:99:227,0,930:2,9,8,0 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 0/1:12,7:19:99:218,0,1029:3,9,7,0 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 0/1:15,4:19:99:202,0,1032:5,10,4,0 chr1 249231026 . A G 79.2 PASS AC=1;AF=0.5;AN=2;DP=194;FractionInformativeReads=1;set=filterInvariant4-filterInvariant5-filterInvariant16-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant29-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant36-filterInvariant40-filterInvariant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,5:14:82:82,0,259:3,6,2,3 chr1 249231048 . T C 51.73 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=82;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:6,4:10:69:69,0,141:2,4,2,2 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 1/1:1,72:73:99:2595,178,0:1,0,42,30 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 0/1:117,106:223:99:3086,0,3383:63,54,66,40 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 0/1:37,24:61:99:521,0,998:21,16,13,11 chr2 224970 . C T 252.65 PASS AC=2;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 1/1:0,53:53:99:1630,158,0:0,0,25,28 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 0/1:12,12:24:99:327,0,298:9,3,8,4 chr2 234130 . T G 4429.58 PASS AC=1;AF=0.589;AN=2;DP=3519;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant28-variant30-variant32-variant34-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,60:114:99:1476,0,1307:31,23,36,24 chr2 239597 . C G 148.09 PASS AC=1;AF=0.591;AN=2;DP=337;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant10-variant13-variant14-variant15-variant16-variant17-variant23-variant26-variant27-variant28-variant29-variant30-variant31-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:8,6:14:99:147,0,156:4,4,2,4 chr2 239736 . C A 247.38 PASS AC=1;AF=0.589;AN=2;DP=386;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant28-variant30-variant32-variant34-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,8:10:19:200,0,19:1,1,5,3 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 0/1:23,18:41:99:444,0,591:14,9,9,9 chr2 240054 . A G 246.09 PASS AC=2;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 1/1:1,60:61:99:1620,173,0:0,1,29,31 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 1/1:0,38:38:99:1097,114,0:0,0,18,20 chr2 240630 . T G 1638.57 PASS AC=1;AF=0.589;AN=2;DP=1537;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant28-variant30-variant32-variant34-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,34:69:99:839,0,966:18,17,20,14 chr2 241669 . A T 4943.19 PASS AC=1;AF=0.589;AN=2;DP=4280;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant28-variant30-variant32-variant34-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,79:161:99:1853,0,2001:45,37,46,33 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 0/1:42,35:77:99:808,0,1100:26,16,19,16 chr2 242732 . T TAAC 361.66 PASS AC=2;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 1/1:0,19:19:60:891,60,0:0,0,15,4 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 0/1:25,26:51:99:571,0,972:13,12,15,11 chr2 242800 . T C 1725.45 PASS AC=1;AF=0.597;AN=2;DP=1760;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant28-variant30-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,25:51:99:566,0,995:15,11,13,12 chr2 243504 . C T 1187.19 PASS AC=1;AF=0.589;AN=2;DP=1348;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant28-variant30-variant32-variant34-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,19:56:99:422,0,920:23,14,11,8 chr2 243567 . T TA 701.61 PASS AC=2;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 1/1:4,55:59:64:1428,64,0:1,3,29,26 chr2 244568 . AAAAG A,AAAAGAAAG 410.16 PASS AC=0,2;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 2/2:14:42:0,0,12,2 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 0/1:4,2:6:69:69,0,119:3,1,2,0 chr2 256278 . T C 709.82 PASS AC=1;AF=0.589;AN=2;DP=738;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant28-variant30-variant32-variant34-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,12:21:99:315,0,181:4,5,5,7 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 1/1:0,86:86:99:2799,258,0:0,0,52,34 chr2 260677 . G A 6727.8 PASS AC=1;AF=0.589;AN=2;DP=6176;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant28-variant30-variant32-variant34-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:103,110:213:99:2606,0,2338:52,51,64,46 chr2 262553 . T C 356.03 PASS AC=2;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 1/1:0,34:34:99:1007,102,0:0,0,22,12 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 1/1:0,17:17:51:600,51,0:0,0,12,5 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 0/1:47,46:93:99:1156,0,1106:23,24,18,28 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 0/1:10,5:15:99:116,0,238:4,6,1,4 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 1/1:0,166:166:99:5338,496,0:0,0,98,68 chr2 269352 . G A 3026.1 PASS AC=1;AF=0.589;AN=2;DP=3004;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant28-variant30-variant32-variant34-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,56:106:99:1287,0,1170:24,26,25,31 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 0/1:16,13:29:99:328,0,395:10,6,9,4 chr2 271998 . CAA CA,CAAA,C 437.47 PASS AC=1,1,0;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 1/2:58:99:4,3,30,21 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 0/1:72,78:150:99:1832,0,1798:37,35,36,42 chr2 272840 . G A 2390.7 PASS AC=2;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 1/1:0,128:128:99:4016,383,0:0,0,52,76 chr2 272926 . A G 2057.02 PASS AC=2;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 1/1:0,75:75:99:2485,225,0:0,0,39,36 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 1/1:0,97:97:99:2974,291,0:0,0,43,54 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 0/1:8,11:19:99:374,0,254:7,1,10,1 chr2 279705 . C T 8527.06 PASS AC=1;AF=0.593;AN=2;DP=8907;MQ=60;set=variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant28-variant30-variant32-variant34-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:188,160:348:99:3506,0,4647:89,99,80,80 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 1/1:0,18:18:54:549,54,0:0,0,7,11 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 0/1:2,10:12:14:274,0,14:1,1,7,3 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 1/1:0,24:24:72:756,72,0:0,0,15,9 chr2 287448 . TAAAA T,TA,TAA 474.57 PASS AC=1,1,0;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 1/2:31:99:1,0,20,10 chr2 672745 . T C 389.81 PASS AC=1;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 0/1:14,13:27:99:394,0,394:11,3,9,4 chr2 675831 . G T 1364.59 PASS AC=1;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 0/1:22,23:45:99:714,0,698:7,15,5,18 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 1/1:194:99:0,0,80,114 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 1/1:0,53:53:99:2416,165,0:0,0,35,18 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 1/1:0,74:74:99:3526,240,0:0,0,48,26 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 1/1:1,41:42:99:1318,115,0:0,1,29,12 chr2 905385 . GGTCTGGTCTTTCATTTCCTCCCGGCCTCCTCGCCTGCACTGC G 1753.73 PASS AC=1;AF=0.583;AN=2;DP=1235;set=variant4-variant5-variant9-variant11-variant18-variant23-variant31-variant32-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,40:102:99:1274,0,2387:30,32,19,21 chr2 905442 . A T 1749.06 PASS AC=1;AF=0.577;AN=2;DP=896;set=variant4-variant5-variant9-variant11-variant13-variant18-variant23-variant31-variant32-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,35:76:99:1234,0,1489:18,23,17,18 chr2 905497 . C T 276.38 PASS AC=1;AF=0.556;AN=2;DP=231;set=variant4-variant9-variant11-variant18-variant23-variant36-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,6:25:99:160,0,604:4,15,2,4 chr2 905889 . C G 262.33 PASS AC=1;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 0/1:25,18:43:99:533,0,598:9,16,10,8 chr2 905967 . A G 458.14 PASS AC=1;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 0/1:20,21:41:99:474,0,563:8,12,9,12 chr2 946507 . G C 194.51 PASS AC=1;AF=0.618;AN=2;DP=171;MQ=60;set=variant2-variant7-variant9-variant11-variant12-variant15-variant18-variant22-variant23-variant26-variant31-variant34-variant36-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:70:70,0,121:3,2,2,1 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 1/1:0,4:4:12:136,12,0:0,0,1,3 chr2 1079130 . G A 2636.32 PASS AC=2;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 1/1:0,46:46:99:2147,150,0:0,0,29,17 chr2 1079132 . G A 2636.32 PASS AC=2;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 1/1:0,50:50:99:2147,150,0:0,0,32,18 chr2 1079143 . A G 804.84 PASS AC=2;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 1/1:0,62:62:99:1828,184,0:0,0,37,25 chr2 1079320 . C T 1059.38 PASS AC=2;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 1/1:0,67:67:99:2015,201,0:0,0,26,41 chr2 1093965 . G A 3485.21 PASS AC=1;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 0/1:44,45:89:99:978,0,1081:24,20,23,22 chr2 1098891 . A G 152.99 PASS AC=2;AF=0.708;AN=2;DP=61;FractionInformativeReads=1;MQ=60;set=variant8-variant11-variant13-variant14-variant15-variant16-variant19-variant23-variant27-variant29-variant31-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:128,12,0:0,0,2,2 chr2 1133188 . G GCACA 929.31 PASS AC=1;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 0/1:22,13:35:99:470,0,1020:19,3,13,0 chr2 1168756 . G A 1103.52 PASS AC=1;AF=0.538;AN=2;DP=3925;MQ=60;set=variant2-variant4-variant6-variant10-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:80,48:128:99:963,0,1886:39,41,24,24 chr2 1168982 . T A 334.23 PASS AC=1;AF=0.548;AN=2;DP=256;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant10-variant15-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant31-variant32-variant33-variant34-variant36-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:70:196,0,70:0,2,0,5 chr2 1204561 . T C 229.37 PASS AC=1;AF=0.542;AN=2;DP=354;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:99:198,0,133:1,2,2,3 chr2 1204570 . G A 305.12 PASS AC=1;AF=0.553;AN=2;DP=309;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant25-variant26-variant31-variant32-variant33-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:275,0,127:1,3,4,3 chr2 1204612 . A G 511.46 PASS AC=1;AF=0.54;AN=2;DP=600;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant10-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:276,0,235:4,2,4,3 chr2 1204615 . C G 511.47 PASS AC=1;AF=0.54;AN=2;DP=614;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant10-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:276,0,235:4,2,4,3 chr2 1204668 . CT C 620.3 PASS AC=1;AF=0.54;AN=2;DP=963;set=variant2-variant4-variant6-variant10-variant14-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:9,14:23:99:377,0,217:6,3,9,5 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 1/1:0,25:25:75:855,75,0:0,0,18,7 chr2 1250878 . T C 482.51 PASS AC=2;AF=0.729;AN=2;DP=985;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:800,75,0:0,0,17,8 chr2 1320143 . C T 1569.42 PASS AC=1;AF=0.694;AN=2;DP=4882;MQ=60;set=variant-variant3-variant5-variant8-variant9-variant10-variant11-variant13-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,67:135:99:1635,0,1582:32,36,35,32 chr2 1320300 . A G 790.81 PASS AC=1;AF=0.7;AN=2;DP=965;MQ=60;set=variant-variant3-variant5-variant8-variant9-variant10-variant11-variant13-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,17:28:99:671,0,383:1,10,3,14 chr2 1320304 . C A 793.82 PASS AC=1;AF=0.7;AN=2;DP=883;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant8-variant9-variant10-variant11-variant13-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,16:26:99:639,0,386:1,9,3,13 chr2 1320305 . G C 755.14 PASS AC=1;AF=0.7;AN=2;DP=874;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant8-variant9-variant10-variant11-variant13-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,15:24:99:639,0,386:1,8,2,13 chr2 1320332 . T TCCCTTATCTGAAATGCTTGAGACCAGAAGTGTTTGGGA 118.36 PASS AC=1;AF=0.75;AN=2;DP=377;MQ=60;set=variant-variant5-variant8-variant9-variant11-variant13-variant19-variant20-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:96:181,0,96:0,2,1,4 chr2 1418192 . C G 1041.76 PASS AC=1;AF=0.574;AN=2;DP=2220;MQ=60;set=variant-variant4-variant9-variant10-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,54:102:99:1217,0,1121:26,22,30,24 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 1/1:0,17:17:51:674,51,0:0,0,16,1 chr2 1437410 . C T 255.13 PASS AC=2;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 1/1:1,28:29:41:1013,41,0:1,0,5,23 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 0/1:55:99:23,10,9,13 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 1/1:0,63:63:99:1990,189,0:0,0,41,22 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 1/1:0,20:20:60:774,60,0:0,0,17,3 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 0/1:53,33:86:99:747,0,1440:23,30,16,17 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 0/1:30,18:48:99:409,0,758:13,17,9,9 chr2 1460280 . G T 170.94 PASS AC=1;AF=0.63;AN=2;DP=279;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant36-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:210,0,229:1,6,1,6 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 1/1:1,9:10:25:361,25,0:0,1,1,8 chr2 1481155 . G T 718.13 PASS AC=1;AF=0.6;AN=2;DP=2108;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant36-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,31:57:99:853,0,607:11,15,13,18 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 0/1:20,30:50:99:595,0,454:11,9,15,15 chr2 1488668 . T C 309.61 PASS AC=1;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 0/1:12,13:25:99:414,0,343:3,9,2,11 chr2 1491497 . T C 476.5 PASS AC=1;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 0/1:29,24:53:99:696,0,772:19,10,19,5 chr2 1491510 . CA C,CAA 1003.77 PASS AC=0,1;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 0/2:62:99:24,13,19,6 chr2 1497442 . A G 481.1 PASS AC=1;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 0/1:29,26:55:99:672,0,699:18,11,17,9 chr2 1497803 . C T 464.73 PASS AC=1;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 0/1:31,39:70:99:976,0,788:12,19,16,23 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 0/1:3,8:11:62:278,0,62:2,1,7,1 chr2 1499899 . C T 605.83 PASS AC=1;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 0/1:81,40:121:99:958,0,1977:43,38,21,19 chr2 1499927 . A C 785.85 PASS AC=1;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 0/1:83,44:127:99:920,0,2003:40,43,22,22 chr2 1500665 . C T 689.7 PASS AC=1;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 0/1:20,25:45:99:576,0,473:9,11,12,13 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 1/1:0,68:68:99:2279,204,0:0,0,45,23 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 1/1:0,12:12:36:438,36,0:0,0,10,2 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 1/1:0,29:29:87:1305,87,0:0,0,21,8 chr2 1544617 . G A 2321.05 PASS AC=1;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 0/1:83,82:165:99:1916,0,2167:42,41,41,41 chr2 1545110 . G A 300.17 PASS AC=1;AF=0.73;AN=2;DP=749;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-variant36-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,7:23:99:191,0,470:5,11,2,5 chr2 1545134 . G GT 77.12 PASS AC=1;AF=0.5;AN=2;DP=111;MQ=60;set=variant4-variant10-variant20-variant22-variant23-variant29-variant31 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:33:149,0,33:0,3,3,4 chr2 1545310 . A G 290.84 PASS AC=1;AF=0.571;AN=2;DP=200;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant8-variant10-variant12-variant20-variant23-variant24-variant29-variant30-variant31-variant34-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,4:12:99:103,0,202:5,3,3,1 chr2 1546531 . C T 4131.15 PASS AC=1;AF=0.529;AN=2;DP=6526;MQ=60;set=variant2-variant4-variant8-variant10-variant12-variant18-variant20-variant22-variant23-variant24-variant29-variant30-variant31-variant34-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:216,139:355:99:3120,0,5514:99,117,61,78 chr2 1547230 . C T 1043.35 PASS AC=1;AF=0.529;AN=2;DP=1258;MQ=60;set=variant2-variant4-variant8-variant10-variant12-variant18-variant20-variant22-variant23-variant24-variant29-variant30-variant31-variant34-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,37:73:99:905,0,1098:20,16,22,15 chr2 1636053 . A G 1103.41 PASS AC=1;AF=0.5;AN=2;DP=869;MQ=60;set=variant-variant5-variant7-variant10-variant18-variant23-variant28-variant30-variant43 GT:AD:DP:GQ:PL:SB 0/1:47,46:93:99:1182,0,1282:30,17,28,18 chr2 1636553 . C A 1674.21 PASS AC=1;AF=0.5;AN=2;DP=1641;MQ=60;set=variant-variant5-variant7-variant10-variant18-variant23-variant28-variant30-variant43 GT:AD:DP:GQ:PL:SB 0/1:66,62:128:99:1511,0,1710:29,37,23,39 chr2 1636904 . C T 3081.12 PASS AC=1;AF=0.5;AN=2;DP=1806;MQ=60;set=variant-variant5-variant7-variant10-variant18-variant23-variant28-variant30-variant43 GT:AD:DP:GQ:PL:SB 0/1:85,87:172:99:2259,0,2125:38,47,42,45 chr2 1636938 . CT C,CTTT,CTT,CTTTT 602.4 PASS AC=1,0,0,0;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 0/1:156:99:48,54,23,31 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 0/1:53,38:91:99:866,0,1364:24,29,19,19 chr2 1637293 . C T 768.81 PASS AC=1;AF=0.5;AN=2;DP=69;FS=8.288;FractionInformativeReads=1;MQ=60;MQRankSum=-1.357;QD=11.14;ReadPosRankSum=-0.754;SOR=1.069;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:38,31:69:99:797,0,1095:16,22,19,12 chr2 1637531 . A G 1103.48 PASS AC=1;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 0/1:27,28:55:99:714,0,617:13,14,15,13 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 0/1:39,60:99:99:1513,0,931:23,16,33,27 chr2 1639013 . C T 166.13 PASS AC=1;AF=0.5;AN=2;DP=117;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant7-variant10-variant18-variant23-variant30-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:195,0,268:7,2,5,2 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 1/1:0,39:39:99:1890,126,0:0,0,34,5 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 1/1:0,42:42:99:2025,135,0:0,0,36,6 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 0/1:23,25:48:99:1011,0,922:20,3,22,3 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 1/1:0,50:50:99:2278,154,0:0,0,44,6 chr2 1642548 . G A 1097.24 PASS AC=1;AF=0.5;AN=2;DP=503;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant7-variant10-variant18-variant23-variant28-variant30-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,27:53:99:999,0,1002:23,3,23,4 chr2 1642790 . T C 1731.08 PASS AC=1;AF=0.5;AN=2;DP=897;set=variant-variant5-variant7-variant10-variant18-variant23-variant28-variant30-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,52:79:99:1422,0,735:9,18,18,34 chr2 1642803 . CGGGTCTCATTTCAAGGTTTCCTGGGTGTGCACCGCCCCTGATGCTCTGAGCT C 88.73 PASS AC=1;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 0/1:18,5:23:99:177,0,696:3,15,2,3 chr2 1643208 . A G 1545.84 PASS AC=1;AF=0.5;AN=2;DP=1274;MQ=60;set=variant5-variant7-variant10-variant18-variant23-variant28-variant30-variant43 GT:AD:DP:GQ:PL:SB 0/1:74,72:146:99:1744,0,1725:37,37,37,35 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 1/1:0,114:114:99:3531,342,0:0,0,70,44 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 1/1:0,177:177:99:5467,531,0:0,0,99,78 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 0/1:40,52:92:99:1271,0,885:17,23,22,30 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 0/1:26,40:66:99:1202,0,714:21,5,30,10 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 0/1:56,57:113:99:1365,0,1318:32,24,35,22 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 0/1:85,68:153:99:1591,0,2153:47,38,36,32 chr2 1687242 . A ATTGTCTGAGCCACATGTTTTTCATTTTGCTCTCTAATGGATTCAATCCACCCTCCATATATTCTCATTCTTTC 372.55 PASS AC=2;AF=1;AN=2;DP=19;FS=0;MQ=60;set=variant20-variant23-variant37 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:27:362,27,0:0,0,4,2 chr2 1696510 . AAC A 984.85 PASS AC=1;AF=0.586;AN=2;DP=2482;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant11-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant32-variant34-variant36-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,27:52:99:997,0,902:12,13,14,13 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 0/1:23,6:29:99:100,0,600:12,11,4,2 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 0/1:8,6:14:99:106,0,238:2,6,3,3 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 0/1:4,4:8:99:102,0,117:1,3,1,3 chr2 1793988 . AT A 649.74 PASS AC=1;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 0/1:8,13:21:99:309,0,165:4,4,5,8 chr2 1794410 . C T 362.72 PASS AC=1;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 0/1:18,25:43:99:673,0,426:9,9,11,14 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 0/1:39,37:76:99:967,0,1065:16,23,11,26 chr2 1842968 . T A,C 2106.95 PASS AC=0,1;AF=0.121,0.5;AN=2;DP=4783;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant13-variant14-variant16-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/2:161:99:56,33,42,30 chr2 1843285 . A G 343.68 PASS AC=1;AF=0.621;AN=2;DP=615;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant13-variant14-variant16-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:310,0,322:2,8,5,7 chr2 1844458 . T C 824.95 PASS AC=1;AF=0.621;AN=2;DP=1542;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant13-variant14-variant16-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,18:43:99:505,0,669:15,10,12,6 chr2 1844652 . C T 1237.9 PASS AC=1;AF=0.63;AN=2;DP=1774;set=variant-variant3-variant5-variant6-variant9-variant10-variant12-variant13-variant14-variant16-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,26:53:99:939,0,967:12,15,10,16 chr2 1846553 . T G 1356.85 PASS AC=1;AF=0.621;AN=2;DP=4731;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant13-variant14-variant16-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:98,68:166:99:1392,0,2394:51,47,36,32 chr2 1855567 . C A 255.5 PASS AC=1;AF=0.5;AN=2;DP=58;FS=0;FractionInformativeReads=1;MQ=60;set=variant20-variant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:12,8:20:99:278,0,386:2,10,1,7 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 1/1:0,23:23:69:788,69,0:0,0,17,6 chr2 1890173 . A G 529.3 PASS AC=1;AF=0.619;AN=2;DP=894;MQ=60;set=variant3-variant4-variant6-variant9-variant12-variant14-variant15-variant16-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant29-variant30-variant34-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,23:56:99:539,0,766:20,13,10,13 chr2 1925993 . C T 613.39 PASS AC=1;AF=0.5;AN=2;DP=349;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant9-variant10-variant14-variant18-variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:24,14:38:99:445,0,714:18,6,11,3 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 1/1:0,98:98:99:3277,292,0:0,0,48,50 chr2 1946646 . A C 2821.05 PASS AC=1;AF=0.63;AN=2;DP=2369;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant33-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,40:74:99:955,0,850:20,14,26,14 chr2 1946914 . A G 658.35 PASS AC=1;AF=0.66;AN=2;DP=1525;set=variant-variant2-variant3-variant4-variant6-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant20-variant22-variant23-variant25-variant26-variant27-variant30-variant33-variant34-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,18:49:99:358,0,787:13,18,8,10 chr2 1946968 . C T 1058.38 PASS AC=1;AF=0.5;AN=2;DP=677;MQ=60;set=variant2-variant6-variant9-variant14-variant18-variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:45,37:82:99:848,0,1175:24,21,17,20 chr2 1982877 . T G 808.19 PASS AC=1;AF=0.5;AN=2;DP=1016;MQ=60;set=variant2-variant6-variant9-variant10-variant14-variant18-variant23-variant26-variant33-variant34-variant39 GT:AD:DP:GQ:PL:SB 0/1:54,46:100:99:1009,0,1350:31,23,26,20 chr2 1983374 . A C 1029.04 PASS AC=1;AF=0.5;AN=2;DP=2079;MQ=60;set=variant2-variant4-variant6-variant9-variant10-variant14-variant15-variant18-variant22-variant23-variant26-variant33-variant34-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:48,46:94:99:1260,0,1162:29,19,28,18 chr2 1983395 . C T 1095.34 PASS AC=1;AF=0.5;AN=2;DP=1086;MQ=60;set=variant2-variant6-variant9-variant14-variant18-variant23-variant26-variant39 GT:AD:DP:GQ:PL:SB 0/1:50,52:102:99:1454,0,1197:29,21,30,22 chr2 1983619 . A G 416.27 PASS AC=1;AF=0.529;AN=2;DP=984;MQ=60;set=variant2-variant4-variant6-variant9-variant10-variant14-variant15-variant18-variant22-variant23-variant25-variant26-variant33-variant34-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,36:49:99:959,0,221:5,8,12,24 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 0/1:14,4:18:85:85,0,376:5,9,2,2 chr2 3192798 . T C 358.5 PASS AC=2;AF=0.898;AN=2;DP=841;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:418,36,0:0,0,9,3 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 0/1:53,29:82:99:705,0,1353:31,22,18,11 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 1/1:0,9:9:27:356,27,0:0,0,8,1 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 1/1:0,24:24:72:805,72,0:0,0,6,18 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 1/1:0,136:136:99:4357,407,0:0,0,90,46 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 1/1:0,199:199:99:6176,595,0:0,0,124,75 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 1/1:0,81:81:99:2599,242,0:0,0,32,49 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 0/1:33,31:64:99:841,0,935:22,11,15,16 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 0/1:54,58:112:99:1454,0,1440:17,37,24,34 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 1/1:0,4:4:12:180,12,0:0,0,4,0 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 1/1:0,8:8:24:347,24,0:0,0,8,0 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 1/1:0,91:91:99:2726,272,0:0,0,56,35 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 0/1:8,5:13:99:105,0,187:4,4,3,2 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 0/1:4,15:19:93:444,0,93:4,0,9,6 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 0/1:29,12:41:99:292,0,765:17,12,10,2 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 0/1:29,30:59:99:717,0,684:12,17,12,18 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 0/1:10,3:13:83:83,0,386:0,10,0,3 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 0/1:12,11:23:99:346,0,282:8,4,9,2 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 1/1:0,112:112:99:3533,336,0:0,0,69,43 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 1/1:0,47:47:99:2075,142,0:0,0,16,31 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 0/1:10,4:14:99:132,0,304:2,8,0,4 chr2 3392075 . T C 3668.3 PASS AC=2;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 1/1:0,313:313:99:9723,940,0:0,0,153,160 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 0/1:127,125:252:99:3039,0,2773:64,63,61,64 chr2 3392513 . T C 1927.88 PASS AC=2;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 1/1:1,125:126:99:5412,288,0:1,0,57,68 chr2 3392514 . T A 1927.88 PASS AC=2;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 1/1:1,123:124:99:5412,288,0:1,0,55,68 chr2 3393288 . A G 118.65 PASS AC=2;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 1/1:0,12:12:36:540,36,0:0,0,10,2 chr2 3393289 . A C 118.65 PASS AC=2;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 1/1:0,12:12:36:540,36,0:0,0,10,2 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 0/1:78,71:149:99:2702,0,3371:28,50,27,44 chr2 3425514 . G C 1519.09 PASS AC=2;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 1/1:0,91:91:99:2586,272,0:0,0,40,51 chr2 3425948 . T C 309.05 PASS AC=2;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 1/1:0,34:34:99:1187,101,0:0,0,8,26 chr2 3428508 . T G 737.64 PASS AC=2;AF=0.646;AN=2;DP=1175;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant16-variant20-variant21-variant22-variant23-variant25-variant30-variant31-variant33-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1069,96,0:0,0,11,21 chr2 3460870 . T C 112.9 PASS AC=2;AF=0.667;AN=2;DP=173;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant18-variant19-variant21-variant23-variant24-variant26-variant29-variant32-variant33-variant36-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:127,9,0:0,0,3,0 chr2 3469278 . C G 2019.26 PASS AC=1;AF=0.604;AN=2;DP=1749;MQ=60;set=variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant16-variant21-variant23-variant24-variant25-variant26-variant29-variant32-variant33-variant34-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,39:87:99:872,0,1333:31,17,22,17 chr2 3469463 . G C 1197.1 PASS AC=1;AF=0.673;AN=2;DP=2894;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant12-variant14-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant29-variant32-variant33-variant34-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,42:95:99:1015,0,1301:22,31,19,23 chr2 3469702 . A G 570.77 PASS AC=1;AF=0.65;AN=2;DP=767;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,16:33:99:401,0,387:7,10,5,11 chr2 3470115 . T C 2602.62 PASS AC=1;AF=0.648;AN=2;DP=4925;MQ=60;set=variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant29-variant32-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,60:134:99:2217,0,2941:39,35,30,30 chr2 3470124 . G A 4640.03 PASS AC=1;AF=0.646;AN=2;DP=4505;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant29-variant32-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,59:134:99:2175,0,2929:40,35,29,30 chr2 3470186 . G C 2540.84 PASS AC=1;AF=0.667;AN=2;DP=3911;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant12-variant13-variant14-variant16-variant18-variant19-variant21-variant23-variant24-variant26-variant29-variant32-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,48:119:99:1170,0,1735:34,37,21,27 chr2 3470254 . T G 1240.25 PASS AC=1;AF=0.648;AN=2;DP=2469;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant12-variant13-variant14-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant32-variant34-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,30:69:99:769,0,1018:14,25,9,21 chr2 3481637 . T C 769.86 PASS AC=1;AF=0.654;AN=2;DP=935;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant12-filterInvariant13-variant14-variant16-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant32-variant34-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,22:35:99:654,0,279:6,7,7,15 chr2 3481659 . G A 674.34 PASS AC=1;AF=0.667;AN=2;DP=783;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant12-variant14-variant16-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant32-variant34-variant36-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,17:28:99:519,0,290:3,8,6,11 chr2 3481716 . T C 489.72 PASS AC=1;AF=0.654;AN=2;DP=656;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant12-variant13-variant14-variant16-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant32-variant34-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:93:275,0,93:1,3,2,7 chr2 3482722 . C T 2719.23 PASS AC=1;AF=0.563;AN=2;DP=1664;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant14-variant19-variant21-variant23-variant29-variant42 GT:AD:DP:GQ:PL:SB 0/1:86,91:177:99:2038,0,2052:40,46,49,42 chr2 3483181 . C T 4641.75 PASS AC=1;AF=0.556;AN=2;DP=1909;MQ=60;set=variant3-variant4-variant13-variant14-variant19-variant21-variant23-variant29-variant42 GT:AD:DP:GQ:PL:SB 0/1:86,100:186:99:2588,0,2200:30,56,48,52 chr2 3483205 . C T 4791.91 PASS AC=1;AF=0.66;AN=2;DP=4543;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant12-variant13-variant14-variant16-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant32-variant34-variant36-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,89:165:99:2322,0,1864:36,40,43,46 chr2 3483390 . T G 1246.74 PASS AC=1;AF=0.66;AN=2;DP=1597;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant12-variant13-variant14-variant16-variant19-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant32-variant34-variant36-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,21:40:99:548,0,529:5,14,7,14 chr2 3488502 . A G 3210.46 PASS AC=1;AF=0.643;AN=2;DP=6296;MQ=60;set=variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant19-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant32-variant34-variant36-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:109,100:209:99:2229,0,2402:60,49,58,42 chr2 3488871 . C T 307.11 PASS AC=1;AF=0.563;AN=2;DP=181;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant14-variant19-variant21-variant23-variant27-variant42 GT:AD:DP:GQ:PL:SB 0/1:7,14:21:99:387,0,174:2,5,5,9 chr2 3502909 . A ACTT 1454.7 PASS AC=1;AF=0.603;AN=2;DP=2251;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant32-variant34-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,35:65:99:1318,0,2311:14,16,16,19 chr2 3502910 . G T 1463.74 PASS AC=1;AF=0.603;AN=2;DP=2209;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant32-variant34-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,32:62:99:1318,0,2311:14,16,13,19 chr2 3504290 . GTGTACCTGCCGCCGCA G 1382.98 PASS AC=1;AF=0.617;AN=2;DP=2391;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant32-variant34-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,43:85:99:1673,0,6689:28,14,27,16 chr2 3504687 . A G 1415.06 PASS AC=1;AF=0.607;AN=2;DP=5767;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant32-variant34-variant36-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:115,82:197:99:1841,0,2646:63,52,41,41 chr2 3504819 . A G 638.77 PASS AC=1;AF=0.603;AN=2;DP=2669;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant32-variant34-variant36-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,28:75:99:697,0,1168:17,30,10,18 chr2 3504893 . G GA 94.03 PASS AC=1;AF=0.607;AN=2;DP=723;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant32-variant34-variant36-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,7:21:99:171,0,419:1,13,1,6 chr2 3518643 . T C 120.16 PASS AC=1;AF=0.531;AN=2;DP=471;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant8-variant12-variant14-variant17-variant21-variant23-variant26-variant27-variant28-variant37-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:23,14:37:99:363,0,552:8,15,3,11 chr2 3519616 . A G 1242.81 PASS AC=1;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 0/1:8,12:20:99:339,0,206:6,2,9,3 chr2 3519656 . T C 328.19 PASS AC=1;AF=0.531;AN=2;DP=706;MQ=60;set=variant2-variant3-variant4-variant8-variant12-variant14-variant17-variant21-variant23-variant26-variant27-variant28-variant37-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:24,15:39:99:334,0,606:15,9,8,7 chr2 3519739 . C A 709.34 PASS AC=1;AF=0.533;AN=2;DP=1323;MQ=60;set=variant2-variant3-variant4-variant8-variant12-variant14-variant17-variant21-variant23-variant26-variant27-variant28-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:48,24:72:99:505,0,1260:25,23,12,12 chr2 3519839 . A G 1889.53 PASS AC=1;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 0/1:14,30:44:99:707,0,292:5,9,10,20 chr2 3520680 . CTTTT C 2059.83 PASS AC=1;AF=0.533;AN=2;DP=1860;MQ=60;set=variant2-variant3-variant4-variant8-variant12-variant14-variant17-variant21-variant23-variant26-variant27-variant28-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:44,65:109:99:2591,0,2259:16,28,27,38 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 1/1:0,27:27:81:761,81,0:0,0,15,12 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 1/1:0,127:127:99:3981,381,0:0,0,68,59 chr2 3523444 . C A 1393.33 PASS AC=1;AF=0.542;AN=2;DP=2071;MQ=60;set=variant2-variant3-variant4-variant12-variant17-variant21-variant23-variant26-variant27-variant28-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:68,80:148:99:1778,0,1617:31,37,39,41 chr2 3579585 . A G 407.32 PASS AC=1;AF=0.5;AN=2;DP=348;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant11-variant17-variant18-variant21-variant23-variant28-variant29-variant31-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,13:21:99:311,0,205:6,2,7,6 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 0/1:29,26:55:99:710,0,730:16,13,16,10 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 0/1:9,17:26:99:544,0,241:7,2,14,3 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 0/1:16,35:51:99:819,0,356:8,8,17,18 chr2 3605468 . A G 2208.25 PASS AC=1;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 0/1:76,74:150:99:1907,0,1776:31,45,33,41 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 0/1:33,47:80:99:1822,0,1719:9,24,18,29 chr2 3605538 . A C 1272.96 PASS AC=1;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 0/1:28,39:67:99:1592,0,1596:7,21,16,23 chr2 3627648 . G C 1777.87 PASS AC=1;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 0/1:64,35:99:99:662,0,1501:29,35,18,17 chr2 3628679 . G A 675.98 PASS AC=1;AF=0.5;AN=2;DP=79;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant30-variant36 GT:AD:DP:GQ:PL:SB 0/1:11,20:31:99:704,0,359:1,10,2,18 chr2 3652616 . G C 2132.13 PASS AC=1;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 0/1:39,37:76:99:773,0,954:19,20,18,19 chr2 3653279 . C T 543.97 PASS AC=1;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 0/1:14,6:20:99:121,0,376:10,4,3,3 chr2 3653576 . A G 3186.37 PASS AC=1;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 0/1:32,41:73:99:1252,0,1043:19,13,28,13 chr2 3653844 . T C 4314.7 PASS AC=1;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 0/1:67,54:121:99:1398,0,1741:26,41,17,37 chr2 3660752 . T C 1173.47 PASS AC=1;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 0/1:20,17:37:99:551,0,491:13,7,13,4 chr2 3673648 . G A 1245.81 PASS AC=1;AF=0.5;AN=2;DP=1835;MQ=60;set=variant2-variant6-variant15-variant16-variant20-variant23-variant29-variant31-variant32-variant36-variant38-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,66:130:99:1570,0,1414:33,31,31,35 chr2 3685046 . T C 1393.42 PASS AC=2;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 1/1:0,40:40:99:1279,119,0:0,0,28,12 chr2 3685074 . A G 1976.82 PASS AC=2;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 1/1:0,58:58:99:1922,173,0:0,0,40,18 chr2 3774390 . G A 242.9 PASS AC=1;AF=0.5;AN=2;DP=39;FractionInformativeReads=1;MQ=60;set=variant14-variant23-variant36 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:237,0,189:2,2,5,1 chr2 3774394 . C T 239.89 PASS AC=1;AF=0.5;AN=2;DP=43;FractionInformativeReads=1;MQ=60;set=variant14-variant23-variant36 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:268,0,219:4,2,6,1 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 1/1:0,24:24:70:704,70,0:0,0,16,8 chr2 3774448 . T C 295.78 PASS AC=2;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 1/1:0,27:27:81:858,81,0:0,0,17,10 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 1/1:0,70:70:99:1992,209,0:0,0,41,29 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 0/1:14,15:29:99:363,0,365:9,5,11,4 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 1/1:2,17:19:3:371,3,0:1,1,4,13 chr2 3816759 . G T 79.98 PASS AC=1;AF=0.5;AN=2;DP=309;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant9-variant18-variant19-variant22-variant23-variant25-variant26-variant28-variant31-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,13:32:99:361,0,545:11,8,9,4 chr2 3826324 . C T 435.26 PASS AC=1;AF=0.563;AN=2;DP=1056;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant28-variant31-variant34-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,15:37:99:353,0,536:13,9,9,6 chr2 3826387 . T C 699.91 PASS AC=1;AF=0.563;AN=2;DP=1488;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant28-variant31-variant34-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,20:52:99:454,0,742:17,15,13,7 chr2 3826597 . G A 160.84 PASS AC=1;AF=0.563;AN=2;DP=1083;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant26-variant28-variant31-variant34-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,21:36:99:540,0,335:6,9,9,12 chr2 3832358 . T C 328.63 PASS AC=1;AF=0.779;AN=2;DP=431;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,7:8:18:207,0,18:1,0,5,2 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 1/1:0,56:56:99:1742,168,0:0,0,33,23 chr2 5832667 . T C 76.45 PASS AC=1;AF=0.872;AN=2;DP=351;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-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,6:7:24:240,0,24:1,0,5,1 chr2 5834577 . A G 621.31 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=472;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:46,19:65:99:125,0,1019:29,17,0,19 chr2 5835227 . C CT 1488.93 PASS AC=1;AF=0.5;AN=2;DP=402;MQ=60;set=variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:123,73:196:99:1526,0,3080:59,64,35,38 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 0/1:166:99:61,55,14,36 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 0/1:124:99:71,34,11,8 chr2 5839841 . CTTTTT C,CTTTT,CT,CTTT,CTTTTTT 4231.49 PASS AC=0,1,0,0,0;AF=0.33,0.216,0.068,0.011,0.011;AN=2;DP=9341;set=Intersection GT:DP:GQ:SB 0/2:150:99:24,39,29,58 chr2 5840552 . CA CAA,C 2320.18 PASS AC=1,0;AF=0.32,0.18;AN=2;DP=6902;set=variant-variant2-variant3-variant7-variant9-filterInvariant11-filterInvariant13-variant16-variant18-variant21-filterInvariant22-variant23-filterInvariant24-variant26-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-variant32-variant33-variant36-variant37-variant38-filterInvariant40-variant41 GT:DP:GQ:SB 0/1:271:99:88,66,61,56 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 0/1:79,51:130:99:1259,0,1898:38,41,22,29 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 0/1:21,43:64:99:1155,0,536:14,7,22,21 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 1/1:0,22:22:66:948,66,0:0,0,17,5 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 1/1:0,32:32:97:1250,97,0:0,0,23,9 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 1/1:0,8:8:24:279,24,0:0,0,2,6 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 1/1:0,137:137:99:4123,410,0:0,0,86,51 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 1/1:0,167:167:99:4979,501,0:0,0,75,92 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 1/1:1,215:216:99:6058,632,0:1,0,95,120 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 1/1:0,77:77:99:2417,231,0:0,0,39,38 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 1/1:0,74:74:99:2107,221,0:0,0,38,36 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 1/1:0,80:80:99:2439,240,0:0,0,31,49 chr2 7036472 . A T 3018.04 PASS AC=1;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 0/1:105,80:185:99:2239,0,2955:45,60,38,42 chr2 7036529 . T C 3469.4 PASS AC=1;AF=0.5;AN=2;DP=1452;MQ=60;set=variant-variant10-variant22-variant23-variant32-variant40 GT:AD:DP:GQ:PL:SB 0/1:123,113:236:99:3183,0,2968:65,58,68,45 chr2 7036621 . A G 4141.96 PASS AC=1;AF=0.5;AN=2;DP=1909;MQ=60;set=variant-variant10-variant22-variant23-variant32-variant40 GT:AD:DP:GQ:PL:SB 0/1:132,155:287:99:3836,0,3189:61,71,80,75 chr2 7036663 . C CTT,CT 3445.28 PASS AC=1,0;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 0/1:177:99:42,80,20,35 chr2 7036678 . C T 4403.17 PASS AC=1;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 0/1:115,73:188:99:2513,0,3233:38,77,28,45 chr2 7036756 . T C 1419.51 PASS AC=1;AF=0.5;AN=2;DP=526;MQ=60;set=variant-variant10-variant22-variant23-variant32-variant40 GT:AD:DP:GQ:PL:SB 0/1:34,50:84:99:1628,0,1027:11,23,9,41 chr2 7036811 . C T 944.51 PASS AC=1;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 0/1:31,33:64:99:908,0,843:10,21,15,18 chr2 7036838 . G C 766.93 PASS AC=1;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 0/1:26,34:60:99:844,0,673:12,14,15,19 chr2 7037067 . G T 748.35 PASS AC=1;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 0/1:40,30:70:99:1129,0,2393:22,18,16,14 chr2 7037068 . C T 748.35 PASS AC=1;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 0/1:40,30:70:99:1129,0,2393:22,18,16,14 chr2 7037174 . A T 907.38 PASS AC=1;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 0/1:46,44:90:99:1081,0,1079:25,21,22,22 chr2 7038109 . G C 666.93 PASS AC=1;AF=0.5;AN=2;DP=241;set=variant-variant10-variant23-variant32-variant40 GT:AD:DP:GQ:PL:SB 0/1:20,20:40:99:733,0,669:18,2,19,1 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 0/1:75:99:27,23,22,3 chr2 7038428 . C T 155.87 PASS AC=1;AF=0.5;AN=2;DP=7;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.198;QD=22.27;ReadPosRankSum=-0.922;SOR=1.609;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:66:184,0,66:0,2,0,5 chr2 7046272 . TACACACACACACACACAC T,TACACACACACACACAC,TACACACACACAC,TACACACACAC,TACACACACACACAC,TACACAC 792.35 PASS AC=1,0,0,0,0,0;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 0/1:12:76:0,1,11,0 chr2 7046309 . A T 905.03 PASS AC=1;AF=0.594;AN=2;DP=699;set=variant-variant3-variant4-variant7-variant8-variant9-variant11-variant12-variant18-variant22-variant23-variant25-variant28-variant32-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,40:41:8:1210,0,8:0,1,29,11 chr2 7050483 . ATGTGTGTG A,ATGTGTGTGTGTGTG,ATGTGTGTGTGTG,ATGTGTG,ATGTGTGTGTGTGTGTG,ATGTGTGTGTG 925.59 PASS AC=2,0,0,0,0,0;AF=0.202,0.31,0.012,0.06,0.036,0.06;AN=2;DP=2728;set=variant-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-variant33-variant34-variant36-variant37-filterInvariant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:44:99:0,0,19,25 chr2 7076975 . AGTGT AGTGTGTGTGTGTGTGT,AGTGTGTGT,AGTGTGT,AGTGTGTGTGTGTGT,AGTGTGTGTGT,AGT,A,AGTGTGTGTGTGT 652.93 PASS AC=0,1,0,0,1,0,0,0;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 2/5:27:99:1,0,20,6 chr2 7130516 . TACACACACACACACAC TAC,TACACACACAC,TACAC,T,TACACACACACACACACAC,TACACACACACAC,TACACACAC,TACACACACACACACACACACAC,TACACACACACACACACACAC 466.86 PASS AC=0,2,0,0,0,0,0,0,0;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 2/2:8:6:0,1,0,7 chr2 7136862 . C T 85.51 PASS AC=1;AF=0.5;AN=2;DP=6;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.406;QD=14.25;ReadPosRankSum=1.537;SOR=2.093;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:76:114,0,76:2,1,3,0 chr2 7136981 . C T 1068.78 PASS AC=1;AF=0.5;AN=2;DP=509;MQ=60;set=variant8-variant13-variant17-variant23-variant27-variant32-variant34-variant36 GT:AD:DP:GQ:PL:SB 0/1:44,22:66:99:448,0,1215:28,16,12,10 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 1/1:0,93:93:99:3035,279,0:0,0,54,39 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 1/1:0,157:157:99:4473,471,0:0,0,84,73 chr2 7161076 . A G 126.94 PASS AC=1;AF=0.5;AN=2;DP=127;FractionInformativeReads=1;MQ=60;set=variant8-variant17-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:18,9:27:99:243,0,488:6,12,2,7 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 0/1:26,43:69:99:987,0,531:15,11,25,18 chr2 7170388 . CTGTGTGTGTGTGTGTG CTGTGTGTGTG,CTGTG,CTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTG,CTGTGTG,C,CTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTG,CTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTG 409.88 PASS AC=0,1,0,0,0,0,0,0,0,0,0;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 0/2:37:99:8,15,3,11 chr2 7181478 . C T 6069.85 PASS AC=1;AF=0.5;AN=2;DP=3416;MQ=60;set=variant3-variant6-variant13-variant15-variant19-variant21-variant23-variant37 GT:AD:DP:GQ:PL:SB 0/1:208,200:408:99:7663,0,10279:103,105,96,104 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 0/1:209,206:415:99:7681,0,10334:103,106,97,109 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 0/1:31,29:60:99:896,0,825:18,13,21,8 chr2 7184419 . T A 362.07 PASS AC=1;AF=0.5;AN=2;DP=127;MQ=60;set=variant3-variant6-variant13-variant15-variant19-variant21-variant23-variant37 GT:AD:DP:GQ:PL:SB 0/1:5,9:14:99:306,0,134:2,3,1,8 chr2 7187199 . A G 1482.52 PASS AC=1;AF=0.5;AN=2;DP=347;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant13-variant15-variant19-variant21-variant23-variant37 GT:AD:DP:GQ:PL:SB 0/1:12,15:27:99:594,0,732:9,3,10,5 chr2 7187209 . C G 1601 PASS AC=1;AF=0.5;AN=2;DP=382;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant13-variant15-variant19-variant21-variant23-variant37 GT:AD:DP:GQ:PL:SB 0/1:13,17:30:99:634,0,760:10,3,11,6 chr2 7187397 . CTA C 1579.5 PASS AC=1;AF=0.5;AN=2;DP=594;MQ=60;set=variant3-variant6-variant13-variant15-variant19-variant21-variant23-variant37 GT:AD:DP:GQ:PL:SB 0/1:34,22:56:99:670,0,1326:13,21,8,14 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 0/1:10,6:16:99:178,0,279:6,4,5,1 chr2 7243449 . AGTGTGTGT AGT,AGTGT,AGTGTGT,AGTGTGTGTGT,A 1057.25 PASS AC=1,0,0,1,0;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 1/4:72:99:6,3,38,25 chr2 7403641 . TACACACACAC TACACACACACACACAC,TACACACACACAC,TACACACACACACAC,T,TACACACACACACACACAC 643.8 PASS AC=0,1,1,0,0;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 2/3:25:99:0,0,15,10 chr2 7409989 . TTGTG TTG,T 753.33 PASS AC=1,0;AF=0.611,0.014;AN=2;DP=3332;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:61:99:13,22,7,19 chr2 7421557 . C G 466.05 PASS AC=1;AF=0.768;AN=2;DP=1139;FractionInformativeReads=1;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,10:21:99:301,0,361:10,1,9,1 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 0/1:26:99:14,3,9,0 chr2 7540646 . C CA 1654.92 PASS AC=2;AF=0.725;AN=2;DP=3824;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-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:3023,256,0:0,0,39,46 chr2 7540695 . C G 1058.37 PASS AC=1;AF=0.689;AN=2;DP=3078;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,28:64:99:589,0,973:13,23,13,15 chr2 7540784 . T C 347.26 PASS AC=1;AF=0.689;AN=2;DP=723;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:150,0,193:1,5,2,4 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 0/1:50,44:94:99:937,0,1110:26,24,22,22 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 0/1:40,29:69:99:620,0,927:19,21,11,18 chr2 8819143 . GCCA G 3553.68 PASS AC=2;AF=0.909;AN=2;DP=4812;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:3315,243,0:0,0,49,32 chr2 8822892 . CAAAAAAAAAAAA CAAAAAAAAAAA,CAAAAAAAAA,C,CAAAAAAAAAA 293.77 PASS AC=0,1,0,0;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 0/2:28:99:10,4,12,2 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 1/1:42:99:0,0,30,12 chr2 8823163 . T C 753.71 PASS AC=1;AF=0.556;AN=2;DP=418;MQ=60;set=variant5-variant7-variant10-variant14-variant18-variant23-variant27-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:24,22:46:99:568,0,609:8,16,6,16 chr2 8823941 . GA G 2872.64 PASS AC=1;AF=0.556;AN=2;DP=3167;set=variant5-variant7-variant10-variant14-variant18-variant23-variant27-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:114,126:240:99:2934,0,2519:30,84,38,88 chr2 8824668 . CACA CCA,C 62.78 PASS AC=0,1;AF=0.406,0.219;AN=2;DP=492;set=variant3-variant4-variant5-variant7-variant8-variant10-variant21-variant23-filterInvariant24-variant27-variant28-variant32-variant33-variant37-variant39-filterInvariant43 GT:DP:GQ:SB 0/2:32:99:1,14,1,16 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 0/1:19,11:30:99:248,0,677:1,18,0,11 chr2 8824684 . C T 913.2 PASS AC=1;AF=0.556;AN=2;DP=266;set=variant5-variant7-variant10-variant18-variant23-variant27-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:14,15:29:99:583,0,502:1,13,0,15 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 1/1:0,57:57:99:1989,171,0:0,0,29,28 chr2 8872150 . TAAG T 224.54 PASS AC=1;AF=0.5;AN=2;DP=15;FS=6.264;FractionInformativeReads=0.733;MQ=60;MQRankSum=-0.278;QD=14.97;ReadPosRankSum=0.678;SOR=0.061;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:262,0,176:0,4,3,4 chr2 8887910 . A T 68.21 PASS AC=2;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 1/1:0,14:14:42:536,42,0:0,0,12,2 chr2 8890179 . G A 872.02 PASS AC=1;AF=0.5;AN=2;DP=579;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant15-variant23-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:46,71:117:99:1792,0,1187:31,15,47,24 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 1/1:0,49:49:99:1502,147,0:0,0,17,32 chr2 8911010 . T C 427 PASS AC=2;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 1/1:0,34:34:99:1135,102,0:0,0,9,25 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 1/1:0,38:38:99:1305,114,0:0,0,29,9 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 1/1:0,9:9:26:273,26,0:0,0,2,7 chr2 8946568 . G T 43.84 PASS AC=1;AF=0.5;AN=2;DP=51;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant15-variant23-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:31:151,0,31:0,1,0,4 chr2 8977487 . C T 468.12 PASS AC=1;AF=0.609;AN=2;DP=430;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant10-variant13-variant15-variant17-variant19-variant20-variant22-variant23-variant25-variant27-variant30-variant34-variant36-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:250,0,280:5,4,7,0 chr2 8993505 . A C 4359.89 PASS AC=1;AF=0.588;AN=2;DP=4998;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant11-variant15-variant17-variant20-variant22-variant23-variant33-variant37-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:150,134:284:99:3016,0,3597:74,76,70,64 chr2 8995712 . G A 2484.24 PASS AC=1;AF=0.5;AN=2;DP=1967;FractionInformativeReads=1;MQ=60;set=variant5-variant7-variant9-variant15-variant17-variant20-variant23-variant33-variant42 GT:AD:DP:GQ:PL:SB 0/1:103,92:195:99:2135,0,2606:58,45,54,38 chr2 8996728 . A G 862.65 PASS AC=1;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 0/1:9,15:24:99:548,0,323:0,9,0,15 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 1/1:0,93:93:99:3022,279,0:0,0,47,46 chr2 9114601 . T G 1288.38 PASS AC=1;AF=0.5;AN=2;DP=151;FractionInformativeReads=1;MQ=60;set=variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:37,49:86:99:1317,0,887:18,19,26,23 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 1/1:0,73:73:99:3231,223,0:0,0,44,29 chr2 9419415 . C T 4457.88 PASS AC=2;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 1/1:0,72:72:99:3180,217,0:0,0,42,30 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 1/1:0,117:117:99:3752,350,0:0,0,37,80 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 1/1:0,13:13:39:497,39,0:0,0,11,2 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 1/1:0,23:23:69:1035,69,0:0,0,15,8 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 1/1:0,50:50:99:1782,150,0:0,0,13,37 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 1/1:0,167:167:99:5110,500,0:0,0,67,100 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 0/1:9,16:25:99:525,0,308:2,7,7,9 chr2 9546212 . GTGTT G 136.56 PASS AC=1;AF=0.5;AN=2;DP=137;set=variant4-variant16-variant20-variant23-variant31-variant33-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:237,0,189:2,2,3,3 chr2 9546230 . A G 46.72 PASS AC=1;AF=0.5;AN=2;DP=49;set=variant23-variant24-variant27-variant30 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:75:75,0,120:2,1,1,1 chr2 9546245 . C A 100.75 PASS AC=2;AF=0.694;AN=2;DP=196;set=variant2-variant12-variant15-variant16-variant17-variant20-variant22-variant23-variant26-variant28-variant29-variant30-variant33-variant34-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,2,2 chr2 9554562 . CA C 249.45 PASS AC=1;AF=0.667;AN=2;DP=35;FS=0;MQ=60;set=variant6-variant19-variant23 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:42:71,0,42:0,2,0,3 chr2 9558905 . CTT CTTT,CT,C 62.37 PASS AC=0,0,1;AF=0.216,0.284,0.014;AN=2;DP=2378;set=filterInvariant-variant2-filterInvariant3-variant4-filterInvariant5-variant6-variant7-filterInvariant8-variant9-filterInvariant10-variant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant16-variant18-filterInvariant19-variant21-variant22-variant23-variant26-variant28-filterInvariant29-variant30-filterInvariant31-filterInvariant32-variant34-variant36-variant37-filterInvariant38-filterInvariant39-variant40-filterInvariant41-variant42-filterInvariant43-variant44 GT:DP:GQ:SB 0/3:23:99:4,11,2,6 chr2 9597320 . G GTGTGTGT 88.51 PASS AC=1;AF=0.5;AN=2;DP=13;FS=3.09;FractionInformativeReads=0.846;MQ=58.55;MQRankSum=-0.278;QD=6.81;ReadPosRankSum=0.597;SOR=1.981;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:99:126,0,257:2,5,0,4 chr2 9614523 . G A 1284.69 PASS AC=1;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 0/1:39,59:98:99:1491,0,893:25,14,34,25 chr2 9616061 . G A 457.09 PASS AC=1;AF=0.5;AN=2;DP=106;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant23 GT:AD:DP:GQ:PL:SB 0/1:14,16:30:99:343,0,320:10,4,9,7 chr2 9629388 . ATTTT ATTT,AT,ATT,ATTTTT,A 126.61 PASS AC=1,0,0,0,0;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 0/1:23:99:4,6,2,11 chr2 9629854 . CAAAAAAA CAAAAAAAA,CAA,CA,CAAAAAA,CAAAA,CAAAAA,CAAA,C 302.13 PASS AC=0,0,0,0,1,0,0,0;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 0/5:79:99:29,21,21,8 chr2 9658388 . CAAAAAAAAAAAAA CAAAAAAAAAAAA,CAAAAAAAA,CAAAAAAAAAAA,C,CAAAAAAAAAA 32.16 PASS AC=0,1,0,0,0;AF=0.214,0.071,0.071,0.071,0.071;AN=2;DP=86;MQ=60;set=variant6-filterInvariant7-variant23-variant28-variant31-variant34-variant40 GT:DP:GQ:SB 0/2:5:76:1,2,1,1 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 0/1:34,27:61:99:631,0,1040:11,23,8,19 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 0/1:140,94:234:99:3582,0,7218:67,73,34,60 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 0/1:43,46:89:99:1090,0,896:21,22,21,25 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 0/1:25,7:32:99:219,0,698:18,7,7,0 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 1/1:0,133:133:99:4966,400,0:0,0,59,74 chr2 9983686 . G T 909.1 PASS AC=1;AF=0.691;AN=2;DP=2742;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,33:81:99:691,0,1239:21,27,12,21 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 1/1:1,67:68:99:1961,157,0:0,1,26,41 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 0/1:47,35:82:99:1002,0,1420:23,24,20,15 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 0/1:6,4:10:99:150,0,225:5,1,3,1 chr2 9989442 . A G 1932.87 PASS AC=1;AF=0.58;AN=2;DP=2316;MQ=60;set=variant3-variant8-variant9-variant12-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,44:73:99:1086,0,701:14,15,22,22 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 1/1:0,5:5:15:225,15,0:0,0,5,0 chr2 9994288 . C G 229.41 PASS AC=1;AF=0.563;AN=2;DP=255;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant9-variant12-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:195,0,195:5,0,5,0 chr2 10008872 . A G 2482.14 PASS AC=1;AF=0.58;AN=2;DP=4187;MQ=60;set=variant3-variant8-variant9-variant12-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,79:147:99:1927,0,1614:27,41,36,43 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 0/1:10,10:20:99:212,0,225:6,4,6,4 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 0/1:34,27:61:99:724,0,880:22,12,17,10 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 0/1:69,48:117:99:1134,0,1625:38,31,27,21 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 1/1:1,117:118:99:4055,315,0:1,0,67,50 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 1/1:0,60:60:99:2018,180,0:0,0,23,37 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 0/1:55,90:145:99:2178,0,1258:22,33,39,51 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 0/1:53,78:131:99:1870,0,1206:21,32,34,44 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 0/1:30:99:1,9,3,17 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 0/1:50,47:97:99:996,0,1167:21,29,21,26 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 0/1:72,40:112:99:953,0,1814:39,33,23,17 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 0/1:25,29:54:99:812,0,691:16,9,19,10 chr2 10074384 . G A 834.19 PASS AC=1;AF=0.545;AN=2;DP=1204;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant8-variant9-variant12-variant14-variant15-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant32-variant33-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:14,21:35:99:663,0,396:5,9,10,11 chr2 10091952 . G A 1380.87 PASS AC=1;AF=0.5;AN=2;DP=1152;MQ=60;set=variant-variant10-variant14-variant20-variant23-variant29-variant30-variant32-variant34-variant40 GT:AD:DP:GQ:PL:SB 0/1:53,65:118:99:1478,0,1122:24,29,33,32 chr2 10092019 . G A 971.36 PASS AC=1;AF=0.5;AN=2;DP=733;MQ=60;set=variant-variant10-variant14-variant20-variant23-variant29-variant30-variant32-variant34-variant40 GT:AD:DP:GQ:PL:SB 0/1:35,53:88:99:1049,0,728:15,20,21,32 chr2 10092933 . CTTAG C 157.73 PASS AC=1;AF=0.5;AN=2;DP=223;MQ=60;set=variant-variant10-variant14-variant17-variant20-variant22-variant23-variant29-variant30-variant32-variant33-variant34-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:11,5:16:99:177,0,626:9,2,3,2 chr2 10093003 . G A 897.83 PASS AC=1;AF=0.5;AN=2;DP=532;FractionInformativeReads=1;MQ=60;set=variant-variant10-variant14-variant20-variant23-variant29-variant30-variant32-variant34-variant40 GT:AD:DP:GQ:PL:SB 0/1:25,22:47:99:607,0,733:19,6,14,8 chr2 10094992 . A G 755.96 PASS AC=2;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 1/1:0,62:62:99:1789,185,0:0,0,38,24 chr2 10095020 . G GT 648.04 PASS AC=1;AF=0.5;AN=2;DP=849;MQ=60;set=variant-variant10-variant14-variant20-variant23-variant29-variant30-variant32-variant34-variant40 GT:AD:DP:GQ:PL:SB 0/1:48,42:90:99:876,0,1084:28,20,25,17 chr2 10095185 . T C 1504.11 PASS AC=1;AF=0.531;AN=2;DP=2524;MQ=60;set=variant-variant6-variant10-variant14-variant17-variant20-variant22-variant23-variant29-variant30-variant32-variant33-variant34-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:89,82:171:99:1965,0,2053:43,46,39,43 chr2 10095374 . C T 694.39 PASS AC=1;AF=0.5;AN=2;DP=1155;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant15-variant19-variant21-variant23-variant26-variant27-variant32-variant37-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,15:41:99:352,0,765:7,19,4,11 chr2 10101468 . A G 914.84 PASS AC=1;AF=0.531;AN=2;DP=2058;MQ=60;set=variant-variant6-variant10-variant14-variant17-variant20-variant22-variant23-variant29-variant30-variant32-variant33-variant34-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:59,73:132:99:1667,0,1519:27,32,35,38 chr2 10102735 . T C 366.79 PASS AC=1;AF=0.5;AN=2;DP=201;FractionInformativeReads=1;MQ=60;set=variant-variant10-variant14-variant20-variant23-variant29-variant30-variant32-variant34-variant40 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:90:107,0,90:1,3,0,3 chr2 10105535 . T C 874.87 PASS AC=1;AF=0.531;AN=2;DP=1542;MQ=60;set=variant-variant6-variant10-variant14-variant17-variant20-variant22-variant23-variant29-variant30-variant32-variant33-variant34-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:43,53:96:99:1328,0,1007:17,26,21,32 chr2 10105584 . A AT 240.59 PASS AC=1;AF=0.531;AN=2;DP=849;MQ=60;set=variant-variant6-variant10-variant14-variant17-variant20-variant22-variant23-variant29-variant30-variant32-variant33-variant34-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:23,20:43:99:370,0,473:7,16,7,13 chr2 10105644 . T C 241.03 PASS AC=1;AF=0.533;AN=2;DP=251;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant10-variant14-variant17-variant20-variant22-variant23-variant29-variant30-variant32-variant33-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:12,4:16:99:126,0,326:4,8,0,4 chr2 10126123 . A T 736.09 PASS AC=1;AF=0.529;AN=2;DP=663;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant10-variant14-variant20-variant23-variant24-variant26-variant29-variant30-variant32-variant33-variant34-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,14:28:99:518,0,468:12,2,14,0 chr2 10126330 . G A 1725.33 PASS AC=1;AF=0.529;AN=2;DP=1866;MQ=60;set=variant-variant2-variant6-variant10-variant14-variant20-variant23-variant24-variant26-variant29-variant30-variant32-variant33-variant34-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,62:94:99:1704,0,759:14,18,24,38 chr2 10126416 . A G 914.97 PASS AC=2;AF=0.641;AN=2;DP=1138;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,32:32:96:1025,96,0:0,0,9,23 chr2 10130973 . T G 529.17 PASS AC=1;AF=0.529;AN=2;DP=845;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant10-variant14-variant20-variant23-variant24-variant26-variant29-variant30-variant32-variant33-variant34-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,17:45:99:456,0,750:8,20,5,12 chr2 10133728 . T C 1609.22 PASS AC=1;AF=0.5;AN=2;DP=2058;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant15-variant19-variant21-variant23-variant26-variant27-variant32-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,41:86:99:1020,0,1083:23,22,20,21 chr2 10133820 . C T 840.02 PASS AC=1;AF=0.5;AN=2;DP=1057;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant15-variant19-variant21-variant23-variant26-variant27-variant32-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,25:50:99:584,0,638:9,16,10,15 chr2 10135855 . T C 328.54 PASS AC=1;AF=0.5;AN=2;DP=466;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant15-variant19-variant21-variant23-variant26-variant27-variant32-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,7:19:99:177,0,394:10,2,5,2 chr2 10135956 . G A 1134.61 PASS AC=1;AF=0.5;AN=2;DP=1712;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant8-variant11-variant12-variant13-variant15-variant19-variant21-variant23-variant26-variant27-variant32-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,33:66:99:868,0,939:21,12,22,11 chr2 10136592 . T C 95.66 PASS AC=1;AF=0.5;AN=2;DP=224;FractionInformativeReads=1;MQ=60;set=variant-variant10-variant14-variant20-variant23-variant29-variant30-variant32-variant34-variant40 GT:AD:DP:GQ:PL:SB 0/1:11,3:14:90:90,0,377:2,9,0,3 chr2 10140651 . A G 3890.93 PASS AC=1;AF=0.558;AN=2;DP=4095;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant15-variant19-variant21-variant23-variant24-variant26-variant27-variant29-variant32-variant33-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:76,57:133:99:1203,0,1709:41,35,32,25 chr2 10140981 . C T 4805.11 PASS AC=1;AF=0.558;AN=2;DP=4041;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant15-variant19-variant21-variant23-variant24-variant26-variant27-variant29-variant32-variant33-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:54,69:123:99:1528,0,1399:26,28,37,32 chr2 10141191 . G A 2445.5 PASS AC=1;AF=0.558;AN=2;DP=1991;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant15-variant19-variant21-variant23-variant24-variant26-variant27-variant29-variant32-variant33-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,42:68:99:1172,0,617:12,14,24,18 chr2 10142073 . T C 3015.14 PASS AC=2;AF=0.641;AN=2;DP=7162;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,213:213:99:7236,638,0:0,0,91,122 chr2 10142302 . G A 6165.71 PASS AC=1;AF=0.558;AN=2;DP=6111;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant15-variant19-variant21-variant23-variant24-variant26-variant27-variant29-variant32-variant33-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:143,84:227:99:2007,0,3620:59,84,27,57 chr2 10142331 . C T 4271.47 PASS AC=1;AF=0.558;AN=2;DP=4220;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant15-variant19-variant21-variant23-variant24-variant26-variant27-variant29-variant32-variant33-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:101,51:152:99:1272,0,2832:30,71,14,37 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 0/1:104,82:186:99:1931,0,2583:45,59,35,47 chr2 10192851 . G GTT,GT 1187.32 PASS AC=1,0;AF=0.635,0.081;AN=2;DP=2736;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:68:99:19,16,16,17 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 0/1:192,147:339:99:3413,0,4969:102,90,69,78 chr2 10194487 . T C 4029.08 PASS AC=1;AF=0.671;AN=2;DP=13665;set=variant2-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:183,184:367:99:4618,0,4904:81,102,88,96 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 0/1:131,101:232:99:2508,0,3451:49,82,32,69 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 0/1:22,30:52:99:817,0,614:12,10,20,10 chr2 10198113 . C A 527.17 PASS AC=1;AF=0.716;AN=2;DP=1523;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,25:46:99:619,0,477:10,11,9,16 chr2 10225215 . G T 511.26 PASS AC=1;AF=0.538;AN=2;DP=506;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant10-variant14-variant16-variant17-variant20-variant23-variant25-variant30-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:9,24:33:99:653,0,185:6,3,18,6 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 1/1:0,59:59:99:1683,176,0:0,0,39,20 chr2 10226306 . G GC 1385.47 PASS AC=2;AF=0.769;AN=2;DP=3961;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2379,193,0:0,0,27,37 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 0/1:86,67:153:99:1744,0,2190:40,46,28,39 chr2 10264057 . T C 1115.05 PASS AC=1;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 0/1:30,38:68:99:863,0,629:13,17,16,22 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 0/1:6,7:13:99:258,0,196:0,6,0,7 chr2 10270757 . AT ATT,A,ATTT 234.25 PASS AC=1,0,0;AF=0.229,0.229,0.043;AN=2;DP=3616;set=filterInvariant-variant2-filterInvariant3-variant4-variant5-filterInvariant6-filterInvariant7-filterInvariant8-filterInvariant9-variant10-filterInvariant12-filterInvariant13-variant15-filterInvariant16-filterInvariant17-filterInvariant18-variant19-filterInvariant20-filterInvariant21-variant22-variant23-variant24-filterInvariant26-filterInvariant27-filterInvariant32-variant33-variant34-filterInvariant36-filterInvariant37-variant38-variant39-variant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/1:42:99:2,20,5,15 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 0/1:213,197:410:99:4878,0,5489:97,116,87,110 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 0/1:37,39:76:99:1458,0,2240:6,31,10,29 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 1/1:0,49:49:99:1800,153,0:0,0,30,19 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 0/1:69,70:139:99:1674,0,1654:24,45,31,39 chr2 10332539 . A G 309.64 PASS AC=1;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 0/1:12,8:20:99:293,0,438:11,1,8,0 chr2 10332876 . AC A 1003.6 PASS AC=1;AF=0.629;AN=2;DP=1556;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,21:48:99:500,0,666:10,17,9,12 chr2 10333010 . G A 510.54 PASS AC=1;AF=0.588;AN=2;DP=1058;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,19:28:99:534,0,193:4,5,7,12 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 1/1:0,53:53:99:2112,168,0:0,0,33,20 chr2 10443756 . G C 3273.81 PASS AC=1;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 0/1:36,22:58:99:551,0,875:20,16,15,7 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 1/1:0,74:74:99:3375,226,0:0,0,46,28 chr2 10443782 . G GC,GT 4206.2 PASS AC=2,0;AF=0.898,0.102;AN=2;DP=3685;FS=0;MQ=60;set=Intersection GT:DP:GQ:SB 1/1:76:99:0,0,48,28 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 1/1:0,81:81:99:3630,249,0:0,0,49,32 chr2 10537018 . A G 1236.3 PASS AC=2;AF=0.648;AN=2;DP=3610;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant10-variant12-variant13-variant15-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,112:112:99:3506,336,0:0,0,60,52 chr2 10548577 . C T 79.67 PASS AC=1;AF=0.583;AN=2;DP=234;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant7-variant10-variant12-variant13-variant15-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,9:12:59:285,0,59:2,1,6,3 chr2 10548826 . T C 370.84 PASS AC=1;AF=0.696;AN=2;DP=469;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:205,0,317:4,7,4,5 chr2 10559675 . A T 151.36 PASS AC=1;AF=0.595;AN=2;DP=482;MQ=60;set=variant-variant3-variant4-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant23-variant24-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,4:17:99:112,0,418:8,5,4,0 chr2 10560335 . CTT CT,CTTT,CTTTT,CTTTTT,C 105.08 PASS AC=0,0,1,0,0;AF=0.227,0.136,0.136,0.023,0.023;AN=2;DP=1036;set=variant-variant2-filterInvariant3-variant4-filterInvariant5-filterInvariant6-variant7-variant8-filterInvariant11-variant13-variant16-variant17-filterInvariant19-filterInvariant22-variant23-filterInvariant26-variant29-variant31-filterInvariant32-variant33-filterInvariant40-filterInvariant43 GT:DP:GQ:SB 0/3:11:95:1,4,1,5 chr2 10564765 . G A 647.18 PASS AC=1;AF=0.5;AN=2;DP=36;FS=1.654;FractionInformativeReads=1;MQ=60;MQRankSum=0.016;QD=17.98;ReadPosRankSum=-1.282;SOR=1.382;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:14,22:36:99:675,0,381:4,10,4,18 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 0/1:134,159:293:99:3803,0,3094:66,68,78,81 chr2 10580967 . G A 873.25 PASS AC=1;AF=0.5;AN=2;DP=710;FractionInformativeReads=1;MQ=60;set=variant5-variant23-variant29-variant33-variant34-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:46,29:75:99:712,0,1170:22,24,9,20 chr2 10584022 . T C 1492.17 PASS AC=1;AF=0.5;AN=2;DP=422;MQ=60;set=variant5-variant23-variant29-variant33-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:30,26:56:99:693,0,686:13,17,7,19 chr2 10584122 . A G 694.63 PASS AC=1;AF=0.5;AN=2;DP=44;FS=1.276;FractionInformativeReads=0.977;MQ=60;MQRankSum=0.135;QD=15.79;ReadPosRankSum=0.55;SOR=1.071;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:19,24:43:99:723,0,541:12,7,17,7 chr2 10585311 . A C 370.27 PASS AC=1;AF=0.5;AN=2;DP=181;FractionInformativeReads=1;MQ=60;set=variant5-variant23-variant29-variant33-variant34-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:20,10:30:99:238,0,564:8,12,4,6 chr2 10586898 . C T 270.29 PASS AC=1;AF=0.5;AN=2;DP=49;FS=1.128;FractionInformativeReads=1;MQ=60;MQRankSum=0.267;QD=5.52;ReadPosRankSum=-0.906;SOR=0.536;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:33,16:49:99:299,0,847:18,15,8,8 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 0/1:7,4:11:66:66,0,219:2,5,2,2 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 0/1:5,5:10:99:154,0,143:3,2,3,2 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 0/1:58,71:129:99:1654,0,1252:25,33,28,43 chr2 10595578 . T C 2351.6 PASS AC=1;AF=0.591;AN=2;DP=1885;MQ=60;set=variant2-variant4-variant5-variant9-variant10-variant12-variant15-variant21-variant22-variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:60,76:136:99:1853,0,1525:27,33,36,40 chr2 10711112 . G A 1883.2 PASS AC=1;AF=0.571;AN=2;DP=2816;set=variant2-variant7-variant8-variant9-variant12-variant14-variant15-variant17-variant18-variant19-variant23-variant26-variant27-variant31-variant32-variant33-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,55:112:99:1271,0,1514:21,36,27,28 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 1/1:0,71:71:99:2305,212,0:0,0,26,45 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 0/1:26,37:63:99:932,0,656:16,10,22,15 chr2 10717806 . C T 1056.83 PASS AC=1;AF=0.571;AN=2;DP=2035;MQ=60;set=variant2-variant7-variant8-variant9-variant12-variant14-variant15-variant17-variant18-variant19-variant23-variant26-variant27-variant31-variant32-variant33-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,33:78:99:818,0,1159:20,25,15,18 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 0/1:6,5:11:99:148,0,195:4,2,3,2 chr2 10729897 . C T 1757.08 PASS AC=1;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 0/1:16,15:31:99:356,0,419:5,11,5,10 chr2 10741141 . A G 404.24 PASS AC=1;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 0/1:4,5:9:99:139,0,135:0,4,1,4 chr2 10742704 . G A 490.37 PASS AC=1;AF=0.571;AN=2;DP=906;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant9-variant12-variant14-variant15-variant17-variant18-variant19-variant23-variant26-variant27-variant31-variant32-variant33-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,18:36:99:452,0,488:13,5,11,7 chr2 10743153 . C T 688.12 PASS AC=1;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 0/1:14,18:32:99:494,0,400:11,3,13,5 chr2 10743191 . G A 764.45 PASS AC=1;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 0/1:26,26:52:99:680,0,649:17,9,17,9 chr2 10747246 . C G 278.54 PASS AC=1;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 0/1:2,4:6:99:162,0,165:2,0,4,0 chr2 10747271 . A G 648.56 PASS AC=1;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 0/1:2,6:8:99:243,0,159:2,0,6,0 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 1/1:0,85:85:99:3180,256,0:0,0,35,50 chr2 10774531 . C T 428.8 PASS AC=1;AF=0.571;AN=2;DP=780;MQ=60;set=variant2-variant7-variant8-variant9-variant12-variant14-variant15-variant17-variant18-variant19-variant23-variant26-variant27-variant31-variant32-variant33-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,20:38:99:612,0,448:12,6,16,4 chr2 10807748 . C T 74.09 PASS AC=1;AF=0.591;AN=2;DP=370;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant9-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant26-variant27-variant31-variant32-variant33-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:193,0,177:1,5,3,5 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 1/1:0,35:35:99:1575,105,0:0,0,16,19 chr2 10813540 . TTTTAG T 409.57 PASS AC=1;AF=0.5;AN=2;DP=16;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.113;QD=25.6;ReadPosRankSum=0.227;SOR=0.892;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:5,11:16:99:447,0,299:3,2,7,4 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 1/1:0,19:19:57:565,57,0:0,0,7,12 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 0/1:8,8:16:99:190,0,230:6,2,5,3 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 1/1:0,5:5:15:176,15,0:0,0,3,2 chr2 10908893 . A G 1043.01 PASS AC=1;AF=0.6;AN=2;DP=3203;MQ=60;set=variant2-variant5-variant6-variant8-variant9-variant12-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,69:122:99:1602,0,1190:25,28,29,40 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 0/1:27,33:60:99:875,0,615:20,7,23,10 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 0/1:60,54:114:99:1303,0,1604:25,35,18,36 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 0/1:23,29:52:99:972,0,820:1,22,6,23 chr2 10915090 . T A 1676.25 PASS AC=1;AF=0.528;AN=2;DP=2190;MQ=60;set=variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant16-variant17-variant20-variant21-variant22-variant23-variant28-variant31-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:68,68:136:99:1641,0,1430:34,34,36,32 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 1/1:0,66:66:99:1940,198,0:0,0,37,29 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 1/1:0,21:21:63:682,63,0:0,0,7,14 chr2 10978049 . TGCGC TGC,T 85.69 PASS AC=0,2;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 2/2:7:21:0,0,1,6 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 1/1:0,7:7:21:315,21,0:0,0,1,6 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 1/1:0,48:48:99:1681,144,0:0,0,37,11 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 1/1:0,269:269:99:8473,806,0:0,0,126,143 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 0/1:64,73:137:99:1891,0,1892:29,35,30,43 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 1/1:0,66:66:99:2046,197,0:0,0,39,27 chr2 11273123 . TCACACACACACACACACACACACA TCACACACACACACACACACACA,TCACACACACACACACACACACACACACA,TCACACACACACACACACACACACACA,TCACACACACACACACACA,T,TCACACACACACACACACACACACACACACA,TCACACACACACACACACACA,TCACACACACACACACACACACACACACACACACACA,TCACACACACACACACA 78.78 PASS AC=0,1,0,0,0,0,0,0,0;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 0/2:7:58:2,0,5,0 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 0/2:102:99:39,36,17,10 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 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 1/1:0,87:87:99:2559,259,0:0,0,36,51 chr2 11300732 . C T 5598.33 PASS AC=2;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 1/1:0,151:151:99:4542,450,0:0,0,83,68 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 1/1:0,114:114:99:3503,341,0:0,0,49,65 chr2 11300927 . TAAAA TA,T,TAA,TAAA 806.59 PASS AC=2,0,0,0;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 1/1:35:99:0,0,4,31 chr2 11311895 . C T 267.87 PASS AC=1;AF=0.5;AN=2;DP=87;FractionInformativeReads=1;set=variant19-variant21-variant23-variant31-variant40 GT:AD:DP:GQ:PL:SB 0/1:10,4:14:99:135,0,369:9,1,4,0 chr2 11312181 . G A 2351.17 PASS AC=2;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 1/1:0,76:76:99:2353,228,0:0,0,27,49 chr2 11312224 . C T 1482.96 PASS AC=2;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 1/1:0,35:35:99:1418,105,0:0,0,3,32 chr2 11318191 . G GAGA 7340.61 PASS AC=2;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 1/1:0,250:250:99:11276,758,0:0,0,126,124 chr2 11318224 . CCCATTTTGAGG C 11893.7 PASS AC=2;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 1/1:1,194:195:99:8468,546,0:0,1,78,116 chr2 11318457 . G A 2648.36 PASS AC=2;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 1/1:0,84:84:99:3008,252,0:0,0,61,23 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 1/1:0,107:107:99:3698,321,0:0,0,77,30 chr2 11320877 . C T 15519 PASS AC=2;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 1/1:0,400:400:99:12270,1194,0:0,0,197,203 chr2 11321757 . CTT CT,CTTTTTTTTT,CTTT,CTTTTTTTTTT,CTTTTTTTT,C,CTTTTTT 87.74 PASS AC=1,0,0,0,0,0,0;AF=0.35,0.025,0.025,0.025,0.025,0.025,0.025;AN=2;DP=1089;set=filterInvariant2-filterInvariant3-variant4-variant5-filterInvariant8-variant11-filterInvariant14-variant15-filterInvariant19-filterInvariant20-filterInvariant22-filterInvariant23-variant27-filterInvariant30-filterInvariant32-filterInvariant39-variant40-filterInvariant41-variant42-filterInvariant43 GT:DP:GQ:SB 0/1:22:72:0,14,0,8 chr2 11322137 . A AAAAAAC 5796.68 PASS AC=2;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 1/1:3,94:97:99:3060,277,0:1,2,64,30 chr2 11323078 . CTATA CTA,C 3015.38 PASS AC=1,1;AF=0.852,0.023;AN=2;DP=4837;MQ=60;set=Intersection GT:DP:GQ:SB 2/1:101:99:1,2,40,58 chr2 11323276 . T C 2859.59 PASS AC=2;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 1/1:0,87:87:99:2723,261,0:0,0,39,48 chr2 11348364 . C CTAACT 409.21 PASS AC=2;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 1/1:0,12:12:42:621,42,0:0,0,7,5 chr2 11348609 . CAAAT C 1028.15 PASS AC=2;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 1/1:0,10:10:30:450,30,0:0,0,1,9 chr2 11356190 . G A 1101.45 PASS AC=2;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 1/1:0,16:16:48:514,48,0:0,0,10,6 chr2 11357100 . G A 36.95 PASS AC=2;AF=0.717;AN=2;DP=164;FractionInformativeReads=1;set=variant2-variant3-variant4-variant7-variant8-variant9-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:276,24,0:0,0,6,2 chr2 11359031 . G T 1352.23 PASS AC=2;AF=0.875;AN=2;DP=1453;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:601,57,0:0,0,11,8 chr2 11359120 . G T 3095.96 PASS AC=2;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 1/1:0,61:61:99:1793,183,0:0,0,34,27 chr2 11359300 . C T 923.36 PASS AC=2;AF=0.553;AN=2;DP=977;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant9-variant17-variant18-variant19-variant21-variant23-variant27-variant28-variant30-variant31-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:687,63,0:0,0,7,14 chr2 11359399 . A C 181.36 PASS AC=2;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 1/1:0,5:5:15:204,15,0:0,0,0,5 chr2 11484462 . A G,AGCCCG 2107.47 PASS AC=0,2;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 2/2:24:74:0,0,11,13 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 0/1:14,15:29:99:351,0,300:6,8,8,7 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 0/1:11,16:27:99:619,0,437:4,7,3,13 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 0/1:5,6:11:99:153,0,123:5,0,6,0 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 0/1:8,14:22:99:335,0,202:4,4,8,6 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 0/1:26,32:58:99:696,0,652:12,14,14,18 chr2 11718591 . C T 1428.37 PASS AC=1;AF=0.652;AN=2;DP=1605;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant15-variant16-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,31:52:99:816,0,596:5,16,7,24 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 0/1:40,35:75:99:704,0,882:24,16,22,13 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 0/1:80,67:147:99:1552,0,1868:46,34,37,30 chr2 11727507 . G A 1986.52 PASS AC=1;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 0/1:99,97:196:99:2389,0,2499:42,57,44,53 chr2 11727988 . G C 394.5 PASS AC=1;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 0/1:14,9:23:99:198,0,357:5,9,5,4 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 0/1:2,6:8:99:246,0,141:0,2,2,4 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 0/1:2,6:8:99:246,0,141:0,2,2,4 chr2 11728381 . T C 553.45 PASS AC=1;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 0/1:8,11:19:99:438,0,338:4,4,6,5 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 0/1:9,11:20:99:435,0,372:5,4,6,5 chr2 11731774 . T G 1341.55 PASS AC=1;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 0/1:52,58:110:99:1711,0,1331:28,24,38,20 chr2 11731846 . T C 2565.92 PASS AC=1;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 0/1:100,106:206:99:2660,0,2494:57,43,58,48 chr2 11733488 . G T 31.75 PASS AC=1;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 0/1:9,3:12:93:93,0,246:4,5,0,3 chr2 11736037 . A G 246.04 PASS AC=1;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 0/1:3,11:14:56:366,0,56:2,1,10,1 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 1/1:0,243:243:99:7153,728,0:0,0,112,131 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 1/1:0,15:15:45:501,45,0:0,0,11,4 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 1/1:0,12:12:36:510,36,0:0,0,0,12 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 0/1:8,11:19:99:347,0,218:7,1,9,2 chr2 11752319 . CA CAAAA,C,CAA,CAAA,CAAAAA 191.51 PASS AC=2,0,0,0,0;AF=0.273,0.045,0.205,0.136,0.023;AN=2;DP=212;set=variant3-variant4-variant5-variant6-variant8-variant12-variant15-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant33-variant36-variant38-variant43-variant44 GT:DP:GQ:SB 1/1:3:9:0,0,3,0 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 1/1:0,47:47:99:1570,141,0:0,0,19,28 chr2 11755443 . T G 475.52 PASS AC=2;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 1/1:0,43:43:99:1496,129,0:0,0,12,31 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 1/1:0,63:63:99:2004,189,0:0,0,28,35 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 0/1:24,37:61:99:952,0,583:11,13,15,22 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 0/1:15,21:36:99:796,0,567:6,9,7,14 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 0/1:15,20:35:99:753,0,570:6,9,7,13 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 1/1:1,35:36:97:1098,97,0:1,0,9,26 chr2 11781593 . G GGTTTT,GGTTTTGTTTTGTTTT,GGTTTGGTTTTGTTTT,GGTTTTGTTTT 501.12 PASS AC=0,1,0,0;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 0/2:8:99:1,2,1,4 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 1/1:0,8:8:24:319,24,0:0,0,1,7 chr2 11802399 . C T 334.76 PASS AC=1;AF=0.5;AN=2;DP=34;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.344;QD=9.85;ReadPosRankSum=-2.032;SOR=0.693;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:17,17:34:99:363,0,457:5,12,5,12 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 1/1:0,117:117:99:3770,351,0:0,0,53,64 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 0/1:8,9:17:99:338,0,273:1,7,0,9 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 0/1:68,68:136:99:1709,0,1490:36,32,40,28 chr2 11853774 . T C 169.95 PASS AC=2;AF=0.741;AN=2;DP=226;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant15-variant16-variant20-variant21-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:184,15,0:0,0,4,1 chr2 11853988 . A T 917.89 PASS AC=2;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 1/1:0,97:97:99:2830,289,0:0,0,47,50 chr2 11854099 . T C 322.48 PASS AC=2;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 1/1:0,39:39:99:1265,117,0:0,0,13,26 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 1/1:0,78:78:99:2339,235,0:0,0,48,30 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 1/1:0,46:46:99:1517,138,0:0,0,16,30 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 1/1:0,42:42:99:1331,126,0:0,0,27,15 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 1/1:0,86:86:99:2707,258,0:0,0,36,50 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 1/1:0,70:70:99:2076,210,0:0,0,39,31 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 1/1:1,54:55:99:1507,136,0:1,0,33,21 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 1/1:0,28:28:84:987,84,0:0,0,6,22 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 1/1:0,21:21:63:708,63,0:0,0,15,6 chr2 11945108 . GT GTT,G,GTTT 145.75 PASS AC=1,0,0;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 0/1:50:99:22,16,6,6 chr2 11965541 . A G 2834.89 PASS AC=2;AF=0.795;AN=2;DP=9848;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,198:198:99:5873,593,0:0,0,104,94 chr2 11977154 . C T 869.59 PASS AC=1;AF=0.5;AN=2;DP=205;FractionInformativeReads=1;MQ=60;set=variant21-variant23-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:15,18:33:99:466,0,377:6,9,7,11 chr2 12164189 . C T 581.72 PASS AC=2;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 1/1:0,51:51:99:1487,153,0:0,0,23,28 chr2 12339169 . G A 461.76 PASS AC=1;AF=0.5;AN=2;DP=149;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant12-variant13-variant23-variant26-variant30-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:138,0,257:6,2,5,0 chr2 12864613 . T A 240.11 PASS AC=1;AF=0.567;AN=2;DP=249;MQ=60;set=variant2-variant3-variant9-variant11-variant22-variant23-variant24-variant26-variant28-variant30-variant31-variant32-variant34-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,6:17:99:216,0,360:10,1,6,0 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 1/1:40:99:0,0,25,15 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 1/1:2,105:107:99:4155,244,0:1,1,59,46 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 1/1:3,289:292:99:8955,780,0:2,1,138,151 chr2 12882023 . A T 2312.68 PASS AC=1;AF=0.5;AN=2;DP=316;FractionInformativeReads=1;MQ=60;set=variant23-variant41 GT:AD:DP:GQ:PL:SB 0/1:97,80:177:99:2341,0,2785:64,33,49,31 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 1/1:0,9:9:27:400,27,0:0,0,2,7 chr2 14775299 . GA G 1851.07 PASS AC=1;AF=0.5;AN=2;DP=399;MQ=60;set=variant23-variant24-variant27 GT:AD:DP:GQ:PL:SB 0/1:74,64:138:99:1888,0,2185:37,37,29,35 chr2 14778337 . CAA CAAA,CA,C 74.05 PASS AC=0,1,0;AF=0.25,0.167,0.083;AN=2;DP=567;set=filterInvariant3-variant4-variant6-variant7-filterInvariant10-variant13-variant16-variant17-filterInvariant21-variant23-filterInvariant24-variant25-variant33-variant36-filterInvariant38-filterInvariant39-variant40-filterInvariant44 GT:DP:GQ:SB 0/2:18:70:3,3,10,2 chr2 14779227 . TAC TACAC,T,TACACAC 750.09 PASS AC=1,0,0;AF=0.435,0.065,0.022;AN=2;DP=2046;set=variant-variant2-variant4-variant7-variant9-variant11-variant12-filterInvariant14-variant17-variant20-variant23-variant24-variant25-filterInvariant26-variant27-variant29-variant32-variant36-filterInvariant37-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:68:99:20,15,23,10 chr2 14779829 . A G 4492.79 PASS AC=1;AF=0.55;AN=2;DP=6203;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant11-variant12-variant17-variant20-variant23-variant24-variant25-variant27-variant29-variant32-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:159,138:297:99:3220,0,3732:67,92,58,80 chr2 14780038 . T G 1180.91 PASS AC=1;AF=0.55;AN=2;DP=1443;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant11-variant12-variant17-variant20-variant23-variant24-variant25-variant27-variant29-variant32-variant36-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,33:66:99:815,0,858:20,13,17,16 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 0/1:26,16:42:99:284,0,557:14,12,9,7 chr2 15372731 . T G 1819.21 PASS AC=1;AF=0.667;AN=2;DP=1123;MQ=60;set=variant5-variant6-variant13-variant14-variant23-variant26-variant33-variant34-variant39 GT:AD:DP:GQ:PL:SB 0/1:54,45:99:99:1058,0,1368:26,28,20,25 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 1/1:0,11:11:33:495,33,0:0,0,2,9 chr2 15415525 . C T 738.45 PASS AC=1;AF=0.686;AN=2;DP=1682;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,15:29:99:458,0,418:11,3,12,3 chr2 15417280 . ATT A 115.75 PASS AC=1;AF=0.686;AN=2;DP=599;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,14:21:99:478,0,479:1,6,3,11 chr2 15417285 . T A 124.75 PASS AC=1;AF=0.686;AN=2;DP=561;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,14:21:99:478,0,479:1,6,3,11 chr2 15427173 . C T 1469.87 PASS AC=1;AF=0.621;AN=2;DP=3734;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:70,45:115:99:889,0,1848:42,28,26,19 chr2 15448311 . A T 1234.64 PASS AC=1;AF=0.691;AN=2;DP=4701;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,84:141:99:1979,0,1358:36,21,47,37 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 0/1:6,2:8:66:66,0,216:0,6,0,2 chr2 15491994 . GCACACACACACA G,GCA,GCACACACACA,GCACA,GCACACACACACACACACACA,GCACACACA 1434.63 PASS AC=0,0,1,0,0,0;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 0/3:56:99:26,16,9,5 chr2 15691791 . G T 3264.99 PASS AC=2;AF=0.559;AN=2;DP=1528;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant9-variant10-variant13-variant16-variant21-variant23-variant24-variant26-variant33-variant34-variant36-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2401,245,0:0,0,31,51 chr2 15731605 . C T 1708.91 PASS AC=2;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 1/1:0,49:49:99:1572,146,0:0,0,35,14 chr2 15731859 . A C 5555.12 PASS AC=2;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 1/1:1,190:191:99:5547,531,0:1,0,94,96 chr2 15731998 . A G 6690.76 PASS AC=2;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 1/1:0,218:218:99:6870,652,0:0,0,124,94 chr2 15735419 . G A 393.29 PASS AC=1;AF=0.556;AN=2;DP=723;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant11-variant14-variant20-variant23-variant24-variant26-variant27-variant29-variant31-variant34-variant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,23:39:99:659,0,443:4,12,7,16 chr2 15735648 . T C 1101.07 PASS AC=1;AF=0.5;AN=2;DP=1396;MQ=60;set=variant8-variant10-variant15-variant16-variant17-variant19-variant21-variant23-variant25-variant26-variant30-variant31-variant33-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,48:68:99:1248,0,406:10,10,25,23 chr2 15736697 . G A 837.5 PASS AC=1;AF=0.5;AN=2;DP=1030;MQ=60;set=variant8-variant10-variant15-variant16-variant17-variant19-variant21-variant23-variant25-variant26-variant30-variant31-variant33-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,32:61:99:874,0,696:15,14,20,12 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 0/1:6,3:9:99:105,0,163:2,4,0,3 chr2 15744484 . CT C 190.31 PASS AC=1;AF=0.556;AN=2;DP=359;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant11-variant14-variant20-variant23-variant24-variant26-variant27-variant29-variant31-variant34-variant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:76:76,0,174:3,3,2,1 chr2 15746220 . C T 763.54 PASS AC=1;AF=0.5;AN=2;DP=1237;FractionInformativeReads=1;MQ=60;set=variant8-variant15-variant16-variant19-variant21-variant23-variant26-variant30-variant33-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:51,42:93:99:964,0,1294:23,28,20,22 chr2 15747393 . C T 3465.37 PASS AC=2;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 1/1:0,98:98:99:2973,294,0:0,0,36,62 chr2 15753279 . C G 72.18 PASS AC=1;AF=0.5;AN=2;DP=167;MQ=60;set=variant8-variant15-variant16-variant19-variant21-variant23-variant26-variant30-variant33-variant37 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:190,0,154:3,4,5,1 chr2 15768876 . G A 1482.23 PASS AC=1;AF=0.553;AN=2;DP=2084;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant11-variant14-variant20-variant23-variant24-variant26-variant27-variant29-variant31-variant34-variant36-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,42:95:99:984,0,1221:24,29,18,24 chr2 15769607 . C T 352.58 PASS AC=1;AF=0.5;AN=2;DP=84;FS=0;FractionInformativeReads=1;MQ=60;set=variant8-variant15-variant16-variant19-variant21-variant23-variant30-variant33-variant37 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:73:159,0,73:2,0,4,0 chr2 16080769 . G T 1064.55 PASS AC=1;AF=0.5;AN=2;DP=117;FS=0.711;FractionInformativeReads=0.983;MQ=60;MQRankSum=0.082;QD=9.1;ReadPosRankSum=-0.014;SOR=0.816;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:68,47:115:99:1093,0,1705:37,31,27,20 chr2 16731017 . T C 6351.67 PASS AC=2;AF=0.575;AN=2;DP=8648;MQ=60;set=variant-variant2-variant6-variant7-variant11-variant14-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant34-variant36-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,364:364:99:11183,1090,0:0,0,204,160 chr2 16731255 . GT G 3329.02 PASS AC=1;AF=0.565;AN=2;DP=8451;set=variant-variant2-variant6-variant7-variant10-variant11-variant13-variant14-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant34-variant36-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:166,160:326:99:3392,0,3329:66,100,74,86 chr2 16731510 . G A 698.13 PASS AC=1;AF=0.563;AN=2;DP=1293;MQ=60;set=variant-variant2-variant6-variant7-variant10-variant11-variant13-variant14-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant34-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,25:46:99:753,0,588:8,13,11,14 chr2 16731572 . CA CAA,C,CAAA 149.3 PASS AC=2,0,0;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 1/1:26:32:1,1,11,13 chr2 16732275 . G T 4048.43 PASS AC=1;AF=0.565;AN=2;DP=5781;MQ=60;set=variant-variant2-variant6-variant7-variant10-variant11-variant13-variant14-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant34-variant36-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:104,112:216:99:2871,0,2726:44,60,50,62 chr2 16732391 . T G 1529.32 PASS AC=1;AF=0.565;AN=2;DP=2695;MQ=60;set=variant-variant2-variant6-variant7-variant10-variant11-variant13-variant14-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant34-variant36-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,52:111:99:1330,0,1481:25,34,18,34 chr2 16733054 . G A 2808.97 PASS AC=1;AF=0.565;AN=2;DP=5309;MQ=60;set=variant-variant2-variant6-variant7-variant10-variant11-variant13-variant14-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant34-variant36-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:109,114:223:99:2711,0,2618:59,50,61,53 chr2 16733525 . G T 1094.5 PASS AC=1;AF=0.568;AN=2;DP=1979;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant7-variant11-variant13-variant14-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant34-variant36-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,52:104:99:1291,0,1207:30,22,34,18 chr2 16733928 . A G 3070.32 PASS AC=2;AF=0.583;AN=2;DP=4491;MQ=60;set=variant-variant2-variant6-variant7-variant10-variant11-variant13-variant14-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant34-variant36-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,166:166:99:5256,496,0:0,0,94,72 chr2 16734284 . T C 1485.73 PASS AC=2;AF=0.575;AN=2;DP=2281;MQ=60;set=variant-variant2-variant6-variant7-variant11-variant14-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant34-variant36-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3541,348,0:0,0,49,67 chr2 16743453 . A C 803.1 PASS AC=2;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 1/1:0,111:111:99:3422,333,0:0,0,45,66 chr2 16746897 . C G 569.79 PASS AC=1;AF=0.563;AN=2;DP=789;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant7-variant11-variant14-variant15-variant18-variant20-variant21-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:8,19:27:99:660,0,140:5,3,17,2 chr2 17691950 . CA C 2780.24 PASS AC=2;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 1/1:0,96:96:99:2671,288,0:0,0,59,37 chr2 17696573 . C T 3983.54 PASS AC=2;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 1/1:0,129:129:99:4115,387,0:0,0,63,66 chr2 17698678 . A G 1922.25 PASS AC=2;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 1/1:0,58:58:99:2000,174,0:0,0,25,33 chr2 17720520 . G C 607.62 PASS AC=1;AF=0.545;AN=2;DP=1110;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant26-variant27-variant29-variant32-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,19:29:99:476,0,265:5,5,9,10 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 1/1:0,100:100:99:3191,300,0:0,0,65,35 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 0/1:22,17:39:99:506,0,623:8,14,3,14 chr2 17836722 . TCACACACACA TCACACACACACACACACACA,TCACACACACACACACACA,TCACACA,TCACACACACACACA,TCACACACA,T,TCACACACACACA,TCACACACACACACACA,TCA 2518.13 PASS AC=0,0,0,2,0,0,0,0,0;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 4/4:38:10:4,0,27,7 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 0/1:37,37:74:99:1149,0,1301:15,22,22,15 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 0/1:91,80:171:99:1987,0,2266:44,47,38,42 chr2 17845296 . A G 10896.7 PASS AC=2;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 1/1:0,332:332:99:9641,994,0:0,0,165,167 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 0/1:26,31:57:99:831,0,684:12,14,18,13 chr2 17846592 . A T 6526.84 PASS AC=2;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 1/1:0,161:161:99:4720,482,0:0,0,97,64 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 0/1:7,9:16:99:235,0,184:2,5,2,7 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 0/1:31,34:65:99:791,0,746:18,13,19,15 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 0/1:33,31:64:99:895,0,995:20,13,21,10 chr2 17890091 . G GTATA,GTA 52.53 PASS AC=1,0;AF=0.625,0.075;AN=2;DP=205;FS=0;set=variant3-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant19-variant23-variant24-variant25-variant26-variant27-variant28-variant33-variant36-variant37-variant38-variant39 GT:DP:GQ:SB 0/1:6:99:1,2,0,3 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 0/1:19,23:42:99:622,0,449:8,11,8,15 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 0/1:38,44:82:99:1033,0,932:24,14,25,19 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 1/1:0,34:34:99:1336,102,0:0,0,7,27 chr2 17927266 . T C 442.6 PASS AC=1;AF=0.5;AN=2;DP=19;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.447;QD=23.29;ReadPosRankSum=0.57;SOR=0.622;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:6,13:19:99:471,0,213:0,6,1,12 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 0/1:10,6:16:99:201,0,478:0,10,0,6 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 0/1:69,42:111:99:1556,0,3620:41,28,29,13 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 0/1:16,10:26:99:241,0,479:4,12,2,8 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 0/1:39,37:76:99:884,0,1063:20,19,18,19 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 1/1:0,79:79:99:2279,237,0:0,0,37,42 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 0/1:9,11:20:99:350,0,240:2,7,4,7 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 0/1:42,21:63:99:472,0,1189:16,26,12,9 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 0/1:3,2:5:75:75,0,113:0,3,0,2 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 1/2:11:99:0,0,2,9 chr2 17959443 . A G 172.69 PASS AC=1;AF=0.604;AN=2;DP=288;set=variant-variant4-variant6-variant7-variant8-variant9-variant14-variant15-variant16-variant17-variant19-variant21-variant23-variant26-variant27-variant29-variant30-variant32-variant34-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:99:105,0,285:1,5,0,3 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 0/1:51,41:92:99:1042,0,1415:26,25,22,19 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 0/1:62,49:111:99:1246,0,1648:36,26,25,24 chr2 17963171 . C T 1688.33 PASS AC=1;AF=0.5;AN=2;DP=142;FS=1.331;FractionInformativeReads=1;MQ=60;MQRankSum=0.153;QD=11.89;ReadPosRankSum=0.741;SOR=0.579;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:70,72:142:99:1717,0,1726:42,28,41,31 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 0/1:191,188:379:99:4787,0,4602:105,86,104,84 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 0/1:58,74:132:99:1989,0,1473:17,41,22,52 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 0/1:14,9:23:99:253,0,459:12,2,6,3 chr2 17980511 . A T 461.69 PASS AC=1;AF=0.615;AN=2;DP=1127;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant26-variant27-variant29-variant30-variant32-variant34-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,18:45:99:446,0,683:9,18,6,12 chr2 17980541 . C G 441.49 PASS AC=1;AF=0.635;AN=2;DP=838;MQ=60;set=variant-variant3-variant4-variant6-variant7-variant8-variant9-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant26-variant27-variant29-variant30-variant32-variant34-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,16:35:99:401,0,465:8,11,6,10 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 0/1:10,5:15:99:177,0,350:7,3,5,0 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 0/1:29,23:52:99:707,0,786:21,8,19,4 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 0/1:63,52:115:99:1159,0,1635:39,24,30,22 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 0/1:83,81:164:99:1778,0,1874:46,37,43,38 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 0/1:18,13:31:99:370,0,629:2,16,4,9 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 0/1:58,62:120:99:1562,0,1616:24,34,28,34 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 0/1:60,39:99:99:1042,0,1657:34,26,17,22 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 0/1:64,50:114:99:1128,0,1577:27,37,19,31 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 1/1:0,6:6:18:249,18,0:0,0,0,6 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 1/1:0,7:7:21:294,21,0:0,0,5,2 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 1/1:0,148:148:99:4747,444,0:0,0,70,78 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 0/1:56,56:112:99:1406,0,1480:26,30,23,33 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 0/1:54,81:135:99:2214,0,1275:28,26,52,29 chr2 18745466 . C T 468.58 PASS AC=1;AF=0.55;AN=2;DP=348;MQ=60;set=variant-variant2-variant4-variant5-variant9-variant15-variant21-variant22-variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:14,17:31:99:460,0,452:2,12,4,13 chr2 19552913 . C T 1104.45 PASS AC=1;AF=0.5;AN=2;DP=313;FractionInformativeReads=1;MQ=60;set=variant23-variant29-variant37 GT:AD:DP:GQ:PL:SB 0/1:55,47:102:99:1133,0,1406:35,20,31,16 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 1/1:0,100:100:99:3569,301,0:0,0,44,56 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 1/1:0,61:61:99:1826,183,0:0,0,27,34 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 1/1:0,25:25:75:762,75,0:0,0,8,17 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 1/1:0,14:14:42:561,42,0:0,0,13,1 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 1/1:0,18:18:54:652,54,0:0,0,4,14 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 1/1:0,26:26:78:958,78,0:0,0,21,5 chr2 20251075 . G C 198.87 PASS AC=1;AF=0.5;AN=2;DP=84;MQ=60;set=variant8-variant10-variant11-variant23-variant28-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,4:13:64:64,0,483:5,4,4,0 chr2 20251080 . A C 94.22 PASS AC=1;AF=0.5;AN=2;DP=211;MQ=60;set=variant6-variant8-variant10-variant11-variant16-variant23-variant24-variant27-variant28-variant31-variant32-variant34-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,4:13:58:58,0,559:5,4,4,0 chr2 20302490 . GAGAAGA GAGAAGGAGAAGAAGAAGAAGAAGA,GAGAAGAAGAAGA,GAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA,GAGAAGAAGA,G,GAGA,GAGAAGGAGAAGGAGAAGGAGAAGAAGA,GAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA,GAGAAGAAGAAGAAGAAGAAGAAGAAGA 578.62 PASS AC=0,0,0,0,0,1,0,0,0;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 0/6:72:99:43,21,5,3 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 1/1:0,92:92:99:2707,276,0:0,0,51,41 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 0/1:18,32:50:99:994,0,525:11,7,16,16 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 1/1:0,162:162:99:5092,486,0:0,0,88,74 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 0/1:78,79:157:99:1933,0,1785:36,42,30,49 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 0/1:11,7:18:99:177,0,316:8,3,6,1 chr2 20405041 . C G 270.1 PASS AC=1;AF=0.5;AN=2;DP=165;FractionInformativeReads=1;MQ=60;set=variant-variant14-variant17-variant18-variant23-variant37 GT:AD:DP:GQ:PL:SB 0/1:13,17:30:99:466,0,330:9,4,13,4 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 1/1:0,35:35:99:1319,108,0:0,0,25,10 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 1/1:0,52:52:99:1525,155,0:0,0,18,34 chr2 20424062 . G A 459.84 PASS AC=1;AF=0.648;AN=2;DP=399;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant17-variant18-variant19-variant20-variant23-variant25-variant26-variant30-variant33-variant34-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,10:14:99:299,0,141:0,4,3,7 chr2 20449174 . G A 3923.68 PASS AC=1;AF=0.63;AN=2;DP=3155;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant17-variant18-variant19-variant23-variant25-variant26-variant30-variant32-variant33-variant34-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:60,69:129:99:1947,0,1604:38,22,45,24 chr2 20455176 . GT G 430.54 PASS AC=1;AF=0.621;AN=2;DP=812;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant17-variant18-variant19-variant22-variant23-variant25-variant26-variant30-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,12:21:99:184,0,142:1,8,1,11 chr2 20462852 . G C 156.22 PASS AC=1;AF=0.667;AN=2;DP=139;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant15-variant17-variant18-variant23-variant26-variant30-variant32-variant33-variant34-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:75:78,0,75:2,0,2,0 chr2 20525948 . T C 1314.28 PASS AC=1;AF=0.65;AN=2;DP=1211;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant15-variant17-variant18-variant19-variant22-variant23-variant25-variant26-variant30-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,18:37:99:449,0,490:14,5,12,6 chr2 20699667 . C G 216.52 PASS AC=2;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 1/1:0,15:15:45:468,45,0:0,0,10,5 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 1/1:0,117:117:99:3619,351,0:0,0,60,57 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 2/2:9:27:0,0,6,3 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 0/1:73,84:157:99:2037,0,1770:37,36,37,47 chr2 20818193 . G A 1293.97 PASS AC=2;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 1/1:0,69:69:99:2801,213,0:0,0,36,33 chr2 20818199 . G A 574.05 PASS AC=1;AF=0.583;AN=2;DP=393;MQ=60;set=variant2-variant4-variant12-variant23-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:29,42:71:99:981,0,790:17,12,19,23 chr2 20818286 . A C 1709.23 PASS AC=2;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 1/1:0,76:76:99:2173,227,0:0,0,37,39 chr2 20818454 . T A 1933.66 PASS AC=2;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 1/1:0,88:88:99:3449,264,0:0,0,45,43 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 0/1:37,50:87:99:1220,0,957:22,15,23,27 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 1/1:0,31:31:93:1187,93,0:0,0,21,10 chr2 20822486 . G C 2950.38 PASS AC=2;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 1/1:0,45:45:99:1473,135,0:0,0,18,27 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 0/1:9,11:20:99:378,0,264:5,4,5,6 chr2 20823252 . A G 1044.44 PASS AC=2;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 1/1:0,39:39:99:1135,117,0:0,0,19,20 chr2 20823612 . A G 2007.24 PASS AC=2;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 1/1:0,50:50:99:1597,150,0:0,0,27,23 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 1/1:0,72:72:99:2117,215,0:0,0,35,37 chr2 20823816 . G T,A 825.57 PASS AC=2,0;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 1/1:46:99:0,0,20,26 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 1/1:0,38:38:99:1207,114,0:0,0,16,22 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 0/1:53,73:126:99:1776,0,1275:28,25,36,37 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 0/1:55,49:104:99:1251,0,1339:28,27,19,30 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 0/1:41,32:73:99:767,0,1070:17,24,11,21 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 0/1:14,15:29:99:505,0,240:9,5,2,13 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 0/1:16,11:27:99:132,0,525:2,14,9,2 chr2 20836794 . G C 174.1 PASS AC=2;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 1/1:0,31:31:96:1317,96,0:0,0,12,19 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 0/1:17,15:32:99:530,0,336:12,5,2,13 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 0/1:27,11:38:93:93,0,912:14,13,9,2 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 1/1:0,58:58:99:1790,174,0:0,0,35,23 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 1/1:0,60:60:99:1899,180,0:0,0,31,29 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 0/1:39,32:71:99:665,0,1056:20,19,15,17 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 0/1:19,25:44:99:615,0,588:13,6,13,12 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 0/1:58,60:118:99:1475,0,1345:31,27,30,30 chr2 20840412 . A G 1113.85 PASS AC=1;AF=0.583;AN=2;DP=444;MQ=60;set=variant2-variant4-variant12-variant23-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:37,44:81:99:1111,0,896:20,17,24,20 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 0/1:11,18:29:99:607,0,357:2,9,1,17 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 1/1:0,61:61:99:1864,183,0:0,0,22,39 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 1/1:0,33:33:99:1616,108,0:0,0,18,15 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 1/1:1,70:71:99:1956,203,0:0,1,34,36 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 1/1:9:27:0,0,4,5 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 1/1:0,63:63:99:1995,188,0:0,0,29,34 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 1/1:0,139:139:99:4527,415,0:0,0,53,86 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 1/1:0,114:114:99:3341,341,0:0,0,56,58 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 1/1:65:99:0,1,25,39 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 1/1:1,64:65:99:2741,145,0:0,1,25,39 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 1/1:2,60:62:99:2663,136,0:0,2,24,36 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 0/2:32:99:6,13,4,9 chr2 20872960 . A AAT 5786.12 PASS AC=2;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 1/1:0,196:196:99:8903,617,0:0,0,107,89 chr2 20872962 . G GA,A 7404.75 PASS AC=0,2;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 2/2:204:99:0,0,112,92 chr2 20873449 . T C 1654.74 PASS AC=2;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 1/1:0,34:34:99:995,102,0:0,0,12,22 chr2 20883652 . GGTGAA G 1091.35 PASS AC=1;AF=0.607;AN=2;DP=942;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant28-variant30-variant31-variant32-variant33-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,14:27:99:458,0,504:10,3,9,5 chr2 20884135 . TTTAATC T 4773.31 PASS AC=1;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 0/1:116,105:221:99:3988,0,6227:49,67,41,64 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 1/1:0,39:39:99:1402,117,0:0,0,10,29 chr2 20884546 . A C 1255.33 PASS AC=1;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 0/1:56,52:108:99:1228,0,1504:30,26,24,28 chr2 20884586 . G C 1322.5 PASS AC=1;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 0/1:54,57:111:99:1450,0,1282:26,28,27,30 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 1/1:2,140:142:99:4047,376,0:1,1,72,68 chr2 20885321 . C A 6247.35 PASS AC=1;AF=0.556;AN=2;DP=1817;MQ=60;set=variant-variant5-variant7-variant13-variant17-variant21-variant23-variant28-variant44 GT:AD:DP:GQ:PL:SB 0/1:88,101:189:99:2533,0,2442:54,34,54,47 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 1/1:0,24:24:84:1164,84,0:0,0,20,4 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 1/1:0,28:28:84:1164,84,0:0,0,22,6 chr2 21225281 . C T 3009.38 PASS AC=2;AF=0.849;AN=2;DP=4523;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2652,222,0:0,0,34,40 chr2 21225753 . C T 3770.39 PASS AC=1;AF=0.618;AN=2;DP=2102;MQ=60;set=variant-variant2-variant3-variant4-variant9-variant12-variant17-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,50:117:99:1379,0,1795:37,30,26,24 chr2 21227383 . C G 3134.39 PASS AC=1;AF=0.611;AN=2;DP=1706;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant9-variant12-variant17-variant19-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,38:78:99:1163,0,996:19,21,19,19 chr2 21232195 . G A 1183.03 PASS AC=1;AF=0.641;AN=2;DP=3458;MQ=60;set=variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,54:106:99:1574,0,1352:27,25,24,30 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 1/1:0,100:100:99:3838,300,0:0,0,42,58 chr2 21232804 . G A 1216.32 PASS AC=1;AF=0.641;AN=2;DP=3923;MQ=60;set=variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,46:100:99:1134,0,1455:21,33,21,25 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 1/1:0,69:69:99:2174,207,0:0,0,25,44 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 1/1:0,32:32:96:991,96,0:0,0,10,22 chr2 21237238 . A T 847.05 PASS AC=1;AF=0.633;AN=2;DP=198;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant9-variant12-variant17-variant23-variant24-variant25-variant26-variant28-variant31-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:111,0,189:5,0,3,1 chr2 21241744 . C T 2022.97 PASS AC=1;AF=0.618;AN=2;DP=1094;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant9-variant12-variant17-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,24:53:99:619,0,739:17,12,15,9 chr2 21249716 . C T 898.69 PASS AC=1;AF=0.5;AN=2;DP=243;MQ=60;set=variant3-variant12-variant17-variant23-variant31 GT:AD:DP:GQ:PL:SB 0/1:23,19:42:99:477,0,666:17,6,13,6 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 1/1:0,82:82:99:2537,245,0:0,0,30,52 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 1/1:0,30:30:89:1016,89,0:0,0,16,14 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 1/1:16:48:0,0,14,2 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 1/1:0,36:36:99:1578,108,0:0,0,8,28 chr2 21263639 . T G 270.93 PASS AC=1;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 0/1:6,15:21:99:536,0,157:5,1,14,1 chr2 21263900 . G A 1363.8 PASS AC=1;AF=0.522;AN=2;DP=2550;MQ=60;set=variant3-variant7-variant8-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant30-variant32-variant34-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:39,49:88:99:1263,0,963:18,21,17,32 chr2 21265518 . A T 427.39 PASS AC=1;AF=0.529;AN=2;DP=270;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant9-variant12-variant16-variant17-variant22-variant23-variant25-variant27-variant31-variant33-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:178,0,114:1,3,0,5 chr2 21266774 . GGCAGCGCCA G 326.43 PASS AC=1;AF=0.521;AN=2;DP=826;MQ=60;set=variant3-variant5-variant7-variant8-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant27-variant28-variant30-variant32-variant34-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:19,13:32:99:482,0,1577:11,8,10,3 chr2 21350324 . G A 323.83 PASS AC=1;AF=0.524;AN=2;DP=543;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant8-variant11-variant13-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant27-variant28-variant30-variant32-variant34-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:8,12:20:99:405,0,297:8,0,12,0 chr2 21350346 . A C 718.15 PASS AC=1;AF=0.524;AN=2;DP=848;MQ=60;set=variant3-variant7-variant8-variant11-variant13-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant27-variant28-variant30-variant32-variant34-variant36-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:17,20:37:99:767,0,643:17,0,20,0 chr2 21364562 . C T 753.26 PASS AC=1;AF=0.5;AN=2;DP=106;FS=8.109;FractionInformativeReads=1;MQ=60;MQRankSum=-2.605;QD=7.11;ReadPosRankSum=-0.777;SOR=1.121;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:70,36:106:99:781,0,1932:38,32,14,22 chr2 23608319 . A AGCC,AGCCGCC 511.87 PASS AC=1,0;AF=0.56,0.02;AN=2;DP=925;set=variant-variant4-variant9-variant12-variant13-variant15-variant16-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant37-variant39-variant40-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:40:99:17,7,8,8 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 1/1:0,16:16:54:639,54,0:0,0,10,6 chr2 23785517 . A G 262.31 PASS AC=1;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 0/1:9,10:19:99:373,0,486:3,6,4,6 chr2 23785524 . C A 217.56 PASS AC=1;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 0/1:9,9:18:99:351,0,489:3,6,3,6 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 1/1:0,40:40:99:1733,121,0:0,0,17,23 chr2 23918891 . C T 2430.55 PASS AC=1;AF=0.5;AN=2;DP=804;MQ=60;set=variant20-variant23-variant27-variant32 GT:AD:DP:GQ:PL:SB 0/1:85,107:192:99:2549,0,2020:38,47,50,57 chr2 23919207 . G A 889.37 PASS AC=1;AF=0.5;AN=2;DP=304;FractionInformativeReads=1;MQ=60;set=variant20-variant23-variant27-variant32 GT:AD:DP:GQ:PL:SB 0/1:29,38:67:99:838,0,740:17,12,20,18 chr2 23919375 . C T 1618.03 PASS AC=1;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 0/1:31,26:57:99:784,0,845:20,11,11,15 chr2 23919557 . G A 777.08 PASS AC=1;AF=0.5;AN=2;DP=261;FractionInformativeReads=1;MQ=60;set=variant20-variant23-variant27-variant32 GT:AD:DP:GQ:PL:SB 0/1:29,33:62:99:919,0,805:15,14,18,15 chr2 23919630 . C G 1606.93 PASS AC=1;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 0/1:27,17:44:99:427,0,722:12,15,9,8 chr2 23919839 . CG C 832.87 PASS AC=1;AF=0.5;AN=2;DP=259;MQ=60;set=variant20-variant23-variant27-variant32 GT:AD:DP:GQ:PL:SB 0/1:35,29:64:99:731,0,909:16,19,17,12 chr2 23920230 . C A 698.66 PASS AC=1;AF=0.5;AN=2;DP=200;FractionInformativeReads=1;MQ=60;set=variant20-variant23-variant27-variant32 GT:AD:DP:GQ:PL:SB 0/1:20,14:34:99:377,0,448:11,9,10,4 chr2 23920545 . A G 1400.81 PASS AC=1;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 0/1:20,26:46:99:697,0,537:8,12,12,14 chr2 23920579 . T TATC 937.45 PASS AC=1;AF=0.5;AN=2;DP=205;MQ=60;set=variant20-variant23-variant27-variant32 GT:AD:DP:GQ:PL:SB 0/1:29,15:44:99:527,0,1173:12,17,7,8 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 1/1:0,41:41:99:1265,122,0:0,0,17,24 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 1/1:0,36:36:99:1225,108,0:0,0,13,23 chr2 23920646 . G C 959.92 PASS AC=1;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 0/1:15,19:34:99:562,0,477:6,9,8,11 chr2 23925980 . T C 1363.76 PASS AC=1;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 0/1:27,23:50:99:591,0,605:16,11,15,8 chr2 23926659 . T C 5408.35 PASS AC=1;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 0/1:89,81:170:99:1808,0,2045:45,44,39,42 chr2 23929979 . T C 1342.94 PASS AC=1;AF=0.5;AN=2;DP=627;FractionInformativeReads=1;MQ=60;set=variant11-variant16-variant20-variant23-variant25-variant27-variant32 GT:AD:DP:GQ:PL:SB 0/1:33,44:77:99:1068,0,742:18,15,26,18 chr2 23930126 . G A 827.08 PASS AC=1;AF=0.5;AN=2;DP=285;FractionInformativeReads=1;MQ=60;set=variant20-variant23-variant27-variant32 GT:AD:DP:GQ:PL:SB 0/1:33,39:72:99:1045,0,733:16,17,15,24 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 1/1:0,40:40:99:1282,120,0:0,0,24,16 chr2 23931036 . C T 3076.37 PASS AC=1;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 0/1:46,59:105:99:1359,0,991:22,24,30,29 chr2 23973799 . T C 11096.4 PASS AC=1;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 0/1:192,186:378:99:4675,0,4950:90,102,92,94 chr2 24009163 . A G 861.96 PASS AC=1;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 0/1:33,21:54:99:504,0,923:12,21,7,14 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 1/1:0,23:23:69:748,69,0:0,0,16,7 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 1/1:0,176:176:99:5191,527,0:0,0,81,95 chr2 24079058 . CA C,CAA,CAAA,CAAAA 128.69 PASS AC=0,0,1,0;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 0/3:29:99:17,0,9,3 chr2 24103432 . CAA CA,C 74.54 PASS AC=1,0;AF=0.478,0.022;AN=2;DP=810;set=variant-variant4-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant14-variant20-variant21-variant22-variant23-variant27-variant28-filterInvariant30-variant32-filterInvariant33-variant34-variant38-variant39-variant40-variant43 GT:DP:GQ:SB 0/1:38:99:13,9,12,4 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 1/1:0,107:107:99:3020,320,0:0,0,58,49 chr2 24110657 . A T 94.69 PASS AC=1;AF=0.5;AN=2;DP=142;MQ=60;set=variant11-variant12-variant16-variant20-variant23-variant25-variant27-variant32 GT:AD:DP:GQ:PL:SB 0/1:11,3:14:93:93,0,415:10,1,3,0 chr2 24150513 . G GGA,GA,GGGA 293.82 PASS AC=2,0,0;AF=0.694,0.028,0.028;AN=2;DP=257;set=variant2-variant3-variant8-variant11-variant13-variant15-variant16-variant19-variant20-variant23-variant24-variant25-variant31-variant32-variant36-variant37-variant42-variant44 GT:DP:GQ:SB 1/1:5:18:0,0,1,4 chr2 24163300 . C CCT 3089.99 PASS AC=1;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 0/1:19,28:47:99:1062,0,704:10,9,17,11 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 1/1:0,27:27:81:884,81,0:0,0,8,19 chr2 24222942 . A G 1321.34 PASS AC=1;AF=0.5;AN=2;DP=802;MQ=60;set=variant11-variant12-variant16-variant20-variant23-variant25-variant27-variant32 GT:AD:DP:GQ:PL:SB 0/1:49,46:95:99:1143,0,1130:23,26,21,25 chr2 24225489 . T A 32.48 PASS AC=1;AF=0.625;AN=2;DP=17;FS=0;FractionInformativeReads=1;MQ=60;set=variant20-variant23-variant27-variant32 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:31:121,0,31:1,1,3,1 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 1/1:0,18:18:54:555,54,0:0,0,11,7 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 1/1:0,139:139:99:6225,418,0:0,0,73,66 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 1/1:0,7:7:21:193,21,0:0,0,4,3 chr2 24227629 . TTC T 579.11 PASS AC=1;AF=0.5;AN=2;DP=341;MQ=60;set=variant7-variant11-variant12-variant16-variant20-variant23-variant25-variant27-variant32 GT:AD:DP:GQ:PL:SB 0/1:19,19:38:99:713,0,712:9,10,9,10 chr2 24239900 . CTGAAGTG C 3342.36 PASS AC=1;AF=0.5;AN=2;DP=746;MQ=60;set=variant20-variant23-variant27-variant32 GT:AD:DP:GQ:PL:SB 0/1:92,65:157:99:2423,0,6047:26,66,19,46 chr2 24240413 . C T 1881.77 PASS AC=1;AF=0.5;AN=2;DP=117;FS=2.725;FractionInformativeReads=1;MQ=60;MQRankSum=-1.849;QD=16.08;ReadPosRankSum=1.7;SOR=1.063;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:50,67:117:99:1910,0,1279:16,34,17,50 chr2 24244603 . G A 1938.8 PASS AC=1;AF=0.5;AN=2;DP=565;MQ=60;set=variant20-variant23-variant27-variant32 GT:AD:DP:GQ:PL:SB 0/1:68,57:125:99:1311,0,1722:32,36,25,32 chr2 24245167 . G A 913.52 PASS AC=1;AF=0.5;AN=2;DP=434;MQ=60;set=variant20-variant23-variant27-variant32 GT:AD:DP:GQ:PL:SB 0/1:48,53:101:99:1279,0,1162:30,18,30,23 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 1/1:0,84:84:99:2699,250,0:0,0,25,59 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 1/1:0,46:46:99:1514,138,0:0,0,14,32 chr2 24248474 . G A 506.57 PASS AC=1;AF=0.5;AN=2;DP=284;MQ=60;set=variant12-variant18-variant20-variant23-variant27-variant32 GT:AD:DP:GQ:PL:SB 0/1:23,27:50:99:574,0,569:8,15,12,15 chr2 24252417 . T C 2570.52 PASS AC=1;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 0/1:40,38:78:99:1193,0,1145:15,25,11,27 chr2 24252436 . A G 2278.44 PASS AC=1;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 0/1:40,34:74:99:988,0,1099:16,24,11,23 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 1/1:0,27:27:80:910,80,0:0,0,12,15 chr2 24256071 . T C 1174.56 PASS AC=1;AF=0.5;AN=2;DP=687;MQ=60;set=variant12-variant18-variant19-variant20-variant23-variant27-variant32-variant40 GT:AD:DP:GQ:PL:SB 0/1:49,41:90:99:1069,0,1281:23,26,20,21 chr2 24272645 . C T 889.4 PASS AC=1;AF=0.536;AN=2;DP=814;MQ=60;set=variant6-variant7-variant9-variant10-variant14-variant20-variant21-variant23-variant27-variant28-variant32-variant34-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:42,24:66:99:435,0,1020:23,19,14,10 chr2 24277709 . G A 460.51 PASS AC=1;AF=0.533;AN=2;DP=491;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant9-variant10-variant14-variant20-variant21-variant22-variant23-variant27-variant28-variant32-variant34-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,18:34:99:534,0,500:3,13,4,14 chr2 24291445 . C T 265.88 PASS AC=1;AF=0.533;AN=2;DP=492;MQ=60;set=variant6-variant7-variant9-variant10-variant14-variant20-variant21-variant22-variant23-variant27-variant28-variant32-variant34-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,16:35:99:439,0,541:5,14,4,12 chr2 24302246 . C T 325.31 PASS AC=1;AF=0.536;AN=2;DP=362;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant9-variant10-variant20-variant21-variant22-variant23-variant27-variant28-variant32-variant34-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:150,0,151:4,1,4,3 chr2 24307260 . A ACAGGGCAGGG,ACAGGG 1427.14 PASS AC=0,1;AF=0.205,0.364;AN=2;DP=3408;set=variant-variant3-variant5-variant6-variant7-variant9-variant10-variant14-variant18-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant30-variant32-variant34-variant39-variant40-variant43 GT:DP:GQ:SB 0/2:125:99:25,40,20,40 chr2 24342505 . T C 1262.86 PASS AC=1;AF=0.583;AN=2;DP=2866;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant30-variant32-variant34-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,38:83:99:960,0,1110:26,19,23,15 chr2 24344060 . T G 1636.76 PASS AC=1;AF=0.533;AN=2;DP=2184;MQ=60;set=variant6-variant7-variant9-variant10-variant14-variant20-variant21-variant22-variant23-variant27-variant28-variant32-variant34-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:69,82:151:99:2003,0,1652:35,34,40,42 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 1/1:0,70:70:99:2068,209,0:0,0,38,32 chr2 24384424 . T C 2155.9 PASS AC=2;AF=0.955;AN=2;DP=2975;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:1981,201,0:0,0,39,28 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 1/1:0,46:46:99:1685,138,0:0,0,16,30 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 1/1:0,15:15:44:543,44,0:0,0,12,3 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 1/1:1,90:91:99:2666,226,0:0,1,53,37 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 1/1:0,5:5:15:214,15,0:0,0,5,0 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 1/1:0,21:21:63:715,63,0:0,0,15,6 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 1/1:0,24:24:72:743,72,0:0,0,7,17 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 1/1:0,6:6:18:148,18,0:0,0,3,3 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 1/1:0,7:7:21:207,21,0:0,0,3,4 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 1/1:0,29:29:87:921,87,0:0,0,20,9 chr2 24398446 . A T 2518.06 PASS AC=2;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 1/1:0,74:74:99:2072,222,0:0,0,32,42 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 1/1:0,30:30:90:1350,90,0:0,0,15,15 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 1/1:0,153:153:99:4587,458,0:0,0,75,78 chr2 24428859 . T C 775.47 PASS AC=1;AF=0.548;AN=2;DP=1053;MQ=60;set=variant5-variant6-variant7-variant9-variant10-variant12-variant14-variant15-variant16-variant18-variant21-variant22-variant23-variant28-variant31-variant32-variant34-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,20:52:99:515,0,795:22,10,13,7 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 1/1:0,44:44:99:1558,132,0:0,0,15,29 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 1/1:0,36:36:99:1361,108,0:0,0,31,5 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 1/1:0,67:67:99:2302,201,0:0,0,49,18 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 1/1:0,13:13:39:484,39,0:0,0,1,12 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 1/1:0,277:277:99:8162,829,0:0,0,149,128 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 1/1:0,243:243:99:7478,728,0:0,0,116,127 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 1/1:0,51:51:99:1745,153,0:0,0,35,16 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 1/1:0,45:45:99:1400,135,0:0,0,16,29 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 1/1:0,5:5:15:181,15,0:0,0,2,3 chr2 24507757 . ATTTT ATT,A,AT,ATTT 392.18 PASS AC=2,0,0,0;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 1/1:22:40:2,0,1,19 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 1/1:0,42:42:99:1434,126,0:0,0,26,16 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 1/1:0,17:17:51:622,51,0:0,0,2,15 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 1/1:55:86:3,1,29,22 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 1/1:0,21:21:62:582,62,0:0,0,13,8 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 1/1:0,26:26:78:797,78,0:0,0,17,9 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 1/1:0,59:59:99:1715,176,0:0,0,36,23 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 1/1:0,42:42:99:1285,125,0:0,0,26,16 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 1/1:0,66:66:99:1920,198,0:0,0,34,32 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 1/1:0,41:41:99:1195,123,0:0,0,15,26 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 1/1:0,28:28:83:956,83,0:0,0,7,21 chr2 24714923 . C T 911.36 PASS AC=1;AF=0.538;AN=2;DP=529;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant11-variant14-variant20-variant21-variant23-variant25-variant26-variant27-variant29-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,21:29:99:571,0,141:5,3,14,7 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 1/1:0,87:87:99:2882,261,0:0,0,27,60 chr2 24896389 . T G 886.26 PASS AC=1;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 0/1:34,18:52:99:390,0,1029:7,27,6,12 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 1/1:0,11:11:33:445,33,0:0,0,11,0 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 1/1:1,196:197:99:5588,544,0:1,0,81,115 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 1/1:0,27:27:81:997,81,0:0,0,22,5 chr2 24952712 . CT C 390.3 PASS AC=1;AF=0.559;AN=2;DP=1521;set=variant-variant4-variant6-filterInvariant9-variant11-variant14-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant29-variant34-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,23:46:99:379,0,450:6,17,9,14 chr2 24952740 . C CT 1067.7 PASS AC=2;AF=0.92;AN=2;DP=2332;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1476,111,0:0,0,11,26 chr2 24962252 . G A 1414.44 PASS AC=1;AF=0.571;AN=2;DP=556;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant11-variant14-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant29-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,15:24:99:397,0,290:7,2,9,6 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 1/1:1,66:67:99:1963,190,0:1,0,37,29 chr2 24991385 . CAAAA CA,CAAAAAAA,CAA,C,CAAA,CAAAAA 391.35 PASS AC=1,0,0,0,0,0;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 0/1:30:99:9,6,12,3 chr2 24991569 . C G 7175.29 PASS AC=1;AF=0.607;AN=2;DP=2807;MQ=60;set=variant4-variant6-variant11-variant14-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant29-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:90,88:178:99:1990,0,2266:38,52,40,48 chr2 25013062 . T C 2612.09 PASS AC=1;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 0/1:87,82:169:99:2113,0,2188:42,45,43,39 chr2 25022442 . TA T 1010.49 PASS AC=1;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 0/1:14,13:27:99:265,0,287:9,5,9,4 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 1/1:0,26:26:78:851,78,0:0,0,7,19 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 1/1:0,42:42:99:1438,126,0:0,0,30,12 chr2 25042622 . A G 5799.07 PASS AC=1;AF=0.594;AN=2;DP=1656;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant11-variant14-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant29-variant38-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,46:83:99:1153,0,911:18,19,21,25 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 1/1:0,82:82:99:3237,247,0:0,0,38,44 chr2 25044754 . A G 982.24 PASS AC=1;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 0/1:38,27:65:99:1013,0,3227:18,20,10,17 chr2 25044755 . C T 982.24 PASS AC=1;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 0/1:39,27:66:99:1013,0,3227:19,20,10,17 chr2 25044763 . A G 862.29 PASS AC=1;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 0/1:38,26:64:99:977,0,3142:18,20,9,17 chr2 25046090 . T C 821.77 PASS AC=1;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 0/1:12,19:31:99:525,0,276:9,3,13,6 chr2 25046355 . T C 410.02 PASS AC=1;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 0/1:11,13:24:99:363,0,365:5,6,4,9 chr2 25046361 . AT ATTT,ATT,A,ATTTT 530.92 PASS AC=1,0,0,0;AF=0.229,0.329,0.071,0.014;AN=2;DP=767;set=variant-variant2-variant3-variant5-variant7-variant8-filterInvariant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:14:14:0,2,3,9 chr2 25047408 . A G 1089.02 PASS AC=1;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 0/1:92,71:163:99:1487,0,2027:42,50,35,36 chr2 25048847 . A G 976.64 PASS AC=1;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 0/1:24,26:50:99:689,0,668:18,6,17,9 chr2 25050977 . T C 1164.96 PASS AC=1;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 0/1:50,29:79:99:685,0,1404:18,32,11,18 chr2 25057263 . G A 193.54 PASS AC=1;AF=0.667;AN=2;DP=344;MQ=60;set=variant-variant2-variant3-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant18-variant21-variant22-variant23-variant24-variant28-variant29-variant31-variant32-variant33-variant36-variant37-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,10:17:99:275,0,150:5,2,7,3 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 0/1:6,6:12:99:128,0,109:3,3,4,2 chr2 25061270 . GGGGTGGGGTGGGTGGGGT GGGGTGGGGT,G 418.87 PASS AC=2,0;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 1/1:8:24:0,0,8,0 chr2 25061810 . ATT AT,ATTT,A 471.61 PASS AC=1,0,0;AF=0.452,0.016,0.065;AN=2;DP=1881;set=variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-filterInvariant10-variant12-variant13-variant14-variant15-filterInvariant16-variant17-variant18-filterInvariant19-variant20-variant21-variant23-filterInvariant27-variant28-variant29-variant31-variant32-variant34-variant36-filterInvariant37-variant39-filterInvariant40-variant41-filterInvariant44 GT:DP:GQ:SB 0/1:28:99:3,12,2,11 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 0/1:7,20:27:99:502,0,137:4,3,13,7 chr2 25179893 . C T 1739.26 PASS AC=1;AF=0.571;AN=2;DP=824;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant13-variant16-variant18-variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:41,43:84:99:1025,0,1104:27,14,23,20 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 1/1:0,291:291:99:8860,867,0:0,0,131,160 chr2 25314186 . T C 2047.26 PASS AC=2;AF=0.703;AN=2;DP=2653;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,89:89:99:2680,266,0:0,0,48,41 chr2 25344464 . G A 396.89 PASS AC=2;AF=0.567;AN=2;DP=395;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant9-variant13-variant15-variant16-variant18-variant21-variant22-variant23-variant26-variant30-variant32-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:62:759,62,0:0,0,16,5 chr2 25359254 . C T 363.76 PASS AC=2;AF=0.556;AN=2;DP=475;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant7-variant9-variant13-variant15-variant16-variant18-variant21-variant23-variant26-variant28-variant30-variant32-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:811,66,0:0,0,18,4 chr2 25362194 . G A 232.47 PASS AC=2;AF=0.556;AN=2;DP=732;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant9-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant30-variant32-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1377,132,0:0,0,16,28 chr2 25368005 . G A 497.41 PASS AC=2;AF=0.556;AN=2;DP=657;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant9-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant30-variant32-variant38 GT:AD:DP:GQ:PL:SB 1/1:1,48:49:99:1395,102,0:0,1,23,25 chr2 25368030 . T C 616.16 PASS AC=2;AF=0.556;AN=2;DP=704;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant9-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant30-variant32-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1483,153,0:0,0,23,28 chr2 25368951 . GTTT G,GTT,GT,GTTTT 408.36 PASS AC=0,0,2,0;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 3/3:25:14:1,1,9,14 chr2 25369002 . C T 464.98 PASS AC=2;AF=0.556;AN=2;DP=611;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant9-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant30-variant32-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:1131,87,0:0,0,12,17 chr2 25369040 . C T 551.49 PASS AC=2;AF=0.556;AN=2;DP=750;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant9-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant30-variant32-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,33:33:99:1231,99,0:0,0,18,15 chr2 25375112 . C T 317.21 PASS AC=1;AF=0.563;AN=2;DP=115;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant13-variant16-variant18-variant23-variant26-variant38 GT:AD:DP:GQ:PL:SB 0/1:2,10:12:55:330,0,55:1,1,3,7 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 1/1:0,161:161:99:5055,483,0:0,0,79,82 chr2 25377329 . C T 970.55 PASS AC=2;AF=0.556;AN=2;DP=1694;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant9-variant13-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant30-variant32-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:3198,302,0:0,0,38,63 chr2 25384113 . T C 1892.22 PASS AC=1;AF=0.5;AN=2;DP=158;FS=4.799;FractionInformativeReads=1;MQ=60;MQRankSum=-0.612;QD=11.98;ReadPosRankSum=0.19;SOR=1.106;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:84,74:158:99:1920,0,1937:38,46,27,47 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 1/1:0,10:10:33:459,33,0:0,0,3,7 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 0/1:10,13:23:99:277,0,200:8,2,12,1 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 0/1:11,7:18:99:177,0,322:7,4,4,3 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 0/1:65,63:128:99:1541,0,1483:35,30,40,23 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 0/1:27,39:66:99:1069,0,547:16,11,26,13 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 0/1:16,24:40:99:633,0,407:7,9,9,15 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 0/1:26,42:68:99:1175,0,612:16,10,28,14 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 0/1:8,15:23:99:443,0,293:0,8,3,12 chr2 25497684 . A AC 524.34 PASS AC=1;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 0/1:11,17:28:99:602,0,339:8,3,11,6 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 0/1:17,6:23:99:201,0,786:6,11,6,0 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 0/1:19,6:25:99:189,0,1206:7,12,6,0 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 0/1:21,6:27:99:189,0,1170:9,12,6,0 chr2 25523196 . T C 1184.67 PASS AC=1;AF=0.6;AN=2;DP=133;FractionInformativeReads=1;MQ=60;set=variant15-variant23-variant26-variant29-variant36 GT:AD:DP:GQ:PL:SB 0/1:7,15:22:99:511,0,212:1,6,3,12 chr2 25602142 . G A 3121.95 PASS AC=2;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 1/1:0,70:70:99:2203,209,0:0,0,44,26 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 0/1:42,30:72:99:798,0,1083:15,27,10,20 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 0/1:22,22:44:99:522,0,501:10,12,10,12 chr2 25650631 . A G 560.75 PASS AC=1;AF=0.533;AN=2;DP=742;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant8-variant9-variant13-variant16-variant17-variant19-variant23-variant25-variant26-variant28-variant33-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,10:24:99:288,0,422:4,10,2,8 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 1/1:0,18:18:54:732,54,0:0,0,17,1 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 0/1:76,67:143:99:1722,0,1920:31,45,30,37 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 1/1:0,35:35:99:1300,105,0:0,0,13,22 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 0/1:16,9:25:99:166,0,323:5,11,3,6 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 0/1:68,69:137:99:1597,0,1784:33,35,36,33 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 0/1:10,15:25:99:430,0,290:2,8,5,10 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 0/1:18,25:43:99:689,0,526:4,14,8,17 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 0/1:68,69:137:99:1861,0,1878:36,32,36,33 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 0/1:12,8:20:99:178,0,349:4,8,3,5 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 0/1:3,2:5:75:75,0,76:1,2,0,2 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 0/1:8,7:15:99:217,0,254:4,4,3,4 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 1/1:0,16:16:48:517,48,0:0,0,7,9 chr2 26082212 . T C 408.18 PASS AC=1;AF=0.5;AN=2;DP=509;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant7-variant9-variant10-variant11-variant15-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant31-variant32-variant33-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,10:23:99:300,0,269:7,6,8,2 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 0/1:10,15:25:99:374,0,184:5,5,6,9 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 1/1:0,10:10:30:268,30,0:0,0,5,5 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 1/1:0,70:70:99:3079,217,0:0,0,38,32 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 1/1:0,73:73:99:3104,222,0:0,0,40,33 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 1/1:0,260:260:99:8297,779,0:0,0,152,108 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 1/1:0,231:231:99:7401,692,0:0,0,95,136 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 1/1:0,64:64:99:2092,192,0:0,0,34,30 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 1/1:0,23:23:69:827,69,0:0,0,10,13 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 0/1:25:99:6,5,8,6 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 1/1:0,175:175:99:5446,525,0:0,0,95,80 chr2 26204640 . G A 7604.18 PASS AC=1;AF=0.712;AN=2;DP=7881;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:125,116:241:99:2736,0,2863:62,63,57,59 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 1/1:0,90:90:99:2530,267,0:0,0,47,43 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 1/1:0,113:113:99:5051,343,0:0,0,44,69 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 1/1:0,114:114:99:5051,343,0:0,0,44,70 chr2 26321526 . T C 605.88 PASS AC=2;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 1/1:0,53:53:99:1614,159,0:0,0,30,23 chr2 26350136 . G T 1154.69 PASS AC=2;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 1/1:0,69:69:99:2042,207,0:0,0,26,43 chr2 26357748 . G T 825.3 PASS AC=2;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 1/1:0,38:38:99:1147,114,0:0,0,24,14 chr2 26358110 . G C 1906.01 PASS AC=2;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 1/1:0,144:144:99:4606,430,0:0,0,62,82 chr2 26359315 . G A 2717.79 PASS AC=2;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 1/1:0,160:160:99:5157,479,0:0,0,96,64 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 0/1:61,65:126:99:1497,0,1438:29,32,33,32 chr2 26399481 . C G 90.18 PASS AC=1;AF=0.743;AN=2;DP=919;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-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,9:16:99:273,0,146:3,4,2,7 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 0/1:31,30:61:99:753,0,773:22,9,20,10 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 0/1:20,22:42:99:594,0,514:10,10,11,11 chr2 26404775 . A G 453.55 PASS AC=1;AF=0.851;AN=2;DP=407;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-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:201,0,138:3,1,5,2 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 0/1:42,31:73:99:744,0,1006:19,23,14,17 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 0/1:9,15:24:99:418,0,223:4,5,4,11 chr2 26408064 . T C 983.58 PASS AC=2;AF=0.955;AN=2;DP=1212;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:626,69,0:0,0,11,12 chr2 26411674 . G A 1404.47 PASS AC=1;AF=0.633;AN=2;DP=1437;MQ=60;set=variant4-variant8-variant11-variant14-variant17-variant21-variant22-variant23-variant24-variant25-variant28-variant34-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:35,32:67:99:767,0,946:18,17,16,16 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 0/1:31,41:72:99:1072,0,783:17,14,22,19 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 0/1:9,11:20:99:435,0,359:2,7,4,7 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 0/1:4,8:12:99:230,0,105:1,3,3,5 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 0/1:21,14:35:99:340,0,515:10,11,5,9 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 0/1:16,10:26:99:250,0,394:8,8,4,6 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 0/2:26:99:8,4,9,5 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 0/1:5,8:13:99:229,0,127:1,4,3,5 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 0/1:20,20:40:99:526,0,517:14,6,14,6 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 0/1:10,7:17:99:223,0,327:2,8,1,6 chr2 26417829 . G A 644.66 PASS AC=1;AF=0.545;AN=2;DP=423;MQ=60;set=variant11-variant12-variant13-variant14-variant16-variant19-variant23-variant29-variant30-variant33-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,25:39:99:668,0,327:10,4,16,9 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 0/1:36,33:69:99:839,0,838:16,20,13,20 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 0/1:10,6:16:99:202,0,405:0,10,0,6 chr2 26454996 . A G 911.8 PASS AC=1;AF=0.829;AN=2;DP=774;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-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,5:14:99:139,0,326:7,2,4,1 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 0/1:5,11:16:99:311,0,177:4,1,9,2 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 0/1:37,63:100:99:1529,0,879:22,15,37,26 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 0/1:20,21:41:99:530,0,480:8,12,8,13 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 0/1:7,5:12:99:148,0,233:1,6,1,4 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 0/1:43,43:86:99:1043,0,1080:27,16,28,15 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 0/1:20,34:54:99:907,0,445:11,9,19,15 chr2 26467666 . G A 2035.46 PASS AC=1;AF=0.829;AN=2;DP=2303;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-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,21:52:99:431,0,874:17,14,12,9 chr2 26476977 . A G 2102.4 PASS AC=2;AF=0.977;AN=2;DP=3188;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:2155,168,0:0,0,48,8 chr2 26477125 . G GACT 17279.8 PASS AC=2;AF=0.977;AN=2;DP=15219;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,306:306:99:13707,924,0:0,0,141,165 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 0/1:5,12:17:99:351,0,174:4,1,8,4 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 0/1:5,6:11:99:193,0,154:4,1,5,1 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 0/1:49,41:90:99:986,0,1100:25,24,21,20 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 0/1:19,33:52:99:833,0,325:10,9,21,12 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 0/1:64,67:131:99:1628,0,1578:34,30,34,33 chr2 26512957 . G C 11413 PASS AC=2;AF=0.977;AN=2;DP=11530;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,223:223:99:7228,668,0:0,0,106,117 chr2 26532491 . G T 1336.53 PASS AC=1;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 0/1:67,39:106:99:863,0,1632:35,32,16,23 chr2 26532735 . G A 882.19 PASS AC=1;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 0/1:33,52:85:99:1208,0,692:20,13,32,20 chr2 26533023 . C T 844.36 PASS AC=1;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 0/1:63,55:118:99:1266,0,1540:33,30,27,28 chr2 26534801 . G A 1173.68 PASS AC=1;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 0/1:29,38:67:99:1024,0,718:17,12,19,19 chr2 26536299 . C G 1027.28 PASS AC=1;AF=0.574;AN=2;DP=3436;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant9-variant11-variant13-variant14-variant17-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant34-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:49,57:106:99:1397,0,1371:29,20,34,23 chr2 26536555 . T C 584.33 PASS AC=1;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 0/1:19,13:32:99:353,0,631:10,9,5,8 chr2 26536694 . C T 487.73 PASS AC=1;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 0/1:51,46:97:99:1240,0,1371:28,23,29,17 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 1/1:0,78:78:99:2255,233,0:0,0,30,48 chr2 26541158 . G A 145.31 PASS AC=2;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 1/1:0,5:5:15:184,15,0:0,0,1,4 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 1/1:0,8:8:24:267,24,0:0,0,2,6 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 0/1:4,3:7:73:73,0,159:0,4,1,2 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 0/1:14,19:33:99:518,0,370:8,6,12,7 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 0/1:67,50:117:99:1084,0,1719:33,34,23,27 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 0/1:63,43:106:99:1035,0,1466:28,35,17,26 chr2 26606347 . T A 524.32 PASS AC=1;AF=0.734;AN=2;DP=872;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant31-variant33-variant34-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:349,0,290:4,7,6,6 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 1/1:0,40:40:99:1345,120,0:0,0,10,30 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 0/1:13,23:36:99:578,0,344:4,9,8,15 chr2 26612465 . G A 5728.83 PASS AC=1;AF=0.734;AN=2;DP=12538;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant31-variant33-variant34-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:155,183:338:99:4517,0,3912:70,85,83,100 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 1/1:0,418:418:99:12541,1253,0:0,0,209,209 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 0/1:189,194:383:99:4698,0,4375:77,112,74,120 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 1/1:0,153:153:99:6875,461,0:0,0,81,72 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 1/1:0,181:181:99:5440,540,0:0,0,96,85 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 1/1:0,206:206:99:6385,619,0:0,0,115,91 chr2 26615902 . G A 3457.08 PASS AC=1;AF=0.734;AN=2;DP=7668;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant31-variant33-variant34-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:105,93:198:99:2182,0,2707:56,49,45,48 chr2 26616356 . A G 551.2 PASS AC=1;AF=0.734;AN=2;DP=1082;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant31-variant33-variant34-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:352,0,288:5,7,6,6 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 1/1:0,30:30:90:918,90,0:0,0,16,14 chr2 26617209 . A G 194.2 PASS AC=1;AF=0.759;AN=2;DP=235;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant20-variant23-variant24-variant26-variant27-variant31-variant33-variant34-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:149,0,148:3,1,3,1 chr2 26618543 . G A 4345.87 PASS AC=1;AF=0.734;AN=2;DP=8904;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant31-variant33-variant34-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:141,150:291:99:3428,0,3261:66,75,71,79 chr2 26625042 . C A 173.4 PASS AC=1;AF=0.721;AN=2;DP=735;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,8:13:99:199,0,186:1,4,3,5 chr2 26647277 . T G 655.8 PASS AC=2;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 1/1:0,37:37:99:1139,111,0:0,0,14,23 chr2 26652671 . A G 907.03 PASS AC=2;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 1/1:0,24:24:72:776,72,0:0,0,7,17 chr2 26653457 . G A 6755.21 PASS AC=1;AF=0.757;AN=2;DP=6446;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-variant26-variant27-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,77:148:99:1837,0,1752:40,31,47,30 chr2 26663187 . TTG TTGTG,TTGTGTG,T,TTGTGTGTG,TTGTGTGTGTG 159.32 PASS AC=1,1,0,0,0;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 1/2:8:81:0,0,5,3 chr2 26663215 . A G 51.02 PASS AC=1;AF=0.72;AN=2;DP=374;set=variant-variant2-variant4-variant5-variant6-variant8-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant30-variant31-variant33-variant34-variant36-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:116,0,114:2,2,2,2 chr2 26667130 . A G 532.39 PASS AC=1;AF=0.583;AN=2;DP=961;FractionInformativeReads=1;MQ=60;set=variant4-variant8-variant14-variant21-variant22-variant23-variant24-variant25-variant28-variant34-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:31,35:66:99:938,0,935:22,9,21,14 chr2 26667462 . G T 259.2 PASS AC=1;AF=0.5;AN=2;DP=18;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.53;QD=14.4;ReadPosRankSum=2.031;SOR=0.358;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:9,9:18:99:287,0,266:7,2,6,3 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 1/1:0,129:129:99:3895,386,0:0,0,71,58 chr2 26671544 . A G 1679.37 PASS AC=2;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 1/1:0,120:120:99:3569,358,0:0,0,62,58 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 1/1:0,41:41:99:1357,123,0:0,0,18,23 chr2 26677303 . G T 1109.41 PASS AC=2;AF=0.955;AN=2;DP=1518;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:83:868,83,0:0,0,17,11 chr2 26677810 . A G 171.09 PASS AC=2;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 1/1:0,18:18:53:563,53,0:0,0,12,6 chr2 26684423 . G A 437.83 PASS AC=1;AF=0.5;AN=2;DP=25;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.169;QD=17.51;ReadPosRankSum=2.04;SOR=0.446;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:12,13:25:99:466,0,377:10,2,10,3 chr2 26688697 . C T 1414.88 PASS AC=1;AF=0.5;AN=2;DP=105;FS=13.002;FractionInformativeReads=1;MQ=60;MQRankSum=-0.952;QD=13.48;ReadPosRankSum=-2.709;SOR=1.349;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:54,51:105:99:1443,0,1439:24,30,33,18 chr2 26695143 . A G 88.71 PASS AC=2;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 1/1:0,12:12:36:429,36,0:0,0,10,2 chr2 26698682 . G T 331.6 PASS AC=2;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 1/1:0,37:37:99:1272,110,0:0,0,28,9 chr2 26699126 . C G 327.77 PASS AC=2;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 1/1:0,86:86:99:2673,258,0:0,0,38,48 chr2 26699855 . G C 695.52 PASS AC=2;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 1/1:0,58:58:99:1983,174,0:0,0,32,26 chr2 26700700 . G A 1140.36 PASS AC=2;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 1/1:0,120:120:99:3850,358,0:0,0,53,67 chr2 26700819 . TGG T 1666.74 PASS AC=2;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 1/1:0,88:88:99:3894,265,0:0,0,41,47 chr2 26700908 . C G 825.24 PASS AC=2;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 1/1:0,74:74:99:2266,222,0:0,0,33,41 chr2 26702057 . GT G 211.36 PASS AC=2;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 1/1:0,20:20:60:744,60,0:0,0,16,4 chr2 26702412 . G A 1911.84 PASS AC=1;AF=0.5;AN=2;DP=295;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:67,68:135:99:1580,0,1598:31,36,31,37 chr2 26717641 . A G 238.34 PASS AC=2;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 1/1:0,25:25:75:755,75,0:0,0,15,10 chr2 26724442 . A G 550.98 PASS AC=1;AF=0.533;AN=2;DP=637;FractionInformativeReads=1;MQ=60;set=variant4-variant14-variant15-variant18-variant21-variant22-variant23-variant24-variant27-variant29-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,26:44:99:746,0,422:13,5,19,7 chr2 26724725 . T G 2376.89 PASS AC=2;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 1/1:0,80:80:99:2568,240,0:0,0,35,45 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 0/1:83,76:159:99:1785,0,2184:36,47,33,43 chr2 26733500 . C T 2777.68 PASS AC=2;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 1/1:0,112:112:99:3566,335,0:0,0,73,39 chr2 26733677 . G A 2530.82 PASS AC=1;AF=0.5;AN=2;DP=1258;MQ=60;set=variant3-variant10-variant14-variant15-variant23-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,72:151:99:1623,0,1991:32,47,28,44 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 0/1:58,22:80:99:537,0,1513:25,33,6,16 chr2 26739526 . A G 697.84 PASS AC=1;AF=0.5;AN=2;DP=353;FractionInformativeReads=1;MQ=60;set=variant15-variant21-variant22-variant23-variant24-variant40 GT:AD:DP:GQ:PL:SB 0/1:24,23:47:99:625,0,522:11,13,8,15 chr2 26750420 . C G 41.19 PASS AC=1;AF=0.533;AN=2;DP=154;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant7-variant8-variant10-variant13-variant16-variant20-variant23-variant25-variant26-variant32-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:154,0,110:3,1,4,1 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 1/1:0,40:40:99:1313,120,0:0,0,27,13 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 0/1:59,41:100:99:931,0,1561:34,25,20,21 chr2 26750769 . G A 1320.91 PASS AC=1;AF=0.5;AN=2;DP=106;FS=6.193;FractionInformativeReads=1;MQ=60;MQRankSum=-0.497;QD=12.46;ReadPosRankSum=2.725;SOR=0.322;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:50,56:106:99:1349,0,1256:18,32,27,29 chr2 26760509 . C T 371.4 PASS AC=1;AF=0.5;AN=2;DP=56;FractionInformativeReads=1;MQ=60;set=variant10-variant23 GT:AD:DP:GQ:PL:SB 0/1:10,20:30:99:627,0,199:6,4,17,3 chr2 26760593 . G A 1269.51 PASS AC=1;AF=0.5;AN=2;DP=194;FractionInformativeReads=1;MQ=60;set=variant10-variant23 GT:AD:DP:GQ:PL:SB 0/1:53,45:98:99:1043,0,1211:31,22,24,21 chr2 26781685 . CGTGT CGT,C 426.12 PASS AC=1,1;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 2/1:27:99:0,0,6,21 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 0/1:1,3:4:8:123,0,8:0,1,1,2 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 0/1:1,3:4:8:123,0,8:0,1,1,2 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 0/1:152,138:290:99:2985,0,3504:65,87,66,72 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 0/1:31,35:66:99:1005,0,930:12,19,14,21 chr2 26799091 . C A 421.62 PASS AC=1;AF=0.667;AN=2;DP=145;FractionInformativeReads=1;MQ=60;set=variant23-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,20:51:99:450,0,800:12,19,7,13 chr2 26799223 . G A 262.34 PASS AC=1;AF=0.5;AN=2;DP=61;FractionInformativeReads=1;MQ=60;set=variant16-variant23-variant33-variant34 GT:AD:DP:GQ:PL:SB 0/1:8,14:22:99:343,0,212:2,6,6,8 chr2 26800422 . G A 1170.02 PASS AC=1;AF=0.735;AN=2;DP=6058;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:97,64:161:99:1344,0,2334:46,51,32,32 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 0/1:60,62:122:99:1560,0,1474:24,36,24,38 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 1/1:0,68:68:99:2118,204,0:0,0,41,27 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 1/1:0,79:79:99:2381,237,0:0,0,45,34 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 1/1:0,92:92:99:2738,275,0:0,0,40,52 chr2 26804247 . T C 502.05 PASS AC=1;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 0/1:52,37:89:99:847,0,1283:20,32,18,19 chr2 26818006 . T C 1624.67 PASS AC=2;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 1/1:0,187:187:99:5406,560,0:0,0,93,94 chr2 26818021 . C T 1497.22 PASS AC=2;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 1/1:0,184:184:99:5212,550,0:0,0,88,96 chr2 26846282 . T C 1116.67 PASS AC=2;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 1/1:0,74:74:99:2298,221,0:0,0,49,25 chr2 26863503 . C T 1473.83 PASS AC=1;AF=0.5;AN=2;DP=108;FS=3.615;FractionInformativeReads=0.991;MQ=60;MQRankSum=-0.641;QD=13.65;ReadPosRankSum=1.96;SOR=0.423;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:49,58:107:99:1502,0,1188:18,31,26,32 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 0/1:2,10:12:14:211,0,14:1,1,5,5 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 1/1:0,96:96:99:2997,287,0:0,0,47,49 chr2 26952998 . T C 857 PASS AC=1;AF=0.568;AN=2;DP=1176;MQ=60;set=variant3-variant5-variant7-variant8-variant12-variant14-variant15-variant18-variant19-variant22-variant23-variant24-variant25-variant30-variant31-variant34-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,23:56:99:484,0,858:15,18,13,10 chr2 26953354 . G T 2696.29 PASS AC=2;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 1/1:1,108:109:99:3251,316,0:1,0,53,55 chr2 26953540 . A G 3818.36 PASS AC=2;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 1/1:0,116:116:99:3708,347,0:0,0,56,60 chr2 26953582 . T G 4805.9 PASS AC=2;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 1/1:0,99:99:99:4336,301,0:0,0,45,54 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 1/1:0,102:102:99:4459,313,0:0,0,47,55 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 1/1:0,93:93:99:2845,277,0:0,0,46,47 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 1/1:0,96:96:99:3090,291,0:0,0,49,47 chr2 26953850 . C T 2968.94 PASS AC=2;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 1/1:0,96:96:99:3062,287,0:0,0,45,51 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 1/1:0,6:6:18:226,18,0:0,0,3,3 chr2 26954991 . G A 1157.84 PASS AC=1;AF=0.568;AN=2;DP=1692;MQ=60;set=variant3-variant5-variant7-variant8-variant12-variant14-variant15-variant18-variant19-variant22-variant23-variant24-variant25-variant30-variant31-variant34-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,32:54:99:847,0,625:10,12,15,17 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 1/1:0,25:25:75:758,75,0:0,0,10,15 chr2 27001810 . C CT 227.08 PASS AC=1;AF=0.553;AN=2;DP=658;set=variant3-variant8-variant11-variant12-variant14-filterInvariant15-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant31-variant32-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,11:19:99:230,0,137:1,7,4,7 chr2 27003021 . T C 246.86 PASS AC=1;AF=0.604;AN=2;DP=523;MQ=60;set=variant3-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant19-variant21-variant22-variant23-variant24-variant25-variant30-variant31-variant32-variant34-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,12:18:99:364,0,169:3,3,6,6 chr2 27014980 . T C 1616.44 PASS AC=1;AF=0.604;AN=2;DP=2979;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant8-variant11-variant12-variant14-variant15-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,34:96:99:645,0,1522:30,32,19,15 chr2 27015118 . G A 994.06 PASS AC=1;AF=0.604;AN=2;DP=1430;MQ=60;set=variant3-variant7-variant8-variant11-variant12-variant14-variant15-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,25:50:99:529,0,735:7,18,11,14 chr2 27015141 . G GC 626.89 PASS AC=1;AF=0.604;AN=2;DP=972;MQ=60;set=variant3-variant7-variant8-variant11-variant12-variant14-variant15-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:439,0,380:4,9,5,10 chr2 27015610 . CCA C 3832.67 PASS AC=1;AF=0.556;AN=2;DP=1519;MQ=60;set=variant3-variant8-variant12-variant14-variant15-variant23-variant25-variant31-variant42 GT:AD:DP:GQ:PL:SB 0/1:92,71:163:99:2694,0,3737:49,43,35,36 chr2 27015903 . T C 843.77 PASS AC=1;AF=0.604;AN=2;DP=1345;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant8-variant11-variant12-variant14-variant15-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,19:44:99:546,0,694:17,8,14,5 chr2 27015969 . G A 1186.69 PASS AC=1;AF=0.604;AN=2;DP=2738;MQ=60;set=variant3-variant7-variant8-variant11-variant12-variant14-variant15-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,43:96:99:960,0,1389:35,18,26,17 chr2 27016259 . A G 588.75 PASS AC=1;AF=0.604;AN=2;DP=974;MQ=60;set=variant3-variant7-variant8-variant11-variant12-variant14-variant15-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,17:31:99:348,0,397:4,10,8,9 chr2 27016302 . G GT 617.98 PASS AC=1;AF=0.604;AN=2;DP=696;MQ=60;set=variant3-variant7-variant8-variant11-variant12-variant14-variant15-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,13:21:99:389,0,222:3,5,5,8 chr2 27016351 . G A 183.09 PASS AC=1;AF=0.604;AN=2;DP=377;MQ=60;set=variant3-variant7-variant8-variant11-variant12-variant14-variant15-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:67:67,0,202:2,4,1,2 chr2 27016988 . C T 4578.22 PASS AC=1;AF=0.943;AN=2;DP=13801;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:164,130:294:99:3428,0,4205:71,93,53,77 chr2 27017542 . A AT 43.31 PASS AC=1;AF=0.864;AN=2;DP=157;set=variant2-variant3-variant5-variant6-variant9-variant10-variant12-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant31-variant33-variant34-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:42:71,0,42:0,2,0,3 chr2 27150891 . G A 1413.81 PASS AC=1;AF=0.65;AN=2;DP=1366;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,13:42:99:415,0,675:15,14,10,3 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 1/1:0,3:3:9:94,9,0:0,0,2,1 chr2 27157542 . C T 1248.44 PASS AC=1;AF=0.5;AN=2;DP=345;FractionInformativeReads=1;MQ=60;set=variant23-variant26-variant40 GT:AD:DP:GQ:PL:SB 0/1:35,47:82:99:1277,0,918:24,11,33,14 chr2 27157788 . T C 1148.16 PASS AC=1;AF=0.65;AN=2;DP=966;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,16:35:99:486,0,677:2,17,2,14 chr2 27163044 . T C 4288.97 PASS AC=1;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 0/1:93,73:166:99:1711,0,2180:45,48,30,43 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 1/1:0,3:3:9:135,9,0:0,0,0,3 chr2 27164806 . G A 4368.14 PASS AC=1;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 0/1:50,63:113:99:1627,0,1222:28,22,32,31 chr2 27165202 . T C 508.54 PASS AC=1;AF=0.661;AN=2;DP=348;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant12-variant15-variant17-variant18-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:157,0,120:2,3,3,3 chr2 27167784 . C T 955.85 PASS AC=1;AF=0.65;AN=2;DP=976;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,17:28:99:464,0,245:5,6,5,12 chr2 27169540 . T G 500.33 PASS AC=1;AF=0.643;AN=2;DP=295;MQ=60;set=variant2-variant3-variant4-variant6-variant9-variant10-variant12-variant13-variant15-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:74:102,0,74:2,1,3,1 chr2 27169637 . TC T 1334.73 PASS AC=1;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 0/1:19,17:36:99:548,0,657:13,6,12,5 chr2 27169842 . C A 4434.41 PASS AC=1;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 0/1:117,115:232:99:2529,0,2800:61,56,62,53 chr2 27170470 . C CG 2879.49 PASS AC=1;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 0/1:33,33:66:99:847,0,826:13,20,16,17 chr2 27170941 . CCACACA CCA,CCACA,CCACACACA,C,CCACACACACACACACACACACACACACACACACACACACGCACACA 567.18 PASS AC=0,1,0,0,0;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 0/2:16:99:4,4,5,3 chr2 27170982 . C T 1062.45 PASS AC=1;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 0/1:21,15:36:99:467,0,767:12,9,10,5 chr2 27171245 . C T 1999.55 PASS AC=1;AF=0.643;AN=2;DP=1870;MQ=60;set=variant2-variant3-variant4-variant6-variant9-variant10-variant12-variant13-variant15-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:36,27:63:99:693,0,878:17,19,13,14 chr2 27172069 . T C 1977.68 PASS AC=1;AF=0.643;AN=2;DP=1630;MQ=60;set=variant2-variant3-variant4-variant6-variant9-variant10-variant12-variant13-variant15-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,17:43:99:525,0,834:12,14,9,8 chr2 27173249 . G A 869.65 PASS AC=1;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 0/1:10,20:30:99:499,0,216:3,7,8,12 chr2 27173341 . G A 366.33 PASS AC=1;AF=0.69;AN=2;DP=140;FS=0;MQ=60;set=variant2-variant3-variant4-variant6-variant9-variant10-variant12-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant33-variant36-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:62:120,0,62:0,2,0,3 chr2 27237614 . A G 635.51 PASS AC=1;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 0/1:12,7:19:99:137,0,244:7,5,4,3 chr2 27246285 . C T 4255.29 PASS AC=1;AF=0.932;AN=2;DP=9184;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:109,92:201:99:2094,0,2490:54,55,46,46 chr2 27249245 . A G 3903.66 PASS AC=1;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 0/1:67,75:142:99:1777,0,1503:34,33,39,36 chr2 27258251 . T G 469.49 PASS AC=1;AF=0.5;AN=2;DP=352;MQ=60;set=variant23-variant26-variant31-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,19:38:99:498,0,461:8,11,9,10 chr2 27258761 . C G 656.83 PASS AC=1;AF=0.5;AN=2;DP=428;FractionInformativeReads=1;MQ=60;set=variant23-variant26-variant31-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,25:58:99:685,0,934:23,10,16,9 chr2 27259794 . G A 2591.51 PASS AC=1;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 0/1:35,31:66:99:748,0,948:18,17,17,14 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 1/1:0,36:36:99:1165,108,0:0,0,23,13 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 1/1:1,43:44:99:1869,101,0:1,0,13,30 chr2 27263122 . T C 3270.56 PASS AC=1;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 0/1:83,80:163:99:2132,0,2029:37,46,38,42 chr2 27276202 . G A 2104.54 PASS AC=1;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 0/1:25,24:49:99:625,0,552:13,12,17,7 chr2 27279013 . A G 1707.39 PASS AC=1;AF=0.5;AN=2;DP=825;FractionInformativeReads=1;MQ=60;set=variant23-variant26-variant31-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:58,67:125:99:1736,0,1451:24,34,28,39 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 1/1:0,90:90:99:2734,270,0:0,0,57,33 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 1/1:0,37:37:99:1217,111,0:0,0,27,10 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 1/1:0,62:62:99:1745,184,0:0,0,36,26 chr2 27280140 . C A 865.48 PASS AC=1;AF=0.5;AN=2;DP=363;FractionInformativeReads=1;MQ=60;set=variant23-variant26-variant31-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,36:63:99:894,0,655:18,9,18,18 chr2 27280460 . A G 654.9 PASS AC=1;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 0/1:13,11:24:99:410,0,434:2,11,0,11 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 1/1:0,113:113:99:3784,338,0:0,0,63,50 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 0/1:21,33:54:99:895,0,566:6,15,8,25 chr2 27292651 . T C 3108.29 PASS AC=1;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 0/1:55,35:90:99:807,0,1588:23,32,14,21 chr2 27293150 . G T 5936.56 PASS AC=1;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 0/1:89,59:148:99:1308,0,2139:37,52,21,38 chr2 27302165 . T C 1969.14 PASS AC=1;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 0/1:27,45:72:99:1245,0,659:8,19,13,32 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 1/1:0,110:110:99:3348,329,0:0,0,41,69 chr2 27307769 . G C 4260.56 PASS AC=1;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 0/1:83,55:138:99:1271,0,2025:37,46,29,26 chr2 27308020 . C A 563.97 PASS AC=1;AF=0.5;AN=2;DP=93;FractionInformativeReads=1;MQ=60;set=variant7-variant23 GT:AD:DP:GQ:PL:SB 0/1:12,21:33:99:577,0,340:9,3,8,13 chr2 27309659 . A C 1816.24 PASS AC=1;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 0/1:33,25:58:99:724,0,834:20,13,17,8 chr2 27309953 . G A 1591.4 PASS AC=1;AF=0.5;AN=2;DP=86;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.562;QD=18.5;ReadPosRankSum=-1.738;SOR=0.722;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:45,41:86:99:1620,0,4385:19,26,17,24 chr2 27309955 . T A 1591.4 PASS AC=1;AF=0.5;AN=2;DP=86;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.467;QD=18.5;ReadPosRankSum=-0.069;SOR=0.629;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:45,41:86:99:1620,0,4385:19,26,18,23 chr2 27309956 . C A 1591.4 PASS AC=1;AF=0.5;AN=2;DP=86;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=2.594;QD=18.5;ReadPosRankSum=2.326;SOR=0.629;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:45,41:86:99:1620,0,4385:19,26,18,23 chr2 27315252 . G A 4490.7 PASS AC=1;AF=0.655;AN=2;DP=5629;MQ=60;set=variant2-variant3-variant4-variant6-variant9-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:94,86:180:99:2002,0,2280:46,48,45,41 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 1/1:0,82:82:99:2357,245,0:0,0,35,47 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 1/1:0,30:30:90:955,90,0:0,0,20,10 chr2 27323385 . C T 4273.06 PASS AC=1;AF=0.661;AN=2;DP=4277;MQ=60;set=variant2-variant3-variant4-variant6-variant9-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant36-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:68,67:135:99:1740,0,1737:42,26,40,27 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 1/1:0,248:248:99:7607,743,0:0,0,127,121 chr2 27323936 . G GC 2284.68 PASS AC=1;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 0/1:27,46:73:99:1281,0,709:14,13,24,22 chr2 27324036 . G A 2297.4 PASS AC=1;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 0/1:40,46:86:99:1254,0,1077:20,20,26,20 chr2 27324724 . G C 2515.95 PASS AC=1;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 0/1:47,75:122:99:1952,0,1182:24,23,41,34 chr2 27324751 . G T 2359.49 PASS AC=1;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 0/1:58,83:141:99:2076,0,1358:29,29,46,37 chr2 27342067 . G C 109.98 PASS AC=1;AF=0.725;AN=2;DP=154;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant15-variant17-variant18-variant20-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant36-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:118,0,107:1,3,3,3 chr2 27351279 . G A 452.07 PASS AC=1;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 0/1:7,13:20:99:379,0,125:5,2,9,4 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 1/1:0,74:74:99:2485,222,0:0,0,37,37 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 1/1:0,75:75:99:2386,225,0:0,0,42,33 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 0/1:26,22:48:99:657,0,776:8,18,14,8 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 1/1:0,26:26:78:892,78,0:0,0,16,10 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 0/1:20,15:35:99:473,0,714:18,2,13,2 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 0/1:17,25:42:99:792,0,489:8,9,12,13 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 0/1:20,22:42:99:557,0,506:10,10,14,8 chr2 27376376 . C CTCTTT,CTCTTTTCTTTTCTTT,CTCTTTTCTTTTCTTTTCTTT,CTCTTTTCTTT 93.7 PASS AC=2,0,0,0;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 1/1:5:15:0,0,1,4 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 1/1:0,46:46:99:1416,138,0:0,0,26,20 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 1/1:0,78:78:99:2484,233,0:0,0,43,35 chr2 27424636 . G A 3960.28 PASS AC=1;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 0/1:68,103:171:99:2519,0,1667:35,33,55,48 chr2 27426362 . G A 188.22 PASS AC=1;AF=0.568;AN=2;DP=643;MQ=60;set=variant2-variant4-variant11-variant14-variant15-variant16-variant17-variant19-variant23-variant26-variant27-variant28-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:7,6:13:99:172,0,264:2,5,2,4 chr2 27426514 . G C 955.34 PASS AC=2;AF=0.977;AN=2;DP=2867;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1703,159,0:0,0,33,20 chr2 27426878 . C T 373.44 PASS AC=1;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 0/1:3,8:11:82:243,0,82:0,3,4,4 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 1/1:0,55:55:99:1860,165,0:0,0,41,14 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 1/1:0,252:252:99:7222,756,0:0,0,126,126 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 1/1:0,8:8:24:308,24,0:0,0,8,0 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 1/1:0,57:57:99:1838,170,0:0,0,39,18 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 1/1:0,86:86:99:2617,258,0:0,0,44,42 chr2 27430781 . A G 464.21 PASS AC=1;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 0/1:5,7:12:99:223,0,109:2,3,1,6 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 1/1:0,16:16:48:448,48,0:0,0,9,7 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 1/1:0,191:191:99:5859,573,0:0,0,110,81 chr2 27435374 . G A 6037.48 PASS AC=1;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 0/1:113,85:198:99:2022,0,2613:49,64,35,50 chr2 27438710 . G A 319.36 PASS AC=1;AF=0.575;AN=2;DP=228;FractionInformativeReads=1;MQ=60;set=variant4-variant11-variant14-variant15-variant16-variant17-variant19-variant23-variant27-variant28-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,8:11:99:234,0,105:0,3,1,7 chr2 27440013 . CT C 790.21 PASS AC=1;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 0/1:15,23:38:99:618,0,362:6,9,6,17 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 1/1:0,122:122:99:3943,365,0:0,0,68,54 chr2 27445315 . G GT 1774.75 PASS AC=1;AF=0.568;AN=2;DP=3364;MQ=60;set=variant2-variant4-variant11-variant14-variant15-variant16-variant17-variant19-variant23-variant26-variant27-variant28-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:66,74:140:99:2242,0,1930:42,24,43,31 chr2 27448417 . A AC,ACCC 115.51 PASS AC=0,1;AF=0.167,0.417;AN=2;DP=48;set=variant10-variant23-variant27-variant28-variant38-variant41 GT:DP:GQ:SB 0/2:7:99:4,0,1,2 chr2 27449293 . C G 1060.24 PASS AC=1;AF=0.64;AN=2;DP=2073;MQ=60;set=variant2-variant4-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant20-variant23-variant26-variant27-variant28-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,36:64:99:1054,0,867:15,13,20,16 chr2 27460968 . A G 1638.29 PASS AC=1;AF=0.64;AN=2;DP=4069;MQ=60;set=variant2-variant4-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant20-variant23-variant26-variant27-variant28-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:77,65:142:99:1448,0,1863:39,38,32,33 chr2 27462076 . C T 1924.33 PASS AC=1;AF=0.568;AN=2;DP=4129;MQ=60;set=variant2-variant4-variant11-variant14-variant15-variant16-variant17-variant19-variant23-variant26-variant27-variant28-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:87,80:167:99:1721,0,2044:37,50,31,49 chr2 27462405 . T A 747.31 PASS AC=1;AF=0.64;AN=2;DP=2323;MQ=60;set=variant2-variant4-variant10-variant11-variant14-variant15-variant16-variant17-variant19-variant20-variant23-variant26-variant27-variant28-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,51:86:99:1144,0,762:18,17,27,24 chr2 27466258 . CTTT C,CT,CTT,CTTTT 342.9 PASS AC=0,1,0,0;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 0/2:53:99:14,13,8,18 chr2 27466906 . C G 147.64 PASS AC=1;AF=0.5;AN=2;DP=96;MQ=60;set=variant23-variant26-variant31-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,6:18:99:176,0,291:4,8,1,5 chr2 27477627 . AACACACACACAC AACACACAC,AACACACACACACAC,AACACACACAC,AACACACACACACACACAC,AAC,AACACAC,AACACACACACACACAC,A 1079.07 PASS AC=1,0,0,0,0,0,0,0;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 0/1:28:99:11,3,9,5 chr2 27481460 . C T 468.77 PASS AC=1;AF=0.568;AN=2;DP=617;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant11-variant14-variant15-variant16-variant17-variant19-variant23-variant26-variant27-variant28-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:270,0,308:8,3,7,5 chr2 27522543 . CCTATCTATCTAT CCTATCTATCTATCTAT,CCTATCTATCTATCTATCTAT,CCTATCTAT,C 594.56 PASS AC=1,0,0,0;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 0/1:23:99:4,5,5,9 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 1/1:0,130:130:99:4687,397,0:0,0,63,67 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 0/1:2,3:5:76:120,0,76:0,2,2,1 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 0/1:40,39:79:99:779,0,801:22,18,22,17 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 0/1:31,64:95:99:1616,0,672:14,17,28,36 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 0/1:57,53:110:99:1198,0,1509:26,31,25,28 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 0/1:31,26:57:99:718,0,707:17,14,15,11 chr2 27566454 . A G 828 PASS AC=1;AF=0.5;AN=2;DP=553;FractionInformativeReads=1;MQ=60;set=variant23-variant26-variant31-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:54,33:87:99:856,0,1363:25,29,11,22 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 0/1:23,40:63:99:910,0,479:9,14,16,24 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 0/1:76,54:130:99:1365,0,1858:39,37,29,25 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 0/2:10:74:0,4,1,5 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 0/1:73,59:132:99:1468,0,1707:42,31,35,24 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 0/1:47,55:102:99:1611,0,1034:29,18,37,18 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 0/1:51,52:103:99:1148,0,1361:29,22,25,27 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 0/1:17,17:34:99:527,0,484:8,9,6,11 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 0/1:27,15:42:99:549,0,1169:16,11,8,7 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 0/1:22,27:49:99:757,0,637:7,15,8,19 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 0/1:125,128:253:99:3165,0,3093:61,64,60,68 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 0/1:20,32:52:99:828,0,491:10,10,15,17 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 0/1:91,84:175:99:1918,0,2301:54,37,51,33 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 0/1:64,68:132:99:1626,0,1516:29,35,38,30 chr2 27606098 . A G 896.83 PASS AC=2;AF=0.977;AN=2;DP=1618;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1501,126,0:0,0,32,10 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 0/1:12,21:33:99:633,0,320:4,8,7,14 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 0/1:146,118:264:99:2862,0,3537:68,78,54,64 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 0/1:71,79:150:99:1810,0,1659:36,35,35,44 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 0/1:5,4:9:99:146,0,137:1,4,3,1 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 0/1:35,19:54:99:487,0,922:23,12,14,5 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 0/1:56,60:116:99:1878,0,1749:27,29,34,26 chr2 27657335 . C T 823.17 PASS AC=1;AF=0.5;AN=2;DP=191;FractionInformativeReads=1;MQ=60;set=variant7-variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:30,19:49:99:497,0,797:19,11,15,4 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 0/1:35,32:67:99:826,0,798:22,13,20,12 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 0/1:53,37:90:99:875,0,1399:34,19,24,13 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 0/1:41,48:89:99:1388,0,1082:16,25,20,28 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 0/1:91,104:195:99:2595,0,2271:47,44,55,49 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 0/1:20,22:42:99:515,0,521:10,10,10,12 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 0/1:4,9:13:99:366,0,193:1,3,2,7 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 0/1:193,203:396:99:6375,0,5981:72,121,80,123 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 0/1:128,118:246:99:2459,0,2864:49,79,47,71 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 0/1:68,41:109:99:897,0,1726:39,29,27,14 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 0/1:39,39:78:99:921,0,1025:17,22,20,19 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 0/1:13,16:29:99:498,0,352:5,8,4,12 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 0/1:5,6:11:99:180,0,150:2,3,0,6 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 0/1:18,13:31:99:411,0,481:13,5,10,3 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 0/1:37,42:79:99:1006,0,859:12,25,16,26 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 0/1:3,7:10:65:282,0,65:2,1,7,0 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 0/1:52,44:96:99:1007,0,1350:30,22,26,18 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 0/1:9,16:25:99:263,0,139:5,4,9,7 chr2 27704292 . TCA TCACA,T 128.46 PASS AC=1,0;AF=0.389,0.167;AN=2;DP=165;set=variant4-variant5-variant8-variant17-variant22-variant23-variant25-variant37-variant44 GT:DP:GQ:SB 0/1:9:71:0,3,2,4 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 0/1:33,31:64:99:944,0,760:20,13,21,10 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 0/1:46,40:86:99:934,0,1100:23,23,22,18 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 0/1:48,25:73:99:504,0,1289:23,25,11,14 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 0/1:6,7:13:99:235,0,180:1,5,1,6 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 0/1:75,59:134:99:1408,0,1792:38,37,29,30 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 0/1:41,25:66:99:564,0,900:17,24,8,17 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 0/1:82,66:148:99:1604,0,1999:35,47,29,37 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 0/1:91,123:214:99:2915,0,2153:46,45,67,56 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 0/1:45,45:90:99:1118,0,1277:29,16,27,18 chr2 27732642 . CAA CA,CAAAA,C,CAAA 245.95 PASS AC=0,0,0,1;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 0/4:9:33:1,2,1,5 chr2 27789861 . T A 2189.38 PASS AC=1;AF=0.567;AN=2;DP=1931;MQ=60;set=variant-variant3-variant6-variant7-variant19-variant20-variant22-variant23-variant26-variant31-variant34-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:51,71:122:99:1842,0,1283:22,29,34,37 chr2 27801403 . C G 4001.6 PASS AC=1;AF=0.662;AN=2;DP=3158;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,43:81:99:1670,0,1903:17,21,22,21 chr2 27801418 . C A 3925.31 PASS AC=1;AF=0.662;AN=2;DP=3143;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,43:80:99:1670,0,1886:17,20,22,21 chr2 27802805 . A G 2321.38 PASS AC=1;AF=0.571;AN=2;DP=2082;MQ=60;set=variant-variant3-variant6-variant7-variant19-variant20-variant22-variant23-variant26-variant31-variant34-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:64,59:123:99:1392,0,1680:29,35,27,32 chr2 27804432 . T C 532.46 PASS AC=1;AF=0.708;AN=2;DP=3863;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,48:95:99:1293,0,1074:24,23,24,24 chr2 27824168 . G C 1101.95 PASS AC=1;AF=0.567;AN=2;DP=1668;MQ=60;set=variant-variant3-variant6-variant7-variant19-variant20-variant22-variant23-variant26-variant31-variant34-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:54,55:109:99:1326,0,1283:29,25,31,24 chr2 27830990 . G T 2120.96 PASS AC=1;AF=0.662;AN=2;DP=2557;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,41:79:99:1096,0,804:16,22,12,29 chr2 27838058 . C A 2699.85 PASS AC=1;AF=0.662;AN=2;DP=2730;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,44:74:99:1009,0,696:13,17,22,22 chr2 27839107 . T C 3875.27 PASS AC=1;AF=0.662;AN=2;DP=3965;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,66:123:99:1501,0,1280:28,29,34,32 chr2 27844601 . T G 2194.16 PASS AC=1;AF=0.533;AN=2;DP=2786;MQ=60;set=variant-variant3-variant6-variant7-variant19-variant20-variant22-variant23-variant26-variant31-variant34-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:77,78:155:99:2117,0,1996:44,33,45,33 chr2 27851120 . T C 789.9 PASS AC=1;AF=0.647;AN=2;DP=1613;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,27:51:99:702,0,565:14,10,15,12 chr2 27852117 . A AGGTCTT 3848.59 PASS AC=1;AF=0.647;AN=2;DP=4233;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,59:120:99:2418,0,2807:22,39,20,39 chr2 27852118 . A C 3857.48 PASS AC=1;AF=0.647;AN=2;DP=3895;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,61:122:99:2418,0,2807:22,39,20,41 chr2 27852150 . C CG 684.55 PASS AC=1;AF=0.542;AN=2;DP=998;MQ=60;set=variant-variant3-variant6-variant7-variant19-variant20-variant22-variant23-variant26-variant31-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:32,39:71:99:1036,0,801:12,20,17,22 chr2 27852637 . A G 2022.74 PASS AC=1;AF=0.647;AN=2;DP=2320;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,42:74:99:1280,0,905:26,6,28,14 chr2 27855397 . A T 1377.54 PASS AC=1;AF=0.571;AN=2;DP=1628;MQ=60;set=variant-variant3-variant6-variant7-variant19-variant20-variant22-variant23-variant26-variant31-variant34-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:52,60:112:99:1445,0,1263:26,26,32,28 chr2 27857992 . T A 3244.1 PASS AC=1;AF=0.662;AN=2;DP=4113;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,54:105:99:1470,0,1252:29,22,35,19 chr2 27858167 . CT CTTTTTTT,CTT,CTTTTTTTT,C,CTTTTTTTTT,CTTTTTT,CTTTTTTTTTT 1336.45 PASS AC=1,0,0,0,0,0,0;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 0/1:36:99:5,16,6,9 chr2 27861707 . G A 617.11 PASS AC=1;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 0/1:12,21:33:99:540,0,320:9,3,15,6 chr2 27873326 . C G 125.28 PASS AC=1;AF=0.567;AN=2;DP=488;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant16-variant19-variant20-variant22-variant23-variant26-variant31-variant34-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,10:25:99:271,0,430:8,7,5,5 chr2 27873415 . G A 1384.03 PASS AC=1;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 0/1:23,29:52:99:738,0,612:14,9,15,14 chr2 27874332 . A C 5331.76 PASS AC=1;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 0/1:115,94:209:99:2248,0,3007:55,60,47,47 chr2 27874563 . G T 11552.6 PASS AC=1;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 0/1:164,173:337:99:4264,0,3976:75,89,86,87 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 1/1:0,15:15:45:520,45,0:0,0,13,2 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 1/1:0,419:419:99:12305,1254,0:0,0,214,205 chr2 27887034 . C A 2405.98 PASS AC=1;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 0/1:47,64:111:99:1541,0,1245:30,17,34,30 chr2 27905391 . C T 77.33 PASS AC=1;AF=0.7;AN=2;DP=22;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant21-variant23-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:86:86,0,87:0,3,0,3 chr2 27929616 . CT C 211.99 PASS AC=2;AF=0.932;AN=2;DP=1095;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:314,36,0:0,0,5,7 chr2 27930837 . C T 1029.26 PASS AC=1;AF=0.542;AN=2;DP=941;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant19-variant20-variant22-variant23-variant26-variant31-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,31:56:99:868,0,646:10,15,13,18 chr2 27995781 . A C 207.11 PASS AC=1;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 0/1:7,3:10:64:64,0,277:0,7,1,2 chr2 28069713 . T G 298.89 PASS AC=1;AF=0.533;AN=2;DP=245;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant14-variant16-variant19-variant20-variant22-variant23-variant26-variant31-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:8,12:20:99:399,0,264:7,1,10,2 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 0/1:15,13:28:99:347,0,426:4,11,3,10 chr2 28084530 . T TGGG,TG 372.48 PASS AC=1,1;AF=0.25,0.375;AN=2;DP=166;MQ=60;set=variant3-variant5-variant6-variant7-variant23-variant31-variant34-variant37 GT:DP:GQ:SB 2/1:9:99:0,0,3,6 chr2 28117455 . C G 930.1 PASS AC=1;AF=0.5;AN=2;DP=431;FractionInformativeReads=1;MQ=60;set=variant23-variant26-variant40 GT:AD:DP:GQ:PL:SB 0/1:82,47:129:99:958,0,2024:38,44,25,22 chr2 28236120 . C T 2537.07 PASS AC=2;AF=0.625;AN=2;DP=1724;set=variant3-variant6-variant7-variant19-variant20-variant22-variant23-variant26-variant31-variant34-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,152:152:99:4101,453,0:0,0,85,67 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 1/1:0,13:13:39:491,39,0:0,0,1,12 chr2 28634790 . G A 1596.22 PASS AC=1;AF=0.574;AN=2;DP=2957;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant28-variant29-variant30-variant33-variant34-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,28:78:99:698,0,1540:23,27,18,10 chr2 28635740 . T C 2692.03 PASS AC=1;AF=0.645;AN=2;DP=3038;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,46:91:99:1172,0,1149:22,23,20,26 chr2 28636644 . A G 1009.02 PASS AC=1;AF=0.589;AN=2;DP=2863;MQ=60;set=variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant33-variant34-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,41:96:99:956,0,1391:30,25,23,18 chr2 28636740 . A G 1312.88 PASS AC=1;AF=0.603;AN=2;DP=3614;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant33-variant34-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,50:106:99:1148,0,1407:21,35,23,27 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 1/1:0,42:42:99:1214,126,0:0,0,19,23 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 1/2:35:99:1,0,20,14 chr2 28639641 . C G 10120.2 PASS AC=1;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 0/1:123,123:246:99:3087,0,3083:75,48,68,55 chr2 28639816 . CT C,CTT,CTTTT,CTTTTT 142.46 PASS AC=0,1,0,0;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 0/2:91:99:20,43,10,18 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 1/1:0,121:121:99:3755,363,0:0,0,62,59 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 1/1:0,164:164:99:4962,489,0:0,0,79,85 chr2 28748896 . A ACAC 4131.35 PASS AC=1;AF=0.5;AN=2;DP=722;MQ=60;set=variant18-variant23-variant26-variant36 GT:AD:DP:GQ:PL:SB 0/1:79,60:139:99:2271,0,3114:31,48,25,35 chr2 28748916 . A C 4121.95 PASS AC=1;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 0/1:60,77:137:99:1902,0,1602:21,39,29,48 chr2 28752159 . G T 995.87 PASS AC=1;AF=0.5;AN=2;DP=257;FractionInformativeReads=1;MQ=60;set=variant18-variant23-variant26-variant36 GT:AD:DP:GQ:PL:SB 0/1:15,28:43:99:610,0,342:11,4,16,12 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 1/1:0,38:38:99:1218,114,0:0,0,19,19 chr2 28752555 . T C 1977.84 PASS AC=1;AF=0.943;AN=2;DP=3140;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:22,32:54:99:770,0,448:14,8,14,18 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 1/1:0,14:14:42:549,42,0:0,0,3,11 chr2 28752741 . A G 876.22 PASS AC=1;AF=0.943;AN=2;DP=787;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:7,3:10:97:97,0,241:1,6,1,2 chr2 28761257 . A G 1680.07 PASS AC=1;AF=0.92;AN=2;DP=2963;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:25,35:60:99:924,0,622:8,17,10,25 chr2 28761282 . A G 1268.25 PASS AC=1;AF=0.92;AN=2;DP=2241;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:18,25:43:99:646,0,485:5,13,6,19 chr2 28763230 . C A 1255.51 PASS AC=1;AF=0.5;AN=2;DP=332;FractionInformativeReads=1;MQ=60;set=variant18-variant21-variant23-variant26-variant36 GT:AD:DP:GQ:PL:SB 0/1:24,27:51:99:693,0,670:16,8,17,10 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 0/1:75,55:130:99:1214,0,1782:38,37,27,28 chr2 28771452 . CTA C,CTATATA 1691.59 PASS AC=1,1;AF=0.955,0.023;AN=2;DP=2420;MQ=60;set=Intersection GT:DP:GQ:SB 1/2:33:99:0,0,15,18 chr2 28771624 . T G 4325.26 PASS AC=1;AF=0.932;AN=2;DP=5223;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:31,50:81:99:1198,0,694:19,12,25,25 chr2 28771897 . T C 572.23 PASS AC=1;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 0/1:8,11:19:99:340,0,301:0,8,2,9 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 1/1:0,11:11:33:417,33,0:0,0,10,1 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 1/1:0,55:55:99:2058,166,0:0,0,20,35 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 0/1:10,9:19:99:334,0,560:9,1,8,1 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 0/1:12,11:23:99:374,0,588:11,1,8,3 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 0/1:32,24:56:99:544,0,927:20,12,15,9 chr2 28816425 . T C 345.74 PASS AC=1;AF=0.838;AN=2;DP=385;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-variant29-variant30-variant31-variant32-variant33-variant34-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:3,2:5:68:68,0,113:3,0,2,0 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 0/2:32:99:13,5,11,3 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 0/1:54,55:109:99:1406,0,1309:28,26,26,29 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 0/1:25,33:58:99:1270,0,955:13,12,17,16 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 1/1:0,3:3:9:94,9,0:0,0,1,2 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 0/1:44,38:82:99:957,0,1084:15,29,10,28 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 0/1:89,80:169:99:1996,0,2437:37,52,42,38 chr2 28829201 . G A 280.73 PASS AC=1;AF=0.5;AN=2;DP=50;FractionInformativeReads=1;MQ=60;set=variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:309,0,345:8,4,9,1 chr2 28849435 . T C 761.61 PASS AC=2;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 1/1:0,42:42:99:1405,126,0:0,0,11,31 chr2 28849473 . T C 496.39 PASS AC=2;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 1/1:0,19:19:57:706,57,0:0,0,3,16 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 1/1:0,117:117:99:4149,352,0:0,0,60,57 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 1/1:0,59:59:99:2123,176,0:0,0,13,46 chr2 28999943 . A G 726.88 PASS AC=1;AF=0.5;AN=2;DP=69;FractionInformativeReads=1;MQ=60;set=variant6-variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:14,9:23:99:323,0,437:3,11,0,9 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 1/1:0,43:43:99:1354,128,0:0,0,27,16 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 1/1:0,9:9:27:310,27,0:0,0,2,7 chr2 29023092 . CTTT CTT,CTTTT,C,CT,CTTTTTT,CTTTTTTTTTTTTT 578.73 PASS AC=1,0,0,1,0,0;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 4/1:38:99:1,6,6,25 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 1/1:0,181:181:99:5990,542,0:0,0,81,100 chr2 29024298 . CT C,CTT 58.32 PASS AC=1,0;AF=0.455,0.045;AN=2;DP=1585;MQ=60;set=filterInvariant2-filterInvariant4-filterInvariant6-filterInvariant8-variant10-filterInvariant16-filterInvariant23-filterInvariant27-filterInvariant36-filterInvariant37-variant41 GT:DP:GQ:SB 0/1:98:97:34,49,6,9 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 1/1:0,168:168:99:5273,504,0:0,0,76,92 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 1/1:0,25:25:75:816,75,0:0,0,16,9 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 1/1:0,61:61:99:1806,183,0:0,0,25,36 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 1/1:0,30:30:90:1086,90,0:0,0,7,23 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 1/1:8:23:0,0,1,7 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 1/1:0,21:21:63:825,63,0:0,0,18,3 chr2 29129300 . ATT AT,A,ATTT 45.11 PASS AC=1,0,0;AF=0.5,0.015,0.015;AN=2;DP=2102;set=filterInvariant-variant3-variant4-variant5-variant6-variant9-filterInvariant10-variant11-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-filterInvariant20-variant21-variant22-variant23-filterInvariant24-variant25-filterInvariant26-variant27-variant28-filterInvariant29-filterInvariant32-variant34-filterInvariant37-variant38-variant40-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/1:54:99:24,16,9,5 chr2 29135468 . C G 1863.44 PASS AC=2;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 1/1:0,137:137:99:4061,409,0:0,0,70,67 chr2 29145663 . GTT G,GT,GTTTT,GTTTTT,GTTTTTT,GTTT,GTTTTTTT 1161.83 PASS AC=0,0,0,1,1,0,0;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 4/5:38:99:1,1,29,7 chr2 29145681 . C T 146.53 PASS AC=1;AF=0.5;AN=2;DP=393;set=filterInvariant9-filterInvariant19-variant23-filterInvariant27-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:43,22:65:99:277,0,878:19,24,22,0 chr2 29145683 . G T 72.13 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=69;FS=30.452;FractionInformativeReads=0.957;MQ=59.51;MQRankSum=-0.025;QD=1.05;ReadPosRankSum=-1.953;SOR=5.136;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:54,12:66:99:100,0,1653:27,27,12,0 chr2 29145725 . G T 1761.22 PASS AC=2;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 1/1:2,85:87:99:2900,209,0:1,1,39,46 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 1/1:0,53:53:99:1600,159,0:0,0,33,20 chr2 29158613 . CAAAAAAA CA,CAAAA,C,CAA,CAAA,CAAAAAA,CAAAAA 153.24 PASS AC=0,0,0,1,0,0,0;AF=0.173,0.019,0.038,0.385,0.038,0.058,0.038;AN=2;DP=449;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant23-variant26-variant27-variant29-variant31-variant33-variant34-variant36-variant37-variant38-variant41-variant43-variant44 GT:DP:GQ:SB 0/4:12:18:0,2,2,8 chr2 29159666 . G C 456.81 PASS AC=1;AF=0.5;AN=2;DP=99;FractionInformativeReads=1;MQ=60;set=variant6-variant23-variant30-variant34 GT:AD:DP:GQ:PL:SB 0/1:18,14:32:99:503,0,467:12,6,14,0 chr2 29161010 . G A 1448.37 PASS AC=2;AF=0.92;AN=2;DP=3861;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2515,236,0:0,0,31,48 chr2 29169612 . T C 1203.92 PASS AC=2;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 1/1:0,78:78:99:2528,234,0:0,0,46,32 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 0/3:25:50:6,2,8,9 chr2 29221040 . C T 1845.63 PASS AC=1;AF=0.5;AN=2;DP=644;FractionInformativeReads=1;MQ=60;set=variant4-variant9-variant16-variant20-variant23 GT:AD:DP:GQ:PL:SB 0/1:44,63:107:99:1598,0,1088:24,20,36,27 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 1/1:0,101:101:99:2994,301,0:0,0,42,59 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 1/1:0,76:76:99:2542,228,0:0,0,24,52 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 1/1:0,36:36:99:1321,107,0:0,0,8,28 chr2 29240005 . T C 1534.17 PASS AC=2;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 1/1:0,120:120:99:3653,360,0:0,0,62,58 chr2 29245933 . G A 2311.54 PASS AC=2;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 1/1:1,194:195:99:5573,537,0:1,0,98,96 chr2 29246044 . T C 1913.81 PASS AC=2;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 1/1:1,141:142:99:4323,381,0:1,0,58,83 chr2 29247304 . C T 1014.82 PASS AC=2;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 1/1:0,93:93:99:3081,277,0:0,0,39,54 chr2 29268295 . A C 530.21 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1262;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:47,17:64:99:147,0,1803:9,38,17,0 chr2 29275272 . T C 598.01 PASS AC=1;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 0/1:15,41:56:99:1035,0,253:8,7,18,23 chr2 29275318 . T C 777.74 PASS AC=1;AF=0.841;AN=2;DP=2245;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:15,34:49:99:909,0,378:9,6,13,21 chr2 29275612 . A G 637.8 PASS AC=1;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 0/1:28,20:48:99:598,0,726:12,16,9,11 chr2 29275940 . A G 1154.6 PASS AC=1;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 0/1:40,35:75:99:825,0,966:17,23,17,18 chr2 29276010 . G T 333.67 PASS AC=1;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 0/1:18,30:48:99:825,0,464:6,12,15,15 chr2 29276630 . T C 39.79 PASS AC=1;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 0/1:11,7:18:99:204,0,300:7,4,5,2 chr2 29277200 . T C 254.7 PASS AC=1;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 0/1:9,21:30:99:555,0,160:4,5,9,12 chr2 29277355 . C G 229.36 PASS AC=1;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 0/1:9,3:12:93:93,0,299:9,0,2,1 chr2 29277592 . T G 206.9 PASS AC=1;AF=0.5;AN=2;DP=187;MQ=60;set=variant6-variant23-variant31-variant34 GT:AD:DP:GQ:PL:SB 0/1:25,18:43:99:346,0,712:7,18,10,8 chr2 29279251 . A AT 632.14 PASS AC=2;AF=1;AN=2;DP=1506;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:711,75,0:0,0,12,13 chr2 29280153 . G T 49.19 PASS AC=1;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 0/1:19,13:32:99:364,0,508:11,8,9,4 chr2 29280261 . A G 490.11 PASS AC=1;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 0/1:42,29:71:99:643,0,963:23,19,16,13 chr2 29280745 . G A 435.94 PASS AC=1;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 0/1:9,16:25:99:484,0,251:3,6,6,10 chr2 29280761 . C T 380.24 PASS AC=1;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 0/1:9,11:20:99:329,0,260:4,5,5,6 chr2 29280791 . G A 375.72 PASS AC=1;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 0/1:13,14:27:99:296,0,344:7,6,6,8 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 1/1:0,13:13:39:437,39,0:0,0,5,8 chr2 29281584 . G C 60.2 PASS AC=1;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 0/1:9,8:17:99:147,0,235:6,3,4,4 chr2 29281759 . T TTGTG,TTG 1399.93 PASS AC=0,1;AF=0.214,0.286;AN=2;DP=760;set=variant-variant4-variant6-variant23-variant31-variant34-variant42 GT:DP:GQ:SB 0/2:76:99:36,4,19,17 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 0/1:97,34:131:99:459,0,3362:60,37,24,10 chr2 29281800 . T G,TGG 5450.61 PASS AC=0,1;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 0/2:138:99:46,33,42,17 chr2 29281804 . T G,TGG,TGGGTGG,TGTGG 6417.9 PASS AC=1,0,0,0;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 0/1:151:99:48,35,46,22 chr2 29281867 . A G 3121.64 PASS AC=1;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 0/1:100,104:204:99:2618,0,2897:40,60,46,58 chr2 29283072 . C T 346.67 PASS AC=1;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 0/1:20,37:57:99:1012,0,518:8,12,16,21 chr2 29283421 . G A 589.29 PASS AC=1;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 0/1:37,22:59:99:526,0,993:15,22,7,15 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 1/1:0,89:89:99:2757,267,0:0,0,47,42 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 1/1:0,65:65:99:2088,195,0:0,0,29,36 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 1/1:0,47:47:99:1596,141,0:0,0,24,23 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 1/1:0,58:58:99:1902,174,0:0,0,33,25 chr2 29285210 . C T 1914.03 PASS AC=1;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 0/1:34,51:85:99:1327,0,934:21,13,27,24 chr2 29285254 . C T 1020.25 PASS AC=1;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 0/1:48,69:117:99:1750,0,1271:32,16,40,29 chr2 29285575 . C T 2008.05 PASS AC=1;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 0/1:51,32:83:99:836,0,1385:19,32,12,20 chr2 29285631 . A G 1810.9 PASS AC=1;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 0/1:39,19:58:99:419,0,989:14,25,9,10 chr2 29285713 . C T 1499.12 PASS AC=1;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 0/1:18,14:32:99:328,0,482:8,10,6,8 chr2 29286031 . T C 1932.53 PASS AC=1;AF=0.5;AN=2;DP=929;FractionInformativeReads=1;MQ=60;set=variant6-variant23-variant30-variant34-variant36 GT:AD:DP:GQ:PL:SB 0/1:102,91:193:99:2154,0,2446:49,53,43,48 chr2 29286072 . G A 3501.56 PASS AC=1;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 0/1:78,89:167:99:2180,0,1728:33,45,39,50 chr2 29286193 . T C 1529.43 PASS AC=1;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 0/1:23,29:52:99:717,0,653:9,14,11,18 chr2 29286364 . C T 427.83 PASS AC=1;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 0/1:25,14:39:99:275,0,712:13,12,8,6 chr2 29286509 . T C 227.36 PASS AC=1;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 0/1:14,17:31:99:452,0,463:6,8,7,10 chr2 29286670 . T C 238.29 PASS AC=1;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 0/1:19,12:31:99:287,0,508:10,9,7,5 chr2 29286905 . G T 436.71 PASS AC=1;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 0/1:31,29:60:99:667,0,748:15,16,12,17 chr2 29287192 . G A 438.34 PASS AC=1;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 0/1:24,22:46:99:616,0,567:12,12,15,7 chr2 29287227 . T C 1015.94 PASS AC=1;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 0/1:30,31:61:99:1191,0,1305:16,14,16,15 chr2 29287229 . A G 1015.94 PASS AC=1;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 0/1:30,30:60:99:1191,0,1305:16,14,15,15 chr2 29287708 . C T 493.19 PASS AC=1;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 0/1:27,31:58:99:728,0,768:14,13,14,17 chr2 29287926 . C CGCT 837.84 PASS AC=1;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 0/1:45,43:88:99:1670,0,1858:22,23,19,24 chr2 29288109 . A G 115.56 PASS AC=1;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 0/1:11,6:17:99:175,0,374:1,10,2,4 chr2 29294629 . C T 1720.47 PASS AC=1;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 0/1:117,103:220:99:2285,0,2891:59,58,51,52 chr2 29294754 . G C 1558.37 PASS AC=1;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 0/1:80,75:155:99:1984,0,2215:39,41,33,42 chr2 29295016 . A G 2487.17 PASS AC=1;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 0/1:92,88:180:99:2102,0,2297:43,49,43,45 chr2 29295676 . G A 1800.93 PASS AC=1;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 0/1:89,65:154:99:1480,0,2333:42,47,30,35 chr2 29296870 . C T 3451.09 PASS AC=1;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 0/1:144,132:276:99:3111,0,3517:66,78,61,71 chr2 29297068 . C T 1544.45 PASS AC=1;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 0/1:56,43:99:99:1021,0,1447:25,31,16,27 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 0/1:11,5:16:99:118,0,343:9,2,3,2 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 0/1:28,9:37:99:210,0,764:13,15,4,5 chr2 29356669 . A G 1651.49 PASS AC=1;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 0/1:43,37:80:99:1016,0,1073:17,26,14,23 chr2 29366830 . A G 781.51 PASS AC=1;AF=0.615;AN=2;DP=2391;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant13-variant14-variant15-variant17-variant18-variant19-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:47,47:94:99:1135,0,1019:20,27,20,27 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 1/1:0,45:45:99:1993,135,0:0,0,15,30 chr2 29383256 . G T 1408.21 PASS AC=1;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 0/1:56,60:116:99:1395,0,1365:25,31,25,35 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 1/1:0,39:39:99:1245,117,0:0,0,13,26 chr2 29386646 . G C 1038.33 PASS AC=1;AF=0.625;AN=2;DP=2489;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant34-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,33:73:99:833,0,1066:28,12,21,12 chr2 29390299 . AG A 852.51 PASS AC=1;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 0/1:53,21:74:99:626,0,1877:29,24,12,9 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 1/1:0,269:269:99:8140,804,0:0,0,154,115 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 1/1:0,138:138:99:4235,414,0:0,0,65,73 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 1/1:0,62:62:99:1974,186,0:0,0,40,22 chr2 29429888 . G A 2318.33 PASS AC=1;AF=0.797;AN=2;DP=2242;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-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,24:49:99:801,0,634:15,10,18,6 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 1/1:0,108:108:99:3269,324,0:0,0,50,58 chr2 29449819 . C T 1175.11 PASS AC=2;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 1/1:0,73:73:99:2151,218,0:0,0,43,30 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 0/1:23,9:32:99:221,0,2219:7,16,9,0 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 0/1:23,9:32:99:206,0,2715:7,16,9,0 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 0/1:27,7:34:99:203,0,2904:7,20,7,0 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 1/1:0,65:65:99:2139,195,0:0,0,34,31 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 1/1:0,87:87:99:3166,261,0:0,0,59,28 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 1/1:0,48:48:99:1655,143,0:0,0,36,12 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 1/1:0,12:12:36:540,36,0:0,0,11,1 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 1/1:0,12:12:36:512,36,0:0,0,11,1 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 1/1:0,21:21:63:860,63,0:0,0,1,20 chr2 29541104 . C T 648.39 PASS AC=1;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 0/1:40,31:71:99:671,0,1082:23,17,21,10 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 1/1:0,88:88:99:2484,263,0:0,0,47,41 chr2 29551161 . G A 406.31 PASS AC=1;AF=0.583;AN=2;DP=837;MQ=60;set=variant2-variant4-variant7-variant8-variant10-variant11-variant13-variant16-variant19-variant21-variant23-variant24-variant26-variant28-variant31-variant32-variant33-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,24:46:99:566,0,528:14,8,14,10 chr2 29754721 . T C 810.8 PASS AC=1;AF=0.553;AN=2;DP=1633;MQ=60;set=variant-variant2-variant3-variant4-variant8-variant12-variant14-variant17-variant18-variant19-variant23-variant25-variant28-variant29-variant32-variant34-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,43:76:99:1198,0,926:26,7,29,14 chr2 29917940 . C G 552.83 PASS AC=2;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 1/1:0,56:56:99:1643,168,0:0,0,28,28 chr2 29940529 . A T 1364.21 PASS AC=2;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 1/1:0,92:92:99:2619,275,0:0,0,53,39 chr2 29940820 . C T 321.52 PASS AC=2;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 1/1:0,26:26:78:851,78,0:0,0,7,19 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 1/1:0,64:64:99:2340,192,0:0,0,32,32 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 1/1:0,15:15:45:439,45,0:0,0,6,9 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 0/1:157,202:359:99:5221,0,3750:100,57,125,77 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 0/1:81,89:170:99:2276,0,2004:45,36,46,43 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 0/1:14,11:25:99:263,0,355:7,7,4,7 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 1/1:0,22:22:66:905,66,0:0,0,21,1 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 1/1:0,137:137:99:4142,410,0:0,0,82,55 chr2 30482099 . G A 1071.48 PASS AC=2;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 1/1:0,63:63:99:1795,189,0:0,0,35,28 chr2 30670010 . G A 233.8 PASS AC=1;AF=0.536;AN=2;DP=395;set=variant-variant2-variant5-variant6-variant12-variant13-variant17-variant20-variant23-variant27-variant29-variant30-variant33-variant38 GT:AD:DP:GQ:PL:SB 0/1:20,13:33:99:364,0,544:14,6,10,3 chr2 30670037 . T C 367 PASS AC=1;AF=0.536;AN=2;DP=655;set=variant-variant2-variant5-variant6-variant12-variant13-variant17-variant20-variant23-variant27-variant29-variant30-variant33-variant38 GT:AD:DP:GQ:PL:SB 0/1:29,17:46:99:371,0,639:16,13,11,6 chr2 30682360 . G A 835.6 PASS AC=2;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 1/1:0,52:52:99:1753,156,0:0,0,38,14 chr2 30682470 . A T 1195.65 PASS AC=1;AF=0.525;AN=2;DP=2370;MQ=60;set=variant2-variant3-variant7-variant10-variant11-variant14-variant15-variant18-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant32-variant34-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,67:133:99:1428,0,1496:33,33,33,34 chr2 30682630 . T A 626.02 PASS AC=1;AF=0.538;AN=2;DP=595;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant12-variant13-variant17-variant20-variant23-variant27-variant30-variant33-variant38 GT:AD:DP:GQ:PL:SB 0/1:13,19:32:99:542,0,330:5,8,5,14 chr2 30748321 . A G 1097.67 PASS AC=2;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 1/1:0,37:37:99:1354,110,0:0,0,30,7 chr2 30748373 . T G 1178.2 PASS AC=1;AF=0.545;AN=2;DP=2408;MQ=60;set=variant2-variant3-variant4-variant7-variant9-variant10-variant11-variant14-variant15-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant32-variant34-variant36-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,36:85:99:1000,0,1388:36,13,28,8 chr2 30756196 . A G 1049.95 PASS AC=1;AF=0.5;AN=2;DP=383;FractionInformativeReads=1;MQ=60;set=variant5-variant17-variant20-variant23-variant38 GT:AD:DP:GQ:PL:SB 0/1:32,34:66:99:988,0,877:9,23,11,23 chr2 30756265 . G A 474.74 PASS AC=1;AF=0.5;AN=2;DP=119;FractionInformativeReads=1;MQ=60;set=variant5-variant17-variant20-variant23-variant38 GT:AD:DP:GQ:PL:SB 0/1:9,6:15:99:178,0,275:2,7,1,5 chr2 30775299 . G A 205.58 PASS AC=2;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 1/1:0,14:14:42:450,42,0:0,0,8,6 chr2 30791152 . A G 420.8 PASS AC=2;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 1/1:0,15:15:45:582,45,0:0,0,2,13 chr2 30828792 . G A 438.96 PASS AC=2;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 1/1:0,55:55:99:1577,164,0:0,0,33,22 chr2 30863651 . A T 1991.28 PASS AC=1;AF=0.543;AN=2;DP=3706;MQ=60;set=variant2-variant3-variant4-variant7-variant9-variant10-variant11-variant14-variant15-variant18-variant21-variant22-variant23-variant24-variant27-variant29-variant30-variant32-variant34-variant36-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,69:143:99:1734,0,1941:32,42,33,36 chr2 30864326 . A G 6747.91 PASS AC=2;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 1/1:0,339:339:99:10575,1015,0:0,0,162,177 chr2 30864789 . G A 162.82 PASS AC=2;AF=0.587;AN=2;DP=323;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant24-variant29-variant32-variant34-variant36-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:124,12,0:0,0,1,3 chr2 30864980 . A G 534.68 PASS AC=2;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 1/1:0,45:45:99:1402,135,0:0,0,27,18 chr2 30865266 . CTT C,CT 238.31 PASS AC=1,1;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 1/2:15:87:0,0,9,6 chr2 30865272 . T C 452.07 PASS AC=1;AF=0.5;AN=2;DP=120;set=variant5-variant17-variant20-variant23-variant29-variant38 GT:AD:DP:GQ:PL:SB 0/1:5,10:15:87:219,0,87:4,1,5,5 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 0/1:10,5:15:87:87,0,219:5,5,4,1 chr2 30866992 . C G 2161.76 PASS AC=1;AF=0.5;AN=2;DP=896;MQ=60;set=variant5-variant17-variant20-variant23-variant38 GT:AD:DP:GQ:PL:SB 0/1:95,69:164:99:1748,0,2512:48,47,38,31 chr2 30945896 . A G 1343.25 PASS AC=2;AF=0.638;AN=2;DP=1688;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1313,111,0:0,0,21,16 chr2 30955528 . C A 272.69 PASS AC=2;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 1/1:0,18:18:53:502,53,0:0,0,7,11 chr2 30959100 . C G 103.49 PASS AC=2;AF=0.68;AN=2;DP=276;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant15-variant19-variant20-variant21-variant23-variant27-variant28-variant29-variant30-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:339,24,0:0,0,8,0 chr2 30959262 . G T 3671.58 PASS AC=2;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 1/1:0,122:122:99:3909,366,0:0,0,77,45 chr2 30959562 . G T 225.31 PASS AC=1;AF=0.5;AN=2;DP=73;FractionInformativeReads=1;MQ=60;set=variant2-variant13-variant20-variant23 GT:AD:DP:GQ:PL:SB 0/1:4,9:13:99:318,0,130:0,4,0,9 chr2 30961393 . G A 2186.38 PASS AC=1;AF=0.5;AN=2;DP=658;MQ=60;set=variant2-variant13-variant20-variant23 GT:AD:DP:GQ:PL:SB 0/1:81,74:155:99:1921,0,2038:39,42,34,40 chr2 30973825 . C A 245.63 PASS AC=1;AF=0.597;AN=2;DP=684;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant36-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,9:17:99:305,0,269:6,2,8,1 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 0/1:69,69:138:99:1591,0,1725:32,37,35,34 chr2 30977073 . G A 4284.08 PASS AC=2;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 1/1:0,119:119:99:3452,356,0:0,0,68,51 chr2 30980940 . C T 1517.15 PASS AC=2;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 1/1:0,63:63:99:1966,188,0:0,0,40,23 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 1/1:0,117:117:99:3641,351,0:0,0,61,56 chr2 30999023 . AT A 297.61 PASS AC=1;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 0/1:13,14:27:99:339,0,295:4,9,4,10 chr2 31000370 . G C 491.45 PASS AC=1;AF=0.531;AN=2;DP=589;FractionInformativeReads=1;MQ=60;set=variant4-variant10-variant12-variant13-variant15-variant21-variant23-variant24-variant26-variant27-variant31-variant33-variant34-variant37-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:17,11:28:99:256,0,598:14,3,9,2 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 1/1:0,32:32:96:1133,96,0:0,0,24,8 chr2 31010212 . C T 1078.18 PASS AC=1;AF=0.5;AN=2;DP=1678;MQ=60;set=variant12-variant21-variant23-variant24-variant26-variant29-variant31-variant34-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:55,65:120:99:1737,0,1403:19,36,20,45 chr2 31030024 . C T 106.77 PASS AC=2;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 1/1:0,8:8:24:300,24,0:0,0,7,1 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 1/1:0,22:22:66:754,66,0:0,0,16,6 chr2 31189236 . G A 734.91 PASS AC=1;AF=0.5;AN=2;DP=1039;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant10-variant18-variant23-variant27-variant28-variant32-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:51,43:94:99:1061,0,1338:24,27,17,26 chr2 31189304 . T C 259.52 PASS AC=1;AF=0.5;AN=2;DP=483;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant10-variant18-variant23-variant27-variant28-variant32-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:23,11:34:99:336,0,680:7,16,2,9 chr2 31189345 . G T 384.62 PASS AC=1;AF=0.5;AN=2;DP=312;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant10-variant18-variant23-variant27-variant28-variant32-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:17,10:27:99:216,0,502:5,12,4,6 chr2 31189401 . A G 220.39 PASS AC=1;AF=0.5;AN=2;DP=197;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant10-variant18-variant23-variant27-variant28-variant32-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,6:17:99:135,0,385:0,11,3,3 chr2 31189439 . G A 169.67 PASS AC=1;AF=0.5;AN=2;DP=114;MQ=60;set=variant-variant3-variant10-variant18-variant23-variant27-variant28-variant32-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:108,0,208:0,6,2,3 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 1/1:0,36:36:99:1513,108,0:0,0,10,26 chr2 31348390 . A G 583.95 PASS AC=1;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 0/1:11,3:14:93:93,0,386:2,9,0,3 chr2 31361259 . T TGCCGCCGCC 2396.74 PASS AC=2;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 1/1:2,87:89:99:2773,229,0:1,1,45,42 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 1/1:0,102:102:99:4484,307,0:0,0,48,54 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 1/1:0,97:97:99:2994,291,0:0,0,59,38 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 1/1:0,139:139:99:4191,417,0:0,0,66,73 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 1/1:0,83:83:99:2663,249,0:0,0,45,38 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 1/1:0,17:17:51:596,51,0:0,0,5,12 chr2 31457154 . GGGGACCCCGGCTT G 687.8 PASS AC=1;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 0/1:11,17:28:99:681,0,1465:5,6,9,8 chr2 31457817 . T C 1352.35 PASS AC=1;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 0/1:24,14:38:99:419,0,772:5,19,5,9 chr2 31457981 . T C 520.43 PASS AC=1;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 0/1:6,8:14:99:188,0,120:3,3,3,5 chr2 31467079 . G A 453.27 PASS AC=1;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 0/1:4,3:7:97:97,0,111:3,1,3,0 chr2 31467351 . T A 2152.78 PASS AC=1;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 0/1:28,47:75:99:1208,0,616:11,17,18,29 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 1/1:0,40:40:99:1677,120,0:0,0,2,38 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 1/1:0,62:62:99:1912,186,0:0,0,38,24 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 1/1:0,21:21:63:792,63,0:0,0,18,3 chr2 31489627 . TACACACACACACAC TACACACACACACACAC,TACACACACACACACACAC,TACACACACACAC,TACACACACACACACACACAC,TACACACACAC,TACACACAC,T 963.84 PASS AC=0,0,0,1,0,0,0;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 0/4:40:99:8,10,8,14 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 1/1:0,60:60:99:1893,180,0:0,0,30,30 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 1/1:0,64:64:99:1895,192,0:0,0,34,30 chr2 31557269 . C A 964.71 PASS AC=1;AF=0.542;AN=2;DP=1497;MQ=60;set=variant-variant4-variant7-variant8-variant9-variant11-variant13-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,19:41:99:410,0,562:10,12,11,8 chr2 31557308 . G A 1864.72 PASS AC=1;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 0/1:19,25:44:99:641,0,424:10,9,13,12 chr2 31557347 . T C 2466.35 PASS AC=1;AF=0.63;AN=2;DP=1919;MQ=60;set=variant-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,16:46:99:478,0,874:16,14,10,6 chr2 31558306 . T C 8612.99 PASS AC=1;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 0/1:113,116:229:99:3191,0,2673:54,59,58,58 chr2 31562412 . C T 619.38 PASS AC=1;AF=0.5;AN=2;DP=648;FractionInformativeReads=1;MQ=60;set=variant-variant13-variant16-variant17-variant22-variant23-variant30-variant32 GT:AD:DP:GQ:PL:SB 0/1:43,35:78:99:927,0,1161:22,21,20,15 chr2 31562639 . C T 585.69 PASS AC=1;AF=0.5;AN=2;DP=58;FS=1.019;FractionInformativeReads=1;MQ=60;MQRankSum=-0.795;QD=10.1;ReadPosRankSum=0.747;SOR=0.898;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:35,23:58:99:614,0,836:17,18,10,13 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 1/1:0,97:97:99:3046,291,0:0,0,40,57 chr2 31569471 . A G 1005.13 PASS AC=2;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 1/1:0,15:15:45:613,45,0:0,0,13,2 chr2 31570376 . T C 2273.65 PASS AC=2;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 1/1:0,58:58:99:1821,174,0:0,0,40,18 chr2 31570626 . C T 691.77 PASS AC=2;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 1/1:0,34:34:99:1442,102,0:0,0,7,27 chr2 31570631 . A G 691.77 PASS AC=2;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 1/1:0,28:28:87:1259,87,0:0,0,6,22 chr2 31571241 . G C 3250.88 PASS AC=2;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 1/1:0,95:95:99:3064,285,0:0,0,38,57 chr2 31571786 . A G 2668.28 PASS AC=2;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 1/1:0,60:60:99:1899,180,0:0,0,26,34 chr2 31572398 . A G 943.21 PASS AC=2;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 1/1:0,28:28:84:1055,84,0:0,0,24,4 chr2 31572482 . T TG 2570.32 PASS AC=2;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 1/1:0,71:71:99:2313,214,0:0,0,45,26 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 0/1:6:10:1,1,0,4 chr2 31587235 . G A 1414.14 PASS AC=2;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 1/1:0,44:44:99:1532,131,0:0,0,7,37 chr2 31588288 . T A 1920.54 PASS AC=2;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 1/1:0,104:104:99:2992,310,0:0,0,58,46 chr2 31588437 . C T 414.75 PASS AC=1;AF=0.5;AN=2;DP=229;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant23-variant30 GT:AD:DP:GQ:PL:SB 0/1:23,28:51:99:673,0,677:9,14,10,18 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 0/1:6,24:30:99:808,0,175:6,0,18,6 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 0/1:29,15:44:99:305,0,766:19,10,10,5 chr2 31593125 . T C 262 PASS AC=1;AF=0.5;AN=2;DP=71;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant10-variant23-variant30 GT:AD:DP:GQ:PL:SB 0/1:2,9:11:58:303,0,58:2,0,8,1 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 0/1:17,22:39:99:862,0,994:6,11,7,15 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 0/1:15,22:37:99:865,0,951:6,9,7,15 chr2 31600146 . T C 1102.23 PASS AC=2;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 1/1:0,31:31:93:1203,93,0:0,0,3,28 chr2 31606670 . G A 1493.31 PASS AC=1;AF=0.5;AN=2;DP=529;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant23-variant30 GT:AD:DP:GQ:PL:SB 0/1:45,52:97:99:1249,0,1102:26,19,31,21 chr2 31606985 . AGTGTGT AGTGTGTGTGT,AGTGTGTGTGTGTGTGT,AGTGTGTGTGTGTGT,AGTGTGTGTGTGTGTGTGT,A,AGTGTGTGTGTGT,AGTGTGTGT 52.37 PASS AC=0,0,0,0,0,0,1;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 0/7:5:15:0,1,0,4 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 1/1:0,57:57:99:1819,171,0:0,0,25,32 chr2 31610701 . C T 811.8 PASS AC=1;AF=0.5;AN=2;DP=591;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant23-variant30 GT:AD:DP:GQ:PL:SB 0/1:68,56:124:99:1278,0,1846:31,37,27,29 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 0/1:15,13:28:99:395,0,454:11,4,11,2 chr2 31611143 . C T 1102.83 PASS AC=1;AF=0.5;AN=2;DP=555;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant23-variant30 GT:AD:DP:GQ:PL:SB 0/1:56,54:110:99:1252,0,1296:30,26,29,25 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 0/1:8,3:11:99:99,0,324:0,8,1,2 chr2 31626045 . G C 612.75 PASS AC=1;AF=0.5;AN=2;DP=595;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant10-variant15-variant19-variant23-variant30-variant34-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,19:31:99:574,0,252:5,7,5,14 chr2 31751174 . C CATATATATATATATATAT 298.42 PASS AC=1;AF=0.563;AN=2;DP=303;MQ=60;set=variant3-filterInvariant6-variant14-variant23-variant25-variant32-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,5:30:99:205,0,6218:14,11,3,2 chr2 31751175 . G A 307.46 PASS AC=1;AF=0.563;AN=2;DP=318;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant14-variant23-variant25-variant32-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,6:32:99:202,0,6252:14,12,4,2 chr2 31751178 . A T 179.95 PASS AC=1;AF=0.563;AN=2;DP=330;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant14-variant23-filterInvariant25-variant32-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,6:35:99:164,0,6327:17,12,4,2 chr2 31756631 . G GGGGCATTTAATTCCAAAAAATGAAGGGAA 466 PASS AC=1;AF=0.531;AN=2;DP=397;MQ=60;set=variant-variant3-variant6-variant7-variant10-variant14-variant15-variant23-variant25-variant30-variant31-variant32-variant40-variant42-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,16:20:99:588,0,729:1,3,8,8 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 1/1:0,57:57:99:1817,171,0:0,0,37,20 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 1/1:1,122:123:99:3702,358,0:0,1,75,47 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 1/1:0,153:153:99:4672,459,0:0,0,95,58 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 1/1:0,205:205:99:7281,617,0:0,0,95,110 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 1/1:0,41:41:99:1450,123,0:0,0,11,30 chr2 32148377 . C T 228.84 PASS AC=1;AF=0.545;AN=2;DP=123;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant14-variant23-variant25-variant30-variant31-variant32-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,9:19:99:323,0,339:9,1,9,0 chr2 32148619 . G T 3502.99 PASS AC=1;AF=0.545;AN=2;DP=3309;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant14-variant23-variant25-variant30-variant31-variant32-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:149,130:279:99:3062,0,3409:73,76,70,60 chr2 32148636 . T A 3643.82 PASS AC=1;AF=0.545;AN=2;DP=3356;MQ=60;set=variant-variant3-variant6-variant14-variant23-variant25-variant30-variant31-variant32-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:150,130:280:99:2936,0,3445:71,79,69,61 chr2 32188138 . C T 2010.18 PASS AC=1;AF=0.545;AN=2;DP=1710;MQ=60;set=variant-variant3-variant6-variant14-variant23-variant25-variant30-variant31-variant32-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:75,56:131:99:1322,0,1886:44,31,32,24 chr2 32248479 . C CCATT 711.78 PASS AC=1;AF=0.542;AN=2;DP=462;MQ=60;set=variant-variant3-variant6-variant13-variant14-variant23-variant25-variant30-variant31-variant32-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,16:29:99:633,0,758:9,4,13,3 chr2 32312700 . T C 467.86 PASS AC=1;AF=0.65;AN=2;DP=737;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,11:21:99:345,0,311:2,8,2,9 chr2 32324072 . T C 160.43 PASS AC=1;AF=0.65;AN=2;DP=411;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:232,0,270:0,7,1,6 chr2 32362079 . G GTATA 910.82 PASS AC=1;AF=0.654;AN=2;DP=1427;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:29,36:65:99:1352,0,1456:14,15,15,21 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 1/1:0,9:9:27:310,27,0:0,0,6,3 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 0/1:7,4:11:96:96,0,154:1,6,1,3 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 1/1:0,157:157:99:7175,484,0:0,0,83,74 chr2 32381829 . G A 2681.5 PASS AC=1;AF=0.654;AN=2;DP=4944;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:104,65:169:99:1712,0,2766:52,52,30,35 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 0/1:13,8:21:99:175,0,318:8,5,5,3 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 1/1:0,29:29:87:961,87,0:0,0,18,11 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 1/1:0,16:16:48:554,48,0:0,0,4,12 chr2 32446613 . A G 848.66 PASS AC=1;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 0/1:28,57:85:99:1435,0,646:13,15,28,29 chr2 32447718 . C T 3172.39 PASS AC=1;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 0/1:121,92:213:99:2263,0,3104:63,58,48,44 chr2 32447868 . A G 1964.58 PASS AC=1;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 0/1:61,47:108:99:1259,0,1685:23,38,17,30 chr2 32448506 . C A 4343.74 PASS AC=1;AF=0.5;AN=2;DP=3581;MQ=60;set=variant-variant3-variant13-variant14-variant23-variant25-variant30-variant31-variant32-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:124,132:256:99:3161,0,3155:60,64,62,70 chr2 32449261 . C T 2032.36 PASS AC=1;AF=0.5;AN=2;DP=1591;set=variant-variant3-variant13-variant14-variant23-variant25-variant30-variant31-variant32-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,54:103:99:1576,0,1389:29,20,35,19 chr2 32449871 . ATTTTT AT,A 914.62 PASS AC=1,0;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 0/1:23:99:5,11,1,6 chr2 32449879 . T A,TAAA 537.73 PASS AC=0,1;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 0/2:16:99:2,7,1,6 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 1/1:0,9:9:27:363,27,0:0,0,0,9 chr2 32466029 . A G 1031.5 PASS AC=1;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 0/1:28,21:49:99:476,0,801:16,12,12,9 chr2 32475109 . G A 2107.34 PASS AC=1;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 0/1:72,69:141:99:1623,0,1703:29,43,27,42 chr2 32476390 . T G 1806.37 PASS AC=1;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 0/1:67,101:168:99:2654,0,1700:26,41,49,52 chr2 32481793 . AT A 2769.05 PASS AC=1;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 0/1:58,41:99:99:1542,0,2855:29,29,23,18 chr2 32481795 . T A 2778.11 PASS AC=1;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 0/1:58,41:99:99:1542,0,2855:29,29,23,18 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 1/1:0,22:22:66:627,66,0:0,0,11,11 chr2 32620722 . A T 2555.7 PASS AC=1;AF=0.538;AN=2;DP=800;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant14-variant18-variant20-variant23-variant26-variant30-variant31-variant32-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,20:59:99:441,0,902:17,22,7,13 chr2 32640038 . A C 879.99 PASS AC=1;AF=0.5;AN=2;DP=50;FS=2.545;FractionInformativeReads=1;MQ=60;MQRankSum=-0.369;QD=17.6;ReadPosRankSum=0.635;SOR=0.392;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:17,33:50:99:908,0,368:11,6,18,15 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 1/1:0,13:13:42:620,42,0:0,0,9,4 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 1/1:0,14:14:42:620,42,0:0,0,10,4 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 1/1:0,52:52:99:1749,156,0:0,0,33,19 chr2 32667562 . A G 441.02 PASS AC=1;AF=0.55;AN=2;DP=590;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant11-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant33-variant34-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,9:25:99:285,0,518:3,13,1,8 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 1/1:0,11:11:33:446,33,0:0,0,1,10 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 1/1:1,69:70:99:2161,184,0:1,0,23,46 chr2 32727820 . C T 839.51 PASS AC=1;AF=0.5;AN=2;DP=74;FS=0.887;FractionInformativeReads=1;MQ=60;MQRankSum=-2.158;QD=11.34;ReadPosRankSum=-0.027;SOR=0.515;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:38,36:74:99:868,0,835:22,16,19,17 chr2 32733343 . CTTTTTTTTTTT CTTTTTTT,CTTTTTTTTT,CTTTTTTTTTTTTTT,CTTTTTTTTTTTTT,CTTTTTT,CTTTTT,CT,C,CTTTTTTTTTTTT,CTTTTTTTTTTTTTTTT,CTTTTTTTTTTTTTTT,CTTTTTTTT 383.5 PASS AC=0,1,0,0,0,0,0,0,0,0,0,0;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 0/2:13:99:2,3,0,8 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 0/1:5,3:8:99:108,0,205:1,4,0,3 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 1/1:0,9:9:30:450,30,0:0,0,9,0 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 1/1:0,13:13:39:583,39,0:0,0,11,2 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 1/1:0,13:13:39:583,39,0:0,0,11,2 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 1/1:0,15:15:45:670,45,0:0,0,13,2 chr2 32757201 . C CGTGTGTGTGTGTGTGT,CGTGTGTGTGTGTGT,CGTGTGTGTGTGT,CGTGTGTGTGT,CGTGTGTGT,CGTGTGTGTGTGTGTGTGT,CGTGTGT 367.38 PASS AC=2,0,0,0,0,0,0;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 1/1:8:24:0,0,5,3 chr2 32843295 . A T 439.79 PASS AC=1;AF=0.5;AN=2;DP=1540;set=variant4-variant5-variant6-variant7-variant9-variant11-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant2-variant27 GT:AD:DP:GQ:PL:SB 0/1:40,33:73:99:568,0,1106:26,14,17,16 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 1/1:0,232:232:99:6596,695,0:0,0,120,112 chr2 32860415 . C T 1772.7 PASS AC=2;AF=0.955;AN=2;DP=2732;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:1736,188,0:0,0,29,34 chr2 32865521 . G C 2800.18 PASS AC=1;AF=0.538;AN=2;DP=2619;MQ=60;set=variant-variant4-variant5-variant6-variant10-variant16-variant19-variant22-variant23-variant24-variant29-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:89,73:162:99:1714,0,2134:41,48,30,43 chr2 32875084 . T C 158.44 PASS AC=1;AF=0.5;AN=2;DP=119;FractionInformativeReads=1;MQ=60;set=variant-variant14-variant16-variant18-variant20-variant23-variant30-variant33-variant36-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:259,0,147:4,1,7,0 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 0/2:7:76:1,3,0,3 chr2 32927863 . G A 980.32 PASS AC=1;AF=0.533;AN=2;DP=1126;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant9-variant16-variant19-variant20-variant22-variant23-variant24-variant28-variant29-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:34,37:71:99:1079,0,1018:24,10,30,7 chr2 32958838 . CTT C 1274.45 PASS AC=1;AF=0.533;AN=2;DP=626;MQ=60;set=variant4-variant5-variant6-variant16-variant17-variant19-variant20-variant22-variant23-variant28-variant29-variant33-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:11,25:36:99:983,0,445:8,3,19,6 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 0/1:51,61:112:99:1449,0,1213:19,32,26,35 chr2 32959075 . G A 552.84 PASS AC=1;AF=0.533;AN=2;DP=699;MQ=60;set=variant4-variant5-variant6-variant16-variant17-variant19-variant20-variant22-variant23-variant28-variant29-variant33-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:30,25:55:99:664,0,891:8,22,7,18 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 0/1:32,40:72:99:1122,0,735:20,12,27,13 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 1/1:0,111:111:99:3314,332,0:0,0,67,44 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 0/1:6,3:9:99:100,0,186:1,5,0,3 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 0/1:50,45:95:99:1182,0,1192:25,25,24,21 chr2 33036324 . G A 339.87 PASS AC=1;AF=0.545;AN=2;DP=874;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:303,0,418:2,10,2,8 chr2 33045867 . G GT 822.19 PASS AC=1;AF=0.529;AN=2;DP=1022;MQ=60;set=variant4-variant5-variant6-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant28-variant29-variant33-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:29,18:47:99:416,0,758:16,13,10,8 chr2 33127244 . C CT 3077.95 PASS AC=1;AF=0.553;AN=2;DP=3214;MQ=60;set=variant2-variant3-variant8-variant10-variant14-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant36-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:88,63:151:99:2080,0,3105:39,49,26,37 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 0/1:50,43:93:99:1123,0,1275:30,20,25,18 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 0/1:37,30:67:99:822,0,974:16,21,9,21 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 0/1:24,13:37:99:335,0,659:10,14,4,9 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 0/1:18,5:23:61:61,0,460:10,8,3,2 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 0/1:16,15:31:99:358,0,381:7,9,8,7 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 0/1:6,5:11:99:141,0,170:6,0,5,0 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 0/1:37,23:60:99:599,0,967:19,18,14,9 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 0/1:16,12:28:99:327,0,387:5,11,3,9 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 0/1:35,13:48:99:256,0,849:20,15,7,6 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 0/1:90,68:158:99:1592,0,2317:40,50,27,41 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 1/1:0,22:22:66:571,66,0:0,0,8,14 chr2 33500734 . A G 238.86 PASS AC=1;AF=0.5;AN=2;DP=89;FractionInformativeReads=1;MQ=60;set=variant2-variant17-variant23-variant25-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:150,0,182:5,0,4,1 chr2 33525382 . A C 583.48 PASS AC=2;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 1/1:0,19:19:57:753,57,0:0,0,17,2 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 1/1:0,9:9:27:358,27,0:0,0,8,1 chr2 33540172 . A AT 308.49 PASS AC=2;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 1/1:0,19:19:57:579,57,0:0,0,16,3 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 1/1:0,81:81:99:2440,243,0:0,0,49,32 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 0/1:26,28:54:99:1016,0,903:11,15,8,20 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 0/1:19,23:42:99:907,0,747:7,12,6,17 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 1/1:0,15:15:45:540,45,0:0,0,3,12 chr2 33572555 . G A 982.82 PASS AC=1;AF=0.556;AN=2;DP=603;MQ=60;set=variant6-variant10-variant21-variant22-variant23-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,36:62:99:977,0,727:9,17,14,22 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 1/1:0,296:296:99:8789,886,0:0,0,135,161 chr2 33586464 . C CT,CTT 375.13 PASS AC=1,0;AF=0.557,0.023;AN=2;DP=1732;set=Intersection GT:DP:GQ:SB 0/1:41:70:5,3,20,13 chr2 33614554 . G A 309.89 PASS AC=1;AF=0.556;AN=2;DP=160;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant21-variant23-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:259,0,193:0,5,0,7 chr2 33622448 . T C 636.13 PASS AC=2;AF=0.629;AN=2;DP=1675;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1710,141,0:0,0,9,38 chr2 33622475 . T C 376.56 PASS AC=2;AF=0.63;AN=2;DP=730;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant7-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant24-variant29-variant30-variant32-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:951,69,0:0,0,1,22 chr2 33623288 . T C 31.43 PASS AC=1;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 0/1:5,7:12:99:238,0,177:5,0,5,2 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 0/1:7,8:15:99:271,0,262:7,0,6,2 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 1/1:0,68:68:99:3051,205,0:0,0,44,24 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 1/1:0,68:68:99:3051,205,0:0,0,44,24 chr2 33623720 . A G 1958.42 PASS AC=1;AF=0.604;AN=2;DP=3622;MQ=60;set=variant2-variant3-variant4-variant9-variant12-variant13-variant14-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant29-variant30-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,81:155:99:2408,0,1891:45,29,51,30 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 1/1:0,175:175:99:5685,525,0:0,0,106,69 chr2 33624648 . C G 794.64 PASS AC=1;AF=0.5;AN=2;DP=57;FS=5.642;FractionInformativeReads=1;MQ=60;MQRankSum=0.314;QD=13.94;ReadPosRankSum=1.857;SOR=1.954;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:32,25:57:99:823,0,966:7,25,2,23 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 0/1:24,19:43:99:683,0,981:12,12,7,12 chr2 33643745 . T A 281.07 PASS AC=1;AF=0.5;AN=2;DP=142;MQ=60;set=variant5-variant18-variant23 GT:AD:DP:GQ:PL:SB 0/1:24,18:42:99:684,0,981:12,12,6,12 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 1/1:0,7:7:24:316,24,0:0,0,3,4 chr2 33701829 . T C 40.71 PASS AC=2;AF=0.833;AN=2;DP=15;FS=0;FractionInformativeReads=1;MQ=60;set=variant11-variant23-variant33 GT:AD:DP:GQ:PL:SB 1/1:1,5:6:8:212,8,0:0,1,2,3 chr2 33736857 . G A 4239.47 PASS AC=1;AF=0.943;AN=2;DP=10858;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:122,99:221:99:2204,0,2875:63,59,45,54 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 0/1:32,21:53:99:418,0,830:18,14,11,10 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 0/1:43,29:72:99:670,0,1197:14,29,11,18 chr2 33745336 . T C 401.26 PASS AC=1;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 0/1:4,8:12:99:311,0,104:1,3,3,5 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 0/1:12,8:20:99:253,0,438:9,3,5,3 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 0/1:39,58:97:99:1298,0,815:16,23,28,30 chr2 33787976 . CCTAA C 8913.87 PASS AC=1;AF=0.955;AN=2;DP=7956;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:72,84:156:99:3302,0,2934:44,28,44,40 chr2 33788060 . CTT C 12404.8 PASS AC=1;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 0/1:110,104:214:99:3795,0,4010:57,53,53,51 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 0/1:97,73:170:99:1865,0,2759:41,56,32,41 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 0/1:19,22:41:99:623,0,518:9,10,6,16 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 0/1:139:99:46,40,32,21 chr2 33789694 . G C 2976.64 PASS AC=1;AF=0.5;AN=2;DP=256;FS=0.961;FractionInformativeReads=1;MQ=60;MQRankSum=2.369;QD=11.63;ReadPosRankSum=1.214;SOR=0.776;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:124,132:256:99:3005,0,2861:56,68,57,75 chr2 33809294 . A G 7915.31 PASS AC=1;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 0/1:126,111:237:99:2952,0,3400:60,66,51,60 chr2 33809471 . C G 7128.92 PASS AC=1;AF=0.583;AN=2;DP=1485;FractionInformativeReads=1;MQ=60;set=variant18-variant23-variant27-variant28-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:113,139:252:99:3643,0,2886:62,51,75,64 chr2 33810799 . A G 384.41 PASS AC=1;AF=0.5;AN=2;DP=38;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.009;QD=10.12;ReadPosRankSum=1.009;SOR=0.551;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:20,18:38:99:413,0,491:7,13,7,11 chr2 33952022 . C A 72.28 PASS AC=1;AF=0.8;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-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,9:10:16:279,0,16:1,0,7,2 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 0/1:5,16:21:99:481,0,144:5,0,11,5 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 0/1:91,107:198:99:2780,0,2058:48,43,51,56 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 1/1:0,214:214:99:6793,642,0:0,0,113,101 chr2 35696519 . G A 688.08 PASS AC=1;AF=0.5;AN=2;DP=759;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant11-variant13-variant16-variant21-variant22-variant23-variant30-variant33-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:18,17:35:99:417,0,504:12,6,12,5 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 1/1:0,56:56:99:1525,166,0:0,0,25,31 chr2 36605304 . G A 1297.1 PASS AC=1;AF=0.655;AN=2;DP=1817;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant17-variant21-variant23-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,25:53:99:607,0,707:16,12,13,12 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 0/1:43,33:76:99:691,0,1260:18,25,18,15 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 0/2:28:99:3,11,2,12 chr2 36704144 . C T 722.77 PASS AC=2;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 1/1:2,96:98:99:2923,244,0:1,1,45,51 chr2 36739553 . T C 508.61 PASS AC=2;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 1/1:0,48:48:99:1526,144,0:0,0,14,34 chr2 36740643 . C G 580.65 PASS AC=1;AF=0.586;AN=2;DP=1037;MQ=60;set=variant2-variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant26-variant30-variant32-variant34-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,8:33:99:211,0,741:17,8,6,2 chr2 36756288 . T C 996.81 PASS AC=2;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 1/1:0,74:74:99:2357,221,0:0,0,36,38 chr2 36758856 . T G 190.41 PASS AC=1;AF=0.545;AN=2;DP=518;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant8-variant9-variant10-variant14-variant15-variant18-variant19-variant23-variant25-variant26-variant27-variant28-variant29-variant32-variant33-variant36-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,10:23:99:260,0,307:9,4,7,3 chr2 36771507 . C T 1066.85 PASS AC=1;AF=0.5;AN=2;DP=99;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.268;QD=10.78;ReadPosRankSum=-0.924;SOR=0.692;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:54,45:99:99:1095,0,1376:30,24,25,20 chr2 36771701 . C A 672.51 PASS AC=1;AF=0.591;AN=2;DP=1105;MQ=60;set=variant-variant4-variant5-variant8-variant10-variant13-variant14-variant16-variant19-variant20-variant22-variant23-variant26-variant29-variant30-variant32-variant33-variant36-variant37-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,13:36:99:326,0,713:6,17,4,9 chr2 36775315 . C G 449.09 PASS AC=2;AF=0.763;AN=2;DP=1348;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-variant26-variant29-variant30-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:939,87,0:0,0,20,9 chr2 36775410 . CTT CT,CTTT,CTTTTT,CTTTT,C,CTTTTTT 230.62 PASS AC=0,0,0,1,0,0;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 0/4:49:99:16,18,9,6 chr2 36776049 . GT G 365.26 PASS AC=1;AF=0.587;AN=2;DP=979;MQ=60;set=variant-variant4-variant5-variant8-variant10-variant11-variant14-variant16-variant19-variant20-variant22-variant23-variant26-variant29-variant30-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,11:24:99:309,0,317:5,8,3,8 chr2 36776271 . C G 514.75 PASS AC=1;AF=0.58;AN=2;DP=946;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant26-variant34-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,15:32:99:400,0,496:7,10,8,7 chr2 36776616 . CT C,CTT 196.88 PASS AC=1,0;AF=0.591,0.023;AN=2;DP=818;MQ=60;set=variant-variant4-variant5-variant8-variant10-variant14-variant16-variant18-variant19-variant20-variant22-variant23-variant26-variant29-variant30-variant32-variant33-variant36-variant37-variant38-variant40-variant44 GT:DP:GQ:SB 0/1:33:99:10,6,11,6 chr2 36777209 . T C 940.45 PASS AC=1;AF=0.5;AN=2;DP=579;set=variant14-variant16-variant19-variant23-variant26-variant29-variant-variant33 GT:AD:DP:GQ:PL:SB 0/1:30,30:60:99:917,0,968:17,13,15,15 chr2 36777377 . ATT AT,A 2564.51 PASS AC=0,1;AF=0.432,0.114;AN=2;DP=14734;set=Intersection GT:DP:GQ:SB 0/2:214:99:79,50,37,48 chr2 36777825 . G A 685.95 PASS AC=1;AF=0.591;AN=2;DP=1663;set=variant2-variant3-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant26-variant34-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,30:68:99:757,0,865:22,16,19,11 chr2 36778372 . G A 307.41 PASS AC=1;AF=0.58;AN=2;DP=616;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant8-variant10-variant11-variant14-variant16-variant18-variant19-variant20-variant22-variant23-variant26-variant29-variant30-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,17:22:99:675,0,150:0,5,0,17 chr2 36779144 . T G 738.03 PASS AC=1;AF=0.615;AN=2;DP=1590;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant26-variant34-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,19:48:99:580,0,684:18,11,14,5 chr2 36779606 . T TTTAAA 1867.77 PASS AC=1;AF=0.614;AN=2;DP=2049;MQ=60;set=variant2-variant3-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant26-variant34-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,44:87:99:1773,0,1668:26,17,24,20 chr2 36779655 . A AACTT 2536.3 PASS AC=1;AF=0.614;AN=2;DP=3852;MQ=60;set=variant2-variant3-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant26-variant34-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,75:155:99:2929,0,3111:48,32,43,32 chr2 36781401 . T C 666.44 PASS AC=1;AF=0.63;AN=2;DP=1428;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant26-variant34-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,31:46:99:689,0,403:8,7,17,14 chr2 36782656 . G A 623.9 PASS AC=1;AF=0.636;AN=2;DP=1149;MQ=60;set=variant2-variant3-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant26-variant34-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,12:38:99:290,0,670:17,9,9,3 chr2 36782886 . G A 1557.97 PASS AC=1;AF=0.615;AN=2;DP=3523;MQ=60;set=variant-variant4-variant5-variant8-variant9-variant10-variant11-variant14-variant16-variant19-variant20-variant22-variant23-variant25-variant26-variant29-variant30-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,72:155:99:1616,0,2133:27,56,27,45 chr2 36783127 . T C 481.21 PASS AC=1;AF=0.636;AN=2;DP=831;MQ=60;set=variant2-variant3-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant26-variant34-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,10:24:99:254,0,283:7,7,7,3 chr2 36783215 . C T 859.83 PASS AC=1;AF=0.591;AN=2;DP=1628;MQ=60;set=variant2-variant3-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant26-variant34-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,23:53:99:441,0,730:14,16,12,11 chr2 36805676 . A G 631.61 PASS AC=1;AF=0.604;AN=2;DP=1882;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant26-variant33-variant34-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,46:80:99:1152,0,892:23,11,28,18 chr2 36806021 . G A 792.73 PASS AC=1;AF=0.604;AN=2;DP=1646;MQ=60;set=variant2-variant3-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant26-variant33-variant34-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,37:70:99:1005,0,808:14,19,11,26 chr2 36806051 . A G 382.76 PASS AC=1;AF=0.604;AN=2;DP=1026;MQ=60;set=variant2-variant3-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant26-variant33-variant34-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,18:40:99:525,0,531:10,12,5,13 chr2 36808350 . C T 458.89 PASS AC=1;AF=0.625;AN=2;DP=826;MQ=60;set=variant2-variant3-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant26-variant33-variant34-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:26,13:39:99:340,0,866:22,4,10,3 chr2 36808732 . T G 640.55 PASS AC=2;AF=0.769;AN=2;DP=2598;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-variant29-variant30-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2132,224,0:0,0,34,41 chr2 36810473 . G T 2005.94 PASS AC=1;AF=0.571;AN=2;DP=2841;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant7-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant26-variant33-variant34-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,64:121:99:1445,0,1349:27,30,30,34 chr2 36810586 . T C 569.69 PASS AC=1;AF=0.625;AN=2;DP=1412;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant23-variant24-variant26-variant33-variant34-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,25:50:99:697,0,668:8,17,8,17 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 1/1:0,28:28:84:1035,84,0:0,0,17,11 chr2 36825137 . G A 185.41 PASS AC=2;AF=0.803;AN=2;DP=1007;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-variant29-variant30-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:936,90,0:0,0,9,21 chr2 36825170 . T C 246.54 PASS AC=2;AF=0.88;AN=2;DP=382;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant16-variant18-variant19-variant22-variant23-variant24-variant30-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:485,42,0:0,0,5,9 chr2 36825330 . C CG,CGGCCCAGCCCG 645.07 PASS AC=1,1;AF=0.92,0.068;AN=2;DP=935;MQRankSum=0.693;ReadPosRankSum=-0.945;set=Intersection GT:DP:GQ:SB 1/2:14:99:0,0,6,8 chr2 36923778 . CAAAA CAAA,CAA,CAAAAAA,CA,C 83.04 PASS AC=0,1,0,0,0;AF=0.346,0.308,0.038,0.038,0.038;AN=2;DP=81;set=variant4-variant5-variant15-variant16-variant17-variant20-variant21-variant23-variant25-variant29-variant32-variant38-variant39 GT:DP:GQ:SB 0/2:7:53:2,1,3,1 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 1/1:0,43:43:99:1432,127,0:0,0,32,11 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 1/1:0,17:17:51:765,51,0:0,0,1,16 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 1/1:0,31:31:93:1191,93,0:0,0,27,4 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 1/1:0,98:98:99:3002,294,0:0,0,62,36 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 1/1:1,143:144:99:4759,395,0:1,0,52,91 chr2 36994439 . A C 337.45 PASS AC=1;AF=0.648;AN=2;DP=542;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant19-variant20-variant23-variant24-variant25-variant27-variant29-variant30-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:148,0,159:0,4,0,4 chr2 37000881 . T A 250.98 PASS AC=2;AF=0.643;AN=2;DP=66;FractionInformativeReads=1;MQ=60;set=variant3-variant10-variant23-variant27-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:94,9,0:0,0,1,2 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 1/1:0,30:30:90:962,90,0:0,0,11,19 chr2 37010574 . G A 1494.5 PASS AC=1;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 0/1:70,57:127:99:1252,0,1734:40,30,29,28 chr2 37032529 . G C 352.02 PASS AC=1;AF=0.5;AN=2;DP=99;FractionInformativeReads=1;MQ=60;set=variant23-variant25-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,14:27:99:380,0,417:11,2,9,5 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 1/1:0,253:253:99:8029,758,0:0,0,129,124 chr2 37073027 . AACACACACACACACACACACACGCATGCATGCACACACAC AACACACACACACACACACACGCATGCATGCACACACAC,AACACACAC,AACACACACACACACACACGCATGCATGCACACACAC,A,AACACAC 97.04 PASS AC=1,0,0,0,0;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 0/1:8:99:2,2,3,1 chr2 37073028 . ACACACACACACACACACACACGCATGCATG A 126.25 PASS AC=1;AF=0.65;AN=2;DP=115;set=variant2-variant19-variant22-variant23-variant24-variant26-variant32-variant36-variant38-variant41 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:154,0,197:4,1,2,2 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 1/1:12:8:1,0,5,6 chr2 37073736 . A C 3745.45 PASS AC=1;AF=0.5;AN=2;DP=596;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:158,137:295:99:3247,0,3766:97,61,85,52 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 1/1:0,349:349:99:10188,1045,0:0,0,176,173 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 1/1:1,430:431:99:12656,1280,0:0,1,181,249 chr2 37075376 . GGAGA G 2620.39 PASS AC=1;AF=0.5;AN=2;DP=148;FS=0.627;FractionInformativeReads=1;MQ=60;MQRankSum=-0.119;QD=17.71;ReadPosRankSum=0.96;SOR=0.793;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:77,71:148:99:2658,0,2910:47,30,45,26 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 1/1:0,173:173:99:5332,516,0:0,0,105,68 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 1/1:0,8:8:23:289,23,0:0,0,0,8 chr2 37078095 . A ATT,AT 252.89 PASS AC=0,2;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 2/2:14:41:0,0,10,4 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 1/1:0,45:45:99:1404,135,0:0,0,31,14 chr2 37095139 . G C 105.42 PASS AC=1;AF=0.685;AN=2;DP=375;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant30-variant32-variant33-variant36-variant37-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,7:19:99:230,0,379:2,10,0,7 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 1/1:0,11:11:33:482,33,0:0,0,0,11 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 1/1:0,26:26:78:758,78,0:0,0,16,10 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 37230888 . A G 553.75 PASS AC=1;AF=0.5;AN=2;DP=502;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant10-variant12-variant13-variant16-variant17-variant19-variant22-variant23-variant24-variant27-variant29-variant33-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:9,9:18:99:278,0,227:4,5,2,7 chr2 37232927 . GT G 508.48 PASS AC=1;AF=0.5;AN=2;DP=451;MQ=60;set=variant2-variant10-variant12-variant13-variant19-variant22-variant23-variant27-variant29-variant33-variant37 GT:AD:DP:GQ:PL:SB 0/1:10,21:31:99:811,0,498:3,7,10,11 chr2 37232929 . T G 517.5 PASS AC=1;AF=0.5;AN=2;DP=440;MQ=60;set=variant2-variant10-variant12-variant13-variant19-variant22-variant23-variant27-variant29-variant33-variant37 GT:AD:DP:GQ:PL:SB 0/1:10,21:31:99:811,0,498:3,7,10,11 chr2 37234519 . T C 71.25 PASS AC=2;AF=0.857;AN=2;DP=120;FS=0;set=variant3-variant4-variant5-variant9-variant10-variant11-variant13-variant17-variant19-variant20-variant23-variant24-variant29-variant31-variant32-variant33-variant36-variant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:171,12,0:0,0,0,4 chr2 37246738 . T G 161.22 PASS AC=1;AF=0.607;AN=2;DP=93;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant10-variant18-variant23-variant24-variant26-variant32-variant33-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,3:4:34:74,0,34:1,0,2,1 chr2 37255015 . G A 121.07 PASS AC=1;AF=0.706;AN=2;DP=738;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant29-variant30-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:99:154,0,156:4,0,4,1 chr2 37276993 . TAAA TAA,TAAAA,TAAAAA,T,TA 56.7 PASS AC=1,0,0,0,0;AF=0.367,0.033,0.067,0.033,0.067;AN=2;DP=370;set=filterInvariant-variant5-variant8-variant9-variant12-variant13-variant15-variant17-variant21-filterInvariant23-filterInvariant28-variant30-filterInvariant32-variant41-filterInvariant44 GT:DP:GQ:SB 0/1:14:71:2,5,2,5 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 1/1:0,32:32:96:961,96,0:0,0,23,9 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 1/1:0,62:62:99:1826,186,0:0,0,28,34 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 1/1:0,44:44:99:1325,132,0:0,0,17,27 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 1/1:0,4:4:12:167,12,0:0,0,1,3 chr2 37323427 . A G 1938.77 PASS AC=1;AF=0.5;AN=2;DP=1056;MQ=60;set=variant2-variant12-variant13-variant19-variant22-variant23-variant33-variant37 GT:AD:DP:GQ:PL:SB 0/1:66,56:122:99:1517,0,1763:36,30,33,23 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 1/1:0,177:177:99:5812,538,0:0,0,113,64 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 0/1:18,10:28:99:233,0,465:5,13,3,7 chr2 37325495 . GTA G 471.24 PASS AC=1;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 0/1:4,7:11:99:232,0,147:4,0,6,1 chr2 37325512 . T G 1357.29 PASS AC=1;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 0/1:15,9:24:99:218,0,515:11,4,7,2 chr2 37325780 . A G 1567.42 PASS AC=1;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 0/1:26,35:61:99:968,0,718:9,17,12,23 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 1/1:0,51:51:99:1838,153,0:0,0,28,23 chr2 37327258 . A T 695.55 PASS AC=1;AF=0.5;AN=2;DP=64;FS=2.155;FractionInformativeReads=1;MQ=60;MQRankSum=0.202;QD=10.87;ReadPosRankSum=-0.823;SOR=1.071;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:35,29:64:99:724,0,879:20,15,19,10 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 1/1:1,347:348:99:10438,1013,0:1,0,157,190 chr2 37327806 . C T 5766.65 PASS AC=1;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 0/1:67,94:161:99:2511,0,1708:25,42,39,55 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 1/1:0,290:290:99:9088,868,0:0,0,174,116 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 1/1:1,350:351:99:10435,1040,0:0,1,167,183 chr2 37330146 . CTG CTGTGTG,CTGTGTGTG,C 3548.29 PASS AC=1,0,0;AF=0.426,0.13,0.056;AN=2;DP=3669;set=variant2-variant3-variant4-filterInvariant5-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant30-variant32-variant33-variant36-variant37-variant38-variant40-variant43-variant44 GT:DP:GQ:SB 0/1:114:99:28,31,32,23 chr2 37333662 . C T 5196.49 PASS AC=1;AF=0.5;AN=2;DP=4495;MQ=60;set=variant-variant6-variant14-variant16-variant20-variant23-variant26-variant27-variant31-variant34-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:148,130:278:99:3575,0,3820:72,76,56,74 chr2 37334185 . T TA,TAA 163.12 PASS AC=2,0;AF=0.881,0.012;AN=2;DP=355;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:10:4:1,0,4,5 chr2 37342367 . T G 173.75 PASS AC=2;AF=1;AN=2;DP=7;FS=0;FractionInformativeReads=1;MQ=58.44;QD=24.82;SOR=2.584;set=variant23 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:202,21,0:0,0,6,1 chr2 37342456 . T C 247.45 PASS AC=2;AF=0.977;AN=2;DP=1411;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:90:925,90,0:0,0,17,13 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 1/1:0,89:89:99:3538,267,0:0,0,47,42 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 0/1:37,26:63:99:620,0,1013:22,15,16,10 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 0/1:55,69:124:99:1673,0,1263:31,24,37,32 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 0/1:23,11:34:99:153,0,650:6,17,3,8 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 0/1:22,26:48:99:766,0,499:14,8,17,9 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 0/1:31,32:63:99:794,0,636:15,16,12,20 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 0/1:30,20:50:99:535,0,756:19,11,13,7 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 0/1:24,26:50:99:644,0,603:14,10,17,9 chr2 37415496 . G C 1457.72 PASS AC=1;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 0/1:16,13:29:99:402,0,431:11,5,11,2 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 0/1:14,6:20:99:167,0,375:9,5,5,1 chr2 37425878 . G C 136.72 PASS AC=1;AF=0.5;AN=2;DP=31;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant17-variant23 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:70:70,0,195:0,5,1,2 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 0/1:71,53:124:99:1205,0,1715:36,35,25,28 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 0/1:243:99:85,114,16,28 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 0/1:12,6:18:99:157,0,890:10,2,4,2 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 0/1:14,7:21:99:234,0,958:12,2,5,2 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 0/1:27,23:50:99:502,0,693:18,9,13,10 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 1/1:0,121:121:99:3870,363,0:0,0,73,48 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 0/1:72,87:159:99:2161,0,1760:33,39,41,46 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 0/1:13,11:24:99:382,0,406:10,3,10,1 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 0/1:34,35:69:99:755,0,733:23,11,23,12 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 0/1:75,68:143:99:1505,0,1665:40,35,38,30 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 0/1:106,79:185:99:1944,0,2853:55,51,48,31 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 0/1:91,113:204:99:2509,0,2091:34,57,48,65 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 0/1:28,23:51:99:623,0,811:5,23,5,18 chr2 37483771 . ATTTTTTTTTT ATTTTTT,ATT,A,AT,ATTTTT,ATTT 124.87 PASS AC=0,0,0,0,1,0;AF=0.091,0.136,0.045,0.045,0.273,0.045;AN=2;DP=58;FS=0;set=variant2-variant8-variant11-variant19-variant22-variant23-variant24-variant28-variant31-variant34-variant39 GT:DP:GQ:SB 0/5:6:30:1,0,5,0 chr2 37494505 . AGAG A 43.7 PASS AC=1;AF=0.5;AN=2;DP=3;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.736;QD=14.57;ReadPosRankSum=0.736;SOR=1.179;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:51:81,0,51:1,0,2,0 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 0/1:58,62:120:99:1534,0,1339:29,29,30,32 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 0/1:6,4:10:99:142,0,209:1,5,0,4 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 1/1:0,97:97:99:2924,288,0:0,0,65,32 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 1/1:0,345:345:99:10191,1033,0:0,0,170,175 chr2 37870570 . T A 1055.57 PASS AC=1;AF=0.5;AN=2;DP=223;FractionInformativeReads=1;MQ=60;set=variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:60,47:107:99:1084,0,1483:32,28,23,24 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 0/1:154:99:46,39,38,31 chr2 37898910 . A G 472.98 PASS AC=1;AF=0.5;AN=2;DP=558;MQ=60;set=variant-variant3-variant9-variant14-variant15-variant19-variant20-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant32-variant34-variant36-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,10:22:99:258,0,299:8,4,6,4 chr2 37898959 . C T 328.6 PASS AC=1;AF=0.525;AN=2;DP=564;MQ=60;set=variant-variant3-variant9-variant14-variant15-variant19-variant20-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant32-variant34-variant36-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:336,0,599:5,6,3,6 chr2 37898963 . CG CAG,CGGG,C 682.73 PASS AC=1,0,0;AF=0.864,0.068,0.011;AN=2;DP=1169;MQ=60;set=Intersection GT:DP:GQ:SB 0/1:18:99:4,6,3,5 chr2 37898964 . G GC 316.56 PASS AC=1;AF=0.525;AN=2;DP=583;MQ=60;set=variant-variant3-variant9-variant14-variant15-variant19-variant20-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant32-variant34-variant36-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:306,0,581:4,6,3,5 chr2 37899418 . A G 377.44 PASS AC=1;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 0/1:6,7:13:99:248,0,181:1,5,2,5 chr2 38156133 . G A 3561.5 PASS AC=1;AF=0.966;AN=2;DP=4410;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:44,55:99:99:1722,0,1408:5,39,8,47 chr2 38177525 . A C 1655.5 PASS AC=2;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 1/1:0,30:30:90:1001,90,0:0,0,21,9 chr2 38178406 . A G 2336.49 PASS AC=2;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 1/1:0,72:72:99:2320,216,0:0,0,43,29 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 1/1:0,111:111:99:3285,333,0:0,0,54,57 chr2 38179414 . CTG C 11420.8 PASS AC=2;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 1/1:0,183:183:99:8213,551,0:0,0,108,75 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 1/1:1,305:306:99:9308,875,0:1,0,150,155 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 1/1:0,35:35:99:1106,105,0:0,0,15,20 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 1/1:0,38:38:99:1210,114,0:0,0,17,21 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 0/1:113,101:214:99:2641,0,2961:54,59,48,53 chr2 38297170 . C A 14299.9 PASS AC=1;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 0/1:179,191:370:99:4917,0,4598:78,101,99,92 chr2 38297515 . G T 8591.83 PASS AC=1;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 0/1:102,92:194:99:2372,0,2610:45,57,41,51 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 0/1:63,76:139:99:1834,0,1507:29,34,37,39 chr2 38298150 . A G 3178.86 PASS AC=1;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 0/1:62,52:114:99:1262,0,1514:31,31,27,25 chr2 38298203 . C G 3331.67 PASS AC=1;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 0/1:62,59:121:99:1442,0,1449:28,34,30,29 chr2 38302390 . G C 3563.94 PASS AC=1;AF=0.568;AN=2;DP=2629;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant11-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant28-variant29-variant31-variant33-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,44:103:99:1184,0,1425:29,30,25,19 chr2 38302544 . G A 2986.01 PASS AC=1;AF=0.571;AN=2;DP=2620;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant28-variant29-variant31-variant33-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,37:104:99:837,0,1549:29,38,13,24 chr2 38302794 . C T 292.51 PASS AC=1;AF=0.575;AN=2;DP=327;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant15-variant17-variant18-variant21-variant22-variant23-variant28-variant29-variant31-variant33-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:149,0,154:3,2,4,2 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 1/1:0,105:105:99:4024,328,0:0,0,54,51 chr2 38522144 . CG CGG,C 392.79 PASS AC=0,1;AF=0.35,0.15;AN=2;DP=609;MQ=60;set=variant3-filterInvariant13-filterInvariant15-variant18-variant20-filterInvariant23-variant31-filterInvariant36-variant41-variant44 GT:DP:GQ:SB 0/2:57:74:46,2,8,1 chr2 38526547 . G A 382.32 PASS AC=1;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 0/1:15,10:25:99:213,0,443:6,9,5,5 chr2 38536626 . T G 1148.39 PASS AC=1;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 0/1:42,33:75:99:713,0,1002:20,22,14,19 chr2 38537626 . A C 753.33 PASS AC=1;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 0/1:7,13:20:99:423,0,119:2,5,3,10 chr2 38541581 . C CTAT 112.63 PASS AC=1;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 0/1:3,6:9:99:243,0,110:2,1,6,0 chr2 38542573 . T C 495.84 PASS AC=1;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 0/1:17,9:26:99:264,0,591:2,15,2,7 chr2 38570291 . TAAAAAAAAAAAAA TA,T 75.19 PASS AC=1,0;AF=0.25,0.375;AN=2;DP=21;FS=0;set=variant6-variant21-variant23-variant35 GT:DP:GQ:SB 0/1:4:26:1,0,3,0 chr2 38604351 . A G 1812.03 PASS AC=1;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 0/1:57,55:112:99:1309,0,1450:32,25,30,25 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 0/1:9:99:1,3,0,5 chr2 38709568 . A G 1086.61 PASS AC=1;AF=0.55;AN=2;DP=896;FractionInformativeReads=1;set=variant3-variant9-variant10-variant13-variant15-variant20-variant23-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:38,34:72:99:904,0,952:20,18,21,13 chr2 38808643 . G C 894.09 PASS AC=1;AF=0.5;AN=2;DP=52;FS=4.184;FractionInformativeReads=1;MQ=60;MQRankSum=0.179;QD=17.19;ReadPosRankSum=0.009;SOR=1.395;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:20,32:52:99:922,0,546:9,11,10,22 chr2 38902926 . T C 400.15 PASS AC=1;AF=0.5;AN=2;DP=124;FractionInformativeReads=1;set=variant3-variant6-variant14-variant15-variant23 GT:AD:DP:GQ:PL:SB 0/1:9,11:20:99:332,0,343:9,0,8,3 chr2 38908271 . CA C,CAA 482.25 PASS AC=1,0;AF=0.357,0.143;AN=2;DP=160;MQ=60;set=variant3-variant6-variant14-variant15-variant22-variant23-variant30 GT:DP:GQ:SB 0/1:25:99:8,3,13,1 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 1/1:1,85:86:99:2646,221,0:1,0,37,48 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 1/1:0,26:26:78:942,78,0:0,0,5,21 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 1/1:0,80:80:99:2395,239,0:0,0,38,42 chr2 38961832 . G GA 1340.67 PASS AC=1;AF=0.5;AN=2;DP=5797;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:21,91:112:99:1575,0,137:12,9,46,45 chr2 38971040 . GT GTT,G,GTTT 3166.29 PASS AC=1,0,1;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 1/3:104:99:3,4,44,53 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 1/1:0,227:227:99:10196,683,0:0,0,107,120 chr2 38975936 . TTGAG T 112.63 PASS AC=1;AF=0.5;AN=2;DP=10;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=1.447;QD=11.26;ReadPosRankSum=-0.741;SOR=0.412;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:150,0,372:0,6,0,4 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 1/1:0,60:60:99:2005,180,0:0,0,17,43 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 1/1:0,36:36:99:1418,108,0:0,0,4,32 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 1/1:0,63:63:99:2214,189,0:0,0,17,46 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 1/1:0,28:28:84:875,84,0:0,0,17,11 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 1/1:0,117:117:99:3331,350,0:0,0,64,53 chr2 39025043 . GA GAA,G 414.04 PASS AC=1,0;AF=0.511,0.375;AN=2;DP=1472;set=Intersection GT:DP:GQ:SB 0/1:21:39:0,4,6,11 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 1/1:0,157:157:99:4799,471,0:0,0,71,86 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 1/1:0,84:84:99:2831,252,0:0,0,24,60 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 1/1:0,80:80:99:2365,239,0:0,0,33,47 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 1/1:0,65:65:99:1968,195,0:0,0,40,25 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 1/1:0,22:22:66:666,66,0:0,0,14,8 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 1/1:0,13:13:39:497,39,0:0,0,11,2 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 1/1:0,31:31:93:1094,93,0:0,0,20,11 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 1/1:0,78:78:99:2537,234,0:0,0,49,29 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 1/1:0,20:20:60:610,60,0:0,0,13,7 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 1/1:0,19:19:57:757,57,0:0,0,17,2 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 1/1:0,156:156:99:4865,467,0:0,0,61,95 chr2 39083645 . CTTT CT,CTT,C,CTTTT 93.24 PASS AC=1,0,0,0;AF=0.1,0.375,0.025,0.025;AN=2;DP=688;set=variant-variant2-variant3-filterInvariant4-variant7-variant10-variant11-variant12-variant14-filterInvariant19-variant20-variant23-variant24-variant25-variant27-variant34-variant38-variant40-filterInvariant42-variant43 GT:DP:GQ:SB 0/1:17:99:4,8,2,3 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 1/1:0,46:46:99:1772,138,0:0,0,8,38 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 1/1:0,104:104:99:3734,316,0:0,0,52,52 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 0/1:32:99:0,11,0,21 chr2 39117117 . G A 3636.86 PASS AC=2;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 1/1:0,136:136:99:4093,407,0:0,0,64,72 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 1/1:5,42:47:24:938,24,0:2,3,27,15 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 1/1:0,71:71:99:1969,212,0:0,0,35,36 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 0/1:11,6:17:99:138,0,280:7,4,4,2 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 0/1:29,25:54:99:665,0,705:17,12,17,8 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 0/1:58,80:138:99:2299,0,1351:27,31,41,39 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 0/1:26,25:51:99:590,0,514:8,18,10,15 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 0/1:14,14:28:99:411,0,388:9,5,11,3 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 0/1:35,47:82:99:1427,0,1000:21,14,27,20 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 0/1:30,40:70:99:1248,0,765:12,18,12,28 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 0/1:55,59:114:99:1558,0,1333:25,30,24,35 chr2 39210398 . A T 7839.98 PASS AC=1;AF=0.92;AN=2;DP=22235;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:238,196:434:99:5137,0,6130:105,133,88,108 chr2 39210719 . T TTA 608.05 PASS AC=1;AF=0.909;AN=2;DP=1334;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:18,13:31:99:474,0,708:8,10,5,8 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 0/1:135,138:273:99:3606,0,3113:72,63,69,69 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 0/1:114,128:242:99:3821,0,3319:60,54,67,61 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 0/1:45,55:100:99:2107,0,1705:23,22,33,22 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 0/1:57,75:132:99:1737,0,1292:26,31,35,40 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 0/1:5,6:11:99:170,0,183:0,5,2,4 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 0/1:5,13:18:99:366,0,129:4,1,9,4 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 0/1:8,15:23:99:382,0,233:3,5,3,12 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 0/1:13,4:17:88:88,0,534:2,11,1,3 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 0/1:10,7:17:99:176,0,276:7,3,5,2 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 0/1:3,2:5:75:75,0,149:1,2,1,1 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 0/1:23,26:49:99:718,0,581:7,16,8,18 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 0/1:11,7:18:99:209,0,306:8,3,6,1 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 0/1:22,30:52:99:865,0,604:14,8,18,12 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 0/1:17,24:41:99:939,0,1965:11,6,14,10 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 0/1:6,4:10:96:96,0,156:3,3,1,3 chr2 39402978 . A AG 7469.99 PASS AC=2;AF=0.92;AN=2;DP=15860;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,320:320:99:12804,963,0:0,0,176,144 chr2 39405570 . G A 45.18 PASS AC=1;AF=0.607;AN=2;DP=82;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant6-variant7-variant9-variant11-variant12-variant19-variant20-variant21-variant23-variant31-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:37:81,0,37:1,0,2,0 chr2 39405663 . C G 303.92 PASS AC=1;AF=0.5;AN=2;DP=25;FS=1.721;FractionInformativeReads=1;MQ=60;MQRankSum=-1.333;QD=12.16;ReadPosRankSum=0.299;SOR=0.357;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:13,12:25:99:332,0,438:10,3,8,4 chr2 39406572 . C A 444.25 PASS AC=2;AF=0.898;AN=2;DP=1086;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:650,57,0:0,0,5,14 chr2 39440727 . G C 304.5 PASS AC=2;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 1/1:0,20:20:60:567,60,0:0,0,8,12 chr2 39452861 . C T 1326.16 PASS AC=2;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 1/1:0,58:58:99:1803,174,0:0,0,38,20 chr2 39476482 . T C 2460.87 PASS AC=2;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 1/1:0,45:45:99:1480,135,0:0,0,31,14 chr2 39477170 . T C 4186.78 PASS AC=2;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 1/1:2,150:152:99:4551,404,0:1,1,52,98 chr2 39479122 . G C 240.22 PASS AC=2;AF=0.927;AN=2;DP=518;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-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:555,45,0:0,0,2,13 chr2 39494197 . C T 343.89 PASS AC=2;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 1/1:0,16:16:48:557,48,0:0,0,13,3 chr2 39494469 . C G 237.59 PASS AC=2;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 1/1:0,15:15:45:554,45,0:0,0,2,13 chr2 39507417 . T A 838.37 PASS AC=2;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 1/1:0,68:68:99:1870,203,0:0,0,40,28 chr2 39514136 . T C 557.11 PASS AC=2;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 1/1:0,32:32:96:920,96,0:0,0,13,19 chr2 39514204 . G C 148.54 PASS AC=2;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 1/1:0,5:5:15:181,15,0:0,0,1,4 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 1/1:0,38:38:99:1233,114,0:0,0,25,13 chr2 39536689 . ATT ATTT,ATTTT,ATTTTT,AT,A 60.34 PASS AC=0,1,0,0,0;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 0/2:17:41:0,4,6,7 chr2 39542658 . ATT AT,A 323.77 PASS AC=2,0;AF=0.872,0.051;AN=2;DP=725;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-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:7:21:0,0,0,7 chr2 39553271 . A G 2452.21 PASS AC=2;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 1/1:0,72:72:99:2244,216,0:0,0,43,29 chr2 39558928 . G A 3143.46 PASS AC=2;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 1/1:0,107:107:99:3193,320,0:0,0,51,56 chr2 39564620 . C A 751.96 PASS AC=2;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 1/1:0,46:46:99:1361,138,0:0,0,27,19 chr2 39570427 . T C 1034 PASS AC=2;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 1/1:0,24:24:72:928,72,0:0,0,21,3 chr2 39583446 . A G 3211.29 PASS AC=2;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 1/1:0,82:82:99:2239,244,0:0,0,39,43 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 0/1:5,6:11:91:141,0,91:2,3,2,4 chr2 40339478 . GCC GC,G 4722.76 PASS AC=1,1;AF=0.682,0.307;AN=2;DP=9869;MQ=60;set=Intersection GT:DP:GQ:SB 2/1:213:99:0,1,83,129 chr2 40339798 . CA C,CAAA,CAAAA,CAA 1312.99 PASS AC=0,1,0,0;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 0/2:129:99:39,29,26,35 chr2 40339986 . T C 4023.85 PASS AC=1;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 0/1:149,152:301:99:3749,0,3944:71,78,75,77 chr2 40340671 . CA C 3301.37 PASS AC=1;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 0/1:67,70:137:99:2208,0,2091:27,40,33,37 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 0/1:50,56:106:99:1509,0,1289:20,30,25,31 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 0/1:34,29:63:99:762,0,951:16,18,11,18 chr2 40341660 . C T 461.77 PASS AC=1;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 0/1:49,24:73:99:569,0,1218:25,24,11,13 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 0/1:77,61:138:99:1291,0,2048:37,40,34,27 chr2 40366301 . G A 136.46 PASS AC=1;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 0/1:9,20:29:99:526,0,241:7,2,13,7 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 1/1:0,25:25:75:995,75,0:0,0,3,22 chr2 40402275 . G A 513.67 PASS AC=1;AF=0.842;AN=2;DP=786;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,14:23:99:456,0,259:6,3,8,6 chr2 40402646 . A ATG,ATGTG 49.45 PASS AC=1,0;AF=0.742,0.015;AN=2;DP=518;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant29-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:11:99:0,4,1,6 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 1/1:0,76:76:99:2371,227,0:0,0,48,28 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 1/1:0,60:60:99:1769,180,0:0,0,36,24 chr2 40655563 . CCACACACACACACACA CCACACACACACA,CCACACACACACACA,CCACACA,CCACACACACA,C,CCACACACACACACACACA 1935.28 PASS AC=1,1,0,0,0,0;AF=0.58,0.159,0.136,0.057,0.011,0.011;AN=2;DP=2244;set=Intersection GT:DP:GQ:SB 1/2:32:99:0,0,23,9 chr2 42163538 . G C 624.59 PASS AC=1;AF=0.5;AN=2;DP=232;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant12-variant21-variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:21,17:38:99:520,0,514:9,12,7,10 chr2 42163628 . G T 304.04 PASS AC=1;AF=0.5;AN=2;DP=172;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant12-variant21-variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:18,12:30:99:319,0,458:8,10,6,6 chr2 42164215 . A C 1531.98 PASS AC=1;AF=0.697;AN=2;DP=1702;MQ=60;set=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-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,20:41:99:480,0,572:12,9,8,12 chr2 42164609 . TACACACACGTAC T 56.46 PASS AC=1;AF=0.5;AN=2;DP=125;set=variant12-variant23-filterInvariant26-variant34 GT:AD:DP:GQ:PL:SB 0/1:26,20:46:99:442,0,1334:13,13,13,7 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 0/1:41:79:21,13,5,2 chr2 42165462 . A G 344.71 PASS AC=1;AF=0.545;AN=2;DP=771;MQ=60;set=variant4-variant5-variant6-variant7-variant12-variant13-variant14-variant15-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant34-variant36-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,16:26:99:391,0,202:5,5,10,6 chr2 42165754 . C T 2176.48 PASS AC=2;AF=0.568;AN=2;DP=3566;MQ=60;set=variant4-variant5-variant6-variant7-variant12-variant13-variant14-variant15-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant34-variant36-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,162:162:99:4871,485,0:0,0,86,76 chr2 42165961 . T A 367.6 PASS AC=2;AF=0.568;AN=2;DP=534;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant7-variant12-variant13-variant14-variant15-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant34-variant36-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:765,60,0:0,0,2,18 chr2 42181051 . GCA G,GCACA 107.51 PASS AC=1,0;AF=0.5,0.045;AN=2;DP=483;set=variant5-variant6-variant7-variant10-variant12-variant15-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant29-variant30-variant31-variant33-variant36-variant37-variant40-variant42-variant44 GT:DP:GQ:SB 0/1:13:99:3,3,2,5 chr2 42275074 . G GCGGA 167.25 PASS AC=2;AF=1;AN=2;DP=30;FS=0;MQ=60;set=variant4-variant5-variant8-variant13-variant15-variant20-variant22-variant23-variant29 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:160,12,0:0,0,1,3 chr2 42275080 . G A 106.77 PASS AC=2;AF=1;AN=2;DP=21;FS=0;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant8-variant13-variant22-variant23-variant29 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,0,3 chr2 42275086 . G A 106.77 PASS AC=2;AF=1;AN=2;DP=16;FS=0;FractionInformativeReads=1;MQ=60;set=variant4-variant8-variant13-variant22-variant23-variant29 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:9:135,9,0:0,0,0,2 chr2 42275245 . G A 51.23 PASS AC=1;AF=0.545;AN=2;DP=117;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant8-variant9-variant10-variant12-variant14-variant23-variant29-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:69:70,0,69:2,0,2,0 chr2 42275726 . C G 1436.21 PASS AC=1;AF=0.579;AN=2;DP=1955;set=variant-variant2-variant5-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant18-variant23-variant29-variant31-variant34-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:50,61:111:99:1580,0,1420:39,11,43,18 chr2 42275819 . T C 3820.51 PASS AC=1;AF=0.593;AN=2;DP=7772;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant18-variant19-variant22-variant23-variant26-variant28-variant29-variant31-variant33-variant34-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:159,122:281:99:2853,0,3551:93,66,65,57 chr2 42280300 . G A 209.8 PASS AC=1;AF=0.579;AN=2;DP=468;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant18-variant23-variant29-variant31-variant34-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:147,0,153:4,2,4,2 chr2 42280358 . C T 31.68 PASS AC=1;AF=0.579;AN=2;DP=466;MQ=60;set=variant-variant2-variant5-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant18-variant23-variant29-variant31-variant34-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:8,3:11:90:90,0,312:4,4,1,2 chr2 42282632 . A T 527.74 PASS AC=1;AF=0.579;AN=2;DP=1120;MQ=60;set=variant-variant2-variant5-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant18-variant23-variant29-variant31-variant34-variant37-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,20:43:99:543,0,640:10,13,9,11 chr2 42282829 . C A 381.23 PASS AC=1;AF=0.6;AN=2;DP=353;MQ=60;set=variant-variant2-variant5-variant8-variant9-variant10-variant12-variant14-variant16-variant18-variant23-variant29-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,12:35:99:232,0,598:8,15,5,7 chr2 42285306 . A G 915.01 PASS AC=1;AF=0.596;AN=2;DP=1733;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant16-variant18-variant19-variant23-variant26-variant28-variant29-variant31-variant33-variant34-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,30:84:99:687,0,1365:26,28,15,15 chr2 42285575 . T A 194.75 PASS AC=1;AF=0.577;AN=2;DP=201;MQ=60;set=variant-variant2-variant5-variant8-variant9-variant10-variant12-variant14-variant18-variant23-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,17:23:99:432,0,160:1,5,6,11 chr2 42285642 . G A 49.76 PASS AC=2;AF=0.8;AN=2;DP=23;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant10-variant12-variant23 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:133,18,0:0,0,3,3 chr2 42396456 . C CGCGCGG 536.87 PASS AC=1;AF=0.5;AN=2;DP=146;MQ=60;set=variant-variant6-variant13-variant22-variant23-variant31-variant40 GT:AD:DP:GQ:PL:SB 0/1:19,4:23:99:153,0,1339:14,5,3,1 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 1/1:0,198:198:99:6377,594,0:0,0,101,97 chr2 42491951 . C T 1861.75 PASS AC=1;AF=0.6;AN=2;DP=530;FractionInformativeReads=1;MQ=60;set=variant-variant13-variant20-variant21-variant22-variant23-variant30-variant31-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:19,17:36:99:472,0,527:14,5,12,5 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 1/1:0,85:85:99:2587,254,0:0,0,51,34 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 1/1:0,94:94:99:2661,281,0:0,0,51,43 chr2 42515501 . C T 670.32 PASS AC=1;AF=0.556;AN=2;DP=510;FractionInformativeReads=1;MQ=60;set=variant-variant13-variant20-variant21-variant22-variant23-variant30-variant31-variant40 GT:AD:DP:GQ:PL:SB 0/1:27,26:53:99:678,0,733:10,17,8,18 chr2 42544821 . C T 267.2 PASS AC=1;AF=0.633;AN=2;DP=720;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant36-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,8:18:99:262,0,277:3,7,1,7 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 0/1:199,75:274:99:791,0,3562:85,114,28,47 chr2 42559288 . A G 790.99 PASS AC=1;AF=0.563;AN=2;DP=460;FractionInformativeReads=1;MQ=60;set=variant-variant13-variant20-variant22-variant23-variant30-variant31-variant40 GT:AD:DP:GQ:PL:SB 0/1:25,36:61:99:972,0,804:4,21,14,22 chr2 42560975 . A G 823.52 PASS AC=1;AF=0.718;AN=2;DP=2208;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-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,22:39:99:620,0,436:6,11,12,10 chr2 42577170 . A G 2647.7 PASS AC=1;AF=0.716;AN=2;DP=8262;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-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:74,135:209:99:3750,0,1808:33,41,55,80 chr2 42577803 . T TAAATACACAC 5411.3 PASS AC=1;AF=0.716;AN=2;DP=8841;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-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:125,137:262:99:5575,0,6951:65,60,74,63 chr2 42578143 . A G 361.56 PASS AC=1;AF=0.563;AN=2;DP=298;FractionInformativeReads=1;MQ=60;set=variant-variant13-variant20-variant22-variant23-variant30-variant31-variant40 GT:AD:DP:GQ:PL:SB 0/1:28,11:39:99:369,0,1481:13,15,5,6 chr2 42578149 . A G 403.28 PASS AC=1;AF=0.641;AN=2;DP=1303;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant36-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,10:36:99:339,0,1446:13,13,5,5 chr2 42670398 . A T 5607.57 PASS AC=1;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 0/1:206,192:398:99:4642,0,5007:110,96,104,88 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 1/1:0,127:127:99:5822,391,0:0,0,82,45 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 1/1:0,142:142:99:6303,430,0:0,0,92,50 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 1/1:0,10:10:36:540,36,0:0,0,6,4 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 1/1:0,12:12:36:540,36,0:0,0,6,6 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 1/1:0,12:12:36:540,36,0:0,0,6,6 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 1/1:0,110:110:99:3091,328,0:0,0,49,61 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 1/1:0,23:23:69:859,69,0:0,0,18,5 chr2 42981990 . C T 1595.19 PASS AC=2;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 1/1:2,69:71:99:2063,163,0:1,1,39,30 chr2 42982500 . C A 444.22 PASS AC=2;AF=0.556;AN=2;DP=371;FractionInformativeReads=1;MQ=60;set=variant-variant13-variant19-variant23-variant30-variant31-variant33-variant34-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1032,104,0:0,0,16,19 chr2 42983004 . T C 1769.49 PASS AC=2;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 1/1:1,75:76:99:2427,217,0:1,0,37,38 chr2 42989592 . C T 153.96 PASS AC=2;AF=0.591;AN=2;DP=118;FractionInformativeReads=1;MQ=60;set=variant2-variant13-variant14-variant19-variant23-variant30-variant31-variant34-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:267,24,0:0,0,6,2 chr2 42989744 . G C 1240.22 PASS AC=2;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 1/1:0,81:81:99:2335,243,0:0,0,45,36 chr2 42989994 . G T 1381.82 PASS AC=2;AF=0.577;AN=2;DP=1911;MQ=60;set=variant2-variant13-variant14-variant19-variant23-variant30-variant31-variant33-variant34-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,141:141:99:4550,422,0:0,0,86,55 chr2 42990010 . C A 1601.53 PASS AC=2;AF=0.577;AN=2;DP=2285;MQ=60;set=variant2-variant13-variant14-variant19-variant23-variant30-variant31-variant33-variant34-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,169:170:99:5138,495,0:0,1,104,65 chr2 42990101 . G C 4600.08 PASS AC=2;AF=0.577;AN=2;DP=4495;MQ=60;set=variant2-variant13-variant14-variant19-variant23-variant30-variant31-variant33-variant34-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,321:323:99:9672,919,0:1,1,165,156 chr2 42990336 . T G 1418.96 PASS AC=2;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 1/1:0,142:142:99:4840,426,0:0,0,72,70 chr2 42990522 . C T 1990.22 PASS AC=2;AF=0.577;AN=2;DP=3277;MQ=60;set=variant2-variant13-variant14-variant19-variant23-variant30-variant31-variant33-variant34-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,253:255:99:7165,710,0:1,1,117,136 chr2 42991468 . G C 175.24 PASS AC=2;AF=0.577;AN=2;DP=383;FractionInformativeReads=1;MQ=60;set=variant2-variant13-variant14-variant19-variant23-variant30-variant31-variant33-variant34-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,20:22:17:661,17,0:1,1,7,13 chr2 42996709 . ATGTGTGTGTGTG A,ATG,ATGTG,ATGTGTGTGTGTGTG,ATGTGTGTGTGTGTGTGTGTGTG,ATGTGTG,ATGTGTGTGTGTGTGTG 392.62 PASS AC=0,1,0,0,0,0,0;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 0/2:24:99:9,5,8,2 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 0/1:25,16:41:99:572,0,1097:10,15,11,5 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 0/1:52,52:104:99:1387,0,1400:33,19,35,17 chr2 43011169 . G T 329.82 PASS AC=1;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 0/1:10,14:24:99:393,0,228:3,7,4,10 chr2 43015612 . G T 921.96 PASS AC=1;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 0/1:37,21:58:99:507,0,1114:27,10,14,7 chr2 43015704 . T A 1641.94 PASS AC=1;AF=0.528;AN=2;DP=2353;MQ=60;set=variant2-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant23-variant28-variant30-variant31-variant33-variant34-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:88,56:144:99:1132,0,1908:46,42,34,22 chr2 43015719 . T C 2030.08 PASS AC=1;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 0/1:92,56:148:99:1156,0,2050:44,48,33,23 chr2 43015757 . G A 2165.81 PASS AC=1;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 0/1:75,59:134:99:1351,0,1844:30,45,29,30 chr2 43015902 . G A 322.92 PASS AC=1;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 0/1:4,6:10:99:237,0,144:0,4,0,6 chr2 43019347 . G C 928.19 PASS AC=1;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 0/1:5,6:11:99:190,0,150:4,1,5,1 chr2 43019364 . G C 1230.02 PASS AC=1;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 0/1:7,13:20:99:356,0,213:6,1,9,4 chr2 43019730 . A G 3543.61 PASS AC=1;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 0/1:53,60:113:99:1429,0,1373:18,35,25,35 chr2 43019852 . C T 471.77 PASS AC=1;AF=0.5;AN=2;DP=30;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.215;QD=15.73;ReadPosRankSum=-1.851;SOR=0.941;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:11,19:30:99:500,0,231:4,7,6,13 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 0/1:104:99:29,40,16,19 chr2 43451761 . A C 1689.81 PASS AC=1;AF=0.5;AN=2;DP=205;FS=1.903;FractionInformativeReads=0.902;MQ=60;MQRankSum=0.307;QD=8.24;ReadPosRankSum=2.669;SOR=0.869;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:111,74:185:99:1718,0,2631:66,45,47,27 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 0/1:100,85:185:99:2239,0,2570:49,51,47,38 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 0/1:32,33:65:99:898,0,809:19,13,21,12 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 0/1:18,18:36:99:444,0,502:12,6,13,5 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 0/1:47,30:77:99:727,0,1048:27,20,16,14 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 0/1:8,4:12:75:75,0,168:3,5,1,3 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 0/1:9,5:14:99:133,0,324:1,8,2,3 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 0/1:39,33:72:99:845,0,939:24,15,22,11 chr2 43768545 . T G 157.5 PASS AC=1;AF=0.5;AN=2;DP=118;FractionInformativeReads=1;MQ=60;set=variant3-variant14-variant19-variant21-variant23-variant40 GT:AD:DP:GQ:PL:SB 0/1:3,10:13:98:391,0,98:1,2,0,10 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 0/1:8,10:18:99:229,0,162:6,2,7,3 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 1/1:0,9:9:27:283,27,0:0,0,6,3 chr2 43783241 . C A 43.34 PASS AC=1;AF=0.591;AN=2;DP=142;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant17-variant19-variant21-variant22-variant23-variant24-variant34-variant40 GT:AD:DP:GQ:PL:SB 0/1:7,3:10:64:64,0,205:4,3,1,2 chr2 43783273 . G A 108.15 PASS AC=1;AF=0.559;AN=2;DP=346;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant7-variant8-variant10-variant12-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant34-variant40 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:99:103,0,239:3,4,2,2 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 0/1:10,8:18:99:257,0,307:7,3,6,2 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 0/1:17,8:25:99:263,0,431:6,11,1,7 chr2 43789786 . C G 481.23 PASS AC=2;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 1/1:0,29:29:87:882,87,0:0,0,16,13 chr2 43790259 . T C 2442.96 PASS AC=2;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 1/1:2,204:206:99:6124,566,0:1,1,104,100 chr2 43790347 . A T 2510.2 PASS AC=2;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 1/1:0,189:189:99:5956,566,0:0,0,84,105 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 0/1:84,59:143:99:1604,0,2480:45,39,31,28 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 1/1:0,138:138:99:4495,414,0:0,0,54,84 chr2 43791563 . T C 1361.28 PASS AC=2;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 1/1:0,106:106:99:3607,318,0:0,0,72,34 chr2 43791766 . A G 1986.79 PASS AC=2;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 1/1:0,163:163:99:5425,487,0:0,0,64,99 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 0/1:9,9:18:99:351,0,416:9,0,8,1 chr2 43792546 . G A 355.55 PASS AC=1;AF=0.5;AN=2;DP=71;FractionInformativeReads=1;set=variant8-variant22-variant23-variant24 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:382,0,447:10,0,9,1 chr2 43792570 . CA C,CAA 366.94 PASS AC=0,1;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 0/2:33:99:16,1,12,4 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 0/1:6,8:14:99:305,0,186:5,1,8,0 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 0/1:20,21:41:99:478,0,446:14,6,17,4 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 0/1:34,38:72:99:1012,0,879:17,17,20,18 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 0/1:10:99:1,4,2,3 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 0/1:33,28:61:99:720,0,810:16,17,16,12 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 0/1:23,18:41:99:474,0,631:7,16,6,12 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 0/1:30,30:60:99:684,0,656:16,14,15,15 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 1/1:0,7:7:21:227,21,0:0,0,3,4 chr2 43800174 . A G 823.9 PASS AC=2;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 1/1:0,86:86:99:2764,257,0:0,0,27,59 chr2 43801712 . A G 944.33 PASS AC=2;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 1/1:0,69:69:99:2294,207,0:0,0,36,33 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 1/1:0,7:7:21:231,21,0:0,0,2,5 chr2 43804229 . T C 1335.5 PASS AC=2;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 1/1:0,88:88:99:2600,264,0:0,0,42,46 chr2 43805608 . C G 374.79 PASS AC=1;AF=0.5;AN=2;DP=179;FractionInformativeReads=1;MQ=60;set=variant3-variant14-variant19-variant21-variant23-variant40 GT:AD:DP:GQ:PL:SB 0/1:14,11:25:99:339,0,460:12,2,9,2 chr2 43805739 . C T 1561.63 PASS AC=1;AF=0.5;AN=2;DP=704;MQ=60;set=variant3-variant14-variant19-variant21-variant23-variant40 GT:AD:DP:GQ:PL:SB 0/1:72,61:133:99:1345,0,1644:37,35,34,27 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 0/1:30,39:69:99:1008,0,717:17,13,22,17 chr2 43819139 . A G 1044.07 PASS AC=1;AF=0.5;AN=2;DP=514;FractionInformativeReads=1;MQ=60;set=variant3-variant14-variant19-variant21-variant23-variant40 GT:AD:DP:GQ:PL:SB 0/1:27,41:68:99:993,0,581:12,15,20,21 chr2 43864526 . A G 1061.41 PASS AC=2;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 1/1:0,56:56:99:1759,168,0:0,0,23,33 chr2 43864555 . T C 706.65 PASS AC=2;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 1/1:0,43:43:99:1252,129,0:0,0,20,23 chr2 43871983 . T C 1573.86 PASS AC=2;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 1/1:0,45:45:99:1466,135,0:0,0,14,31 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 0/1:16,7:23:99:239,0,553:3,13,0,7 chr2 43902511 . G C 2120.68 PASS AC=2;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 1/1:0,57:57:99:1788,171,0:0,0,37,20 chr2 43902757 . C G 1822.99 PASS AC=1;AF=0.5;AN=2;DP=261;FractionInformativeReads=1;MQ=60;set=variant14-variant23 GT:AD:DP:GQ:PL:SB 0/1:60,50:110:99:1346,0,1681:32,28,21,29 chr2 43903066 . A G 3874.81 PASS AC=2;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 1/1:0,99:99:99:3309,297,0:0,0,50,49 chr2 43903354 . T C 5603.01 PASS AC=2;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 1/1:0,143:143:99:4340,428,0:0,0,72,71 chr2 43903483 . T C 2633.33 PASS AC=2;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 1/1:0,82:82:99:2550,246,0:0,0,32,50 chr2 43905898 . G GAGGTGGAGGTGC 235.58 PASS AC=2;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 1/1:0,6:6:21:315,21,0:0,0,5,1 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 0/1:12,16:28:99:393,0,369:11,1,10,6 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 0/1:56,77:133:99:2049,0,1342:30,26,40,37 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 0/1:48,43:91:99:969,0,1047:24,24,22,21 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 0/1:12,13:25:99:360,0,306:4,8,3,10 chr2 43937723 . CTTTTT CTTTT,CTTTTTTT,CTTTTTT,CTTTTTTTT,CTTT,C 137.46 PASS AC=1,0,0,0,0,0;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 0/1:26:35:1,7,4,14 chr2 43947728 . C G 991.89 PASS AC=1;AF=0.5;AN=2;DP=65;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.672;QD=15.26;ReadPosRankSum=0.699;SOR=0.828;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:27,38:65:99:1020,0,649:17,10,25,13 chr2 43953664 . A G 572.26 PASS AC=1;AF=0.645;AN=2;DP=1044;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,14:30:99:431,0,546:2,14,2,12 chr2 43968024 . C T 203.88 PASS AC=1;AF=0.5;AN=2;DP=51;FractionInformativeReads=1;MQ=60;set=variant14-variant23 GT:AD:DP:GQ:PL:SB 0/1:19,10:29:99:334,0,629:16,3,10,0 chr2 43968316 . G A 355.6 PASS AC=1;AF=0.5;AN=2;DP=35;FractionInformativeReads=1;MQ=60;set=variant14-variant23 GT:AD:DP:GQ:PL:SB 0/1:8,9:17:99:337,0,265:1,7,1,8 chr2 43973099 . A G 1464.14 PASS AC=1;AF=0.5;AN=2;DP=266;FractionInformativeReads=1;MQ=60;set=variant14-variant23 GT:AD:DP:GQ:PL:SB 0/1:64,44:108:99:1082,0,1536:29,35,17,27 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 1/1:0,20:20:60:664,60,0:0,0,16,4 chr2 43992529 . C G 1946.2 PASS AC=1;AF=0.5;AN=2;DP=191;FractionInformativeReads=1;MQ=60;set=variant14-variant23 GT:AD:DP:GQ:PL:SB 0/1:33,41:74:99:1098,0,794:19,14,20,21 chr2 43993448 . G C 1117.25 PASS AC=1;AF=0.568;AN=2;DP=1390;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant9-variant11-variant13-variant14-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant33-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,23:54:99:626,0,823:16,15,15,8 chr2 43994697 . T A 1008.69 PASS AC=1;AF=0.568;AN=2;DP=1960;MQ=60;set=variant-variant4-variant6-variant9-variant11-variant13-variant14-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant33-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:44,25:69:99:703,0,1269:15,29,6,19 chr2 44001139 . C T 1624.72 PASS AC=1;AF=0.5;AN=2;DP=1929;MQ=60;set=variant4-variant6-variant11-variant13-variant14-variant20-variant23-variant26-variant27-variant31-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:63,52:115:99:1335,0,1628:39,24,33,19 chr2 44001185 . C T 1868.41 PASS AC=1;AF=0.5;AN=2;DP=338;FractionInformativeReads=1;MQ=60;set=variant14-variant23 GT:AD:DP:GQ:PL:SB 0/1:96,66:162:99:1529,0,2511:55,41,39,27 chr2 44001216 . C T 1999.55 PASS AC=1;AF=0.5;AN=2;DP=352;FractionInformativeReads=1;MQ=60;set=variant14-variant23 GT:AD:DP:GQ:PL:SB 0/1:102,70:172:99:1511,0,2576:57,45,38,32 chr2 44004010 . T C 1723.04 PASS AC=1;AF=0.558;AN=2;DP=3030;MQ=60;set=variant-variant4-variant6-variant9-variant11-variant13-variant14-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,55:83:99:1448,0,641:10,18,25,30 chr2 44004099 . T G 275.54 PASS AC=1;AF=0.5;AN=2;DP=428;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant11-variant13-variant14-variant20-variant23-variant26-variant27-variant31-variant36-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,17:23:99:494,0,128:1,5,5,12 chr2 44010620 . G A 1196.05 PASS AC=1;AF=0.58;AN=2;DP=2119;MQ=60;set=variant-variant4-variant6-variant9-variant11-variant13-variant14-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant33-variant34-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:46,29:75:99:660,0,1233:27,19,15,14 chr2 44021826 . T A 4049.6 PASS AC=1;AF=0.58;AN=2;DP=7467;MQ=60;set=variant-variant4-variant6-variant9-variant11-variant13-variant14-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant33-variant34-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:137,131:268:99:3345,0,3288:77,60,69,62 chr2 44022970 . T C 692.51 PASS AC=1;AF=0.5;AN=2;DP=799;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant11-variant13-variant14-variant20-variant23-variant26-variant27-variant31-variant36-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,22:63:99:473,0,1021:26,15,14,8 chr2 44028013 . A T 976.77 PASS AC=1;AF=0.542;AN=2;DP=1584;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant6-variant9-variant11-variant13-variant14-variant17-variant20-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant33-variant34-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,19:42:99:570,0,584:13,10,10,9 chr2 44036689 . A G 181.96 PASS AC=1;AF=0.6;AN=2;DP=209;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant17-variant22-variant23-variant24-variant25-variant27-variant29-variant33-variant34-variant36-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:190,0,188:5,1,5,1 chr2 44036800 . A G 1118.75 PASS AC=1;AF=0.6;AN=2;DP=1279;FractionInformativeReads=1;MQ=60;set=variant-variant9-variant17-variant22-variant23-variant24-variant25-variant27-variant29-variant33-variant34-variant36-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:46,27:73:99:620,0,1107:26,20,14,13 chr2 44036892 . G C 1481.31 PASS AC=1;AF=0.5;AN=2;DP=115;FS=3.441;FractionInformativeReads=0.983;MQ=60;MQRankSum=-0.784;QD=12.88;ReadPosRankSum=-0.686;SOR=0.497;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:56,57:113:99:1510,0,1492:32,24,28,29 chr2 44036922 . T C 2683.24 PASS AC=1;AF=0.6;AN=2;DP=2024;MQ=60;set=variant-variant9-variant17-variant22-variant23-variant24-variant25-variant27-variant29-variant33-variant34-variant36-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:55,83:138:99:2053,0,1336:30,25,49,34 chr2 44039733 . C T 343.57 PASS AC=1;AF=0.5;AN=2;DP=762;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant11-variant13-variant14-variant20-variant23-variant26-variant27-variant31-variant36-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,16:35:99:450,0,503:10,9,7,9 chr2 44039875 . A C 1529.38 PASS AC=1;AF=0.58;AN=2;DP=2765;MQ=60;set=variant-variant4-variant6-variant9-variant11-variant13-variant14-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant31-variant33-variant34-variant36-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,45:86:99:1025,0,888:22,19,24,21 chr2 44054991 . G A 423.24 PASS AC=1;AF=0.5;AN=2;DP=255;FractionInformativeReads=1;MQ=60;set=variant6-variant22-variant23-variant27-variant29-variant39 GT:AD:DP:GQ:PL:SB 0/1:14,17:31:99:406,0,409:10,4,10,7 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 0/1:4,11:15:54:278,0,54:2,2,5,6 chr2 44055527 . T C 45.63 PASS AC=2;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 1/1:0,9:9:27:283,27,0:0,0,5,4 chr2 44065090 . G A 2083.19 PASS AC=1;AF=0.5;AN=2;DP=929;MQ=60;set=variant6-variant22-variant23-variant27-variant29-variant32-variant39 GT:AD:DP:GQ:PL:SB 0/1:63,45:108:99:1061,0,1624:27,36,20,25 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 0/1:31,42:73:99:1101,0,803:17,14,14,28 chr2 44066247 . G C 1358.23 PASS AC=1;AF=0.5;AN=2;DP=550;FractionInformativeReads=1;MQ=60;set=variant6-variant22-variant23-variant27-variant29-variant32-variant39 GT:AD:DP:GQ:PL:SB 0/1:38,36:74:99:816,0,971:17,21,17,19 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 0/1:66,69:135:99:1671,0,1729:26,40,34,35 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 0/1:69,66:135:99:1646,0,1713:27,42,32,34 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 0/1:27,41:68:99:992,0,621:13,14,19,22 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 0/1:9,14:23:99:472,0,198:3,6,2,12 chr2 44073656 . T C 313.72 PASS AC=1;AF=0.5;AN=2;DP=166;FractionInformativeReads=1;MQ=60;set=variant6-variant22-variant23-variant27-variant29-variant32-variant39 GT:AD:DP:GQ:PL:SB 0/1:11,4:15:91:91,0,365:2,9,1,3 chr2 44078853 . G A 3854.9 PASS AC=1;AF=0.5;AN=2;DP=1813;MQ=60;set=variant6-variant22-variant23-variant27-variant29-variant39 GT:AD:DP:GQ:PL:SB 0/1:168,120:288:99:2800,0,4239:77,91,56,64 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 1/1:0,61:61:99:2173,183,0:0,0,16,45 chr2 44079310 . C A 94.73 PASS AC=1;AF=0.5;AN=2;DP=51;FractionInformativeReads=1;MQ=60;set=variant6-variant22-variant23-variant27-variant29-variant39 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:62:77,0,62:2,1,2,1 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 1/1:0,19:19:57:747,57,0:0,0,2,17 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 1/1:0,14:14:42:500,42,0:0,0,11,3 chr2 44101430 . T G 153.33 PASS AC=1;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 0/1:14,10:24:99:216,0,398:11,3,6,4 chr2 44101537 . A AT 1107.45 PASS AC=2;AF=0.577;AN=2;DP=927;MQ=60;set=variant6-variant9-variant20-variant22-variant23-variant26-variant27-variant29-variant31-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:3530,238,0:0,0,44,35 chr2 44101538 . C T 904.47 PASS AC=2;AF=0.771;AN=2;DP=2520;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:3530,238,0:0,0,44,35 chr2 44101649 . G GC,GCCC,GCC 1292.76 PASS AC=0,0,1;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 0/3:45:99:5,18,7,15 chr2 44104925 . T C 7565.61 PASS AC=2;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 1/1:0,233:233:99:6799,697,0:0,0,112,121 chr2 44114282 . CAAAAA CAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAA,CAAA,C,CAAAA,CAA,CAAAAAAAAAA 85.69 PASS AC=0,0,0,0,0,1,0,0,0,0;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 0/6:7:29:2,0,3,2 chr2 44116836 . C T 1801.87 PASS AC=2;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 1/1:0,77:77:99:2355,230,0:0,0,43,34 chr2 44123672 . TC T 432.98 PASS AC=2;AF=0.587;AN=2;DP=600;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant14-variant15-variant18-variant22-variant23-variant26-variant27-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:688,51,0:0,0,11,6 chr2 44145374 . G T 1357.23 PASS AC=2;AF=0.625;AN=2;DP=2658;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant14-variant15-variant18-variant22-variant23-variant26-variant27-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:2893,291,0:0,0,50,47 chr2 44152180 . G A 2885.92 PASS AC=2;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 1/1:1,97:98:99:2881,258,0:1,0,48,49 chr2 44161854 . GA GAA,G 556 PASS AC=1,0;AF=0.563,0.031;AN=2;DP=810;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant18-variant22-variant23-variant26-variant27-variant31-variant38-variant39-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:39:99:12,7,12,8 chr2 44172444 . A C 1832.69 PASS AC=2;AF=0.611;AN=2;DP=3527;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant14-variant15-variant18-variant22-variant23-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,95:95:99:2818,284,0:0,0,49,46 chr2 44173422 . T G 682.69 PASS AC=2;AF=0.615;AN=2;DP=1422;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant14-variant15-variant18-variant22-variant23-variant26-variant27-variant29-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1822,174,0:0,0,21,37 chr2 44175366 . A C 1714.08 PASS AC=1;AF=0.6;AN=2;DP=2017;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant18-variant22-variant23-variant26-variant27-variant31-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,56:105:99:1312,0,1316:23,26,27,29 chr2 44177701 . G C 1329.16 PASS AC=1;AF=0.615;AN=2;DP=1073;MQ=60;set=variant3-variant4-variant8-variant9-variant18-variant23-variant26-variant27-variant31-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,17:49:99:327,0,723:17,15,9,8 chr2 44186498 . A C 341.96 PASS AC=1;AF=0.633;AN=2;DP=164;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant18-variant22-variant23-variant26-variant27-variant31-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:236,0,153:0,4,0,6 chr2 44187829 . A C 432.64 PASS AC=1;AF=0.807;AN=2;DP=2201;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:20,23:43:99:582,0,526:7,13,8,15 chr2 44201259 . T C 967.7 PASS AC=1;AF=0.6;AN=2;DP=978;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant18-variant22-variant23-variant26-variant27-variant31-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,23:47:99:580,0,713:18,6,15,8 chr2 44201376 . T C 1201.82 PASS AC=1;AF=0.5;AN=2;DP=823;FractionInformativeReads=1;MQ=60;set=variant9-variant14-variant15-variant23-variant32-variant34-variant36-variant42 GT:AD:DP:GQ:PL:SB 0/1:51,55:106:99:1306,0,1144:26,25,26,29 chr2 44202426 . A G 541.39 PASS AC=1;AF=0.6;AN=2;DP=411;MQ=60;set=variant3-variant4-variant5-variant8-variant9-variant18-variant22-variant23-variant26-variant27-variant31-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,19:39:99:483,0,641:3,17,5,14 chr2 44209477 . C T 818.13 PASS AC=1;AF=0.807;AN=2;DP=2931;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:23,34:57:99:798,0,498:12,11,18,16 chr2 44396235 . T G 3526.53 PASS AC=1;AF=0.864;AN=2;DP=4903;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:28,45:73:99:1189,0,639:11,17,24,21 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 0/1:32,46:78:99:1869,0,1520:18,14,27,19 chr2 44460270 . G A 1662.6 PASS AC=1;AF=0.531;AN=2;DP=1643;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant7-variant9-variant10-variant11-variant17-variant20-variant23-variant24-variant33-variant34-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,50:90:99:1307,0,1005:14,26,19,31 chr2 44471326 . CAT C 76.65 PASS AC=2;AF=0.792;AN=2;DP=70;FS=0;MQ=60;set=variant2-variant6-variant9-variant10-variant20-variant23-variant24-variant33-variant34-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:76,6,0:0,0,1,1 chr2 44471409 . T G 538.19 PASS AC=1;AF=0.533;AN=2;DP=501;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant7-variant9-variant10-variant11-variant20-variant23-variant24-variant33-variant34-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,8:23:99:207,0,382:10,5,5,3 chr2 44502788 . A C 4137.5 PASS AC=1;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 0/1:114,112:226:99:2578,0,2626:65,49,59,53 chr2 44508095 . T C 927.67 PASS AC=1;AF=0.5;AN=2;DP=200;MQ=60;set=variant23-variant31-variant41 GT:AD:DP:GQ:PL:SB 0/1:35,37:72:99:956,0,869:15,20,11,26 chr2 44508835 . G A 526.57 PASS AC=1;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 0/1:13,3:16:87:87,0,463:2,11,0,3 chr2 44512971 . G A 3208.95 PASS AC=1;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 0/1:31,27:58:99:716,0,914:17,14,12,15 chr2 44527323 . G A 211.67 PASS AC=1;AF=0.5;AN=2;DP=10;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.633;QD=21.17;ReadPosRankSum=1.036;SOR=1.085;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:240,0,143:0,4,0,6 chr2 44531081 . G T 190.65 PASS AC=1;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 0/1:9,7:16:99:220,0,290:8,1,6,1 chr2 44531484 . C T 308.47 PASS AC=1;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 0/1:9,22:31:99:716,0,269:2,7,3,19 chr2 44541706 . G C 1922.28 PASS AC=1;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 0/1:58,45:103:99:1590,0,3994:29,29,17,28 chr2 44541725 . C T 1871.62 PASS AC=1;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 0/1:48,37:85:99:1478,0,3928:22,26,13,24 chr2 44541731 . C CCA 934.16 PASS AC=1;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 0/1:47,36:83:99:1393,0,3930:21,26,13,23 chr2 44541917 . AAT A 1654.87 PASS AC=1;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 0/1:30,40:70:99:1409,0,1015:16,14,18,22 chr2 44544814 . A G 93.42 PASS AC=1;AF=0.5;AN=2;DP=8;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.684;QD=11.68;ReadPosRankSum=0.956;SOR=0.582;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:72:122,0,72:2,1,3,2 chr2 44544914 . A C 484.41 PASS AC=1;AF=0.5;AN=2;DP=110;FractionInformativeReads=1;MQ=60;set=variant11-variant21-variant23 GT:AD:DP:GQ:PL:SB 0/1:12,8:20:99:177,0,321:8,4,5,3 chr2 44544955 . G A 166.1 PASS AC=1;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 0/1:15,13:28:99:264,0,397:9,6,7,6 chr2 44545234 . GTTT GTT,GT,G,GTTTT 463.84 PASS AC=1,0,0,0;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 0/1:76:99:14,23,14,25 chr2 44545576 . T C 2375.56 PASS AC=1;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 0/1:81,86:167:99:2217,0,1897:50,31,51,35 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 0/1:153,78:231:99:2610,0,50929:74,79,27,51 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 0/1:136,71:207:99:2679,0,50719:65,71,21,50 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 0/1:137,70:207:99:2566,0,50168:63,74,22,48 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 0/1:135,66:201:99:2569,0,49988:62,73,21,45 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 0/1:131,61:192:99:2413,0,49107:60,71,21,40 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 0/1:129,58:187:99:2293,0,48639:60,69,19,39 chr2 44546016 . C T 1256.34 PASS AC=1;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 0/1:24,50:74:99:1624,0,673:17,7,31,19 chr2 44546632 . CATTT C 3061.5 PASS AC=1;AF=0.5;AN=2;DP=552;MQ=60;set=variant11-variant21-variant23 GT:AD:DP:GQ:PL:SB 0/1:101,78:179:99:2943,0,5128:45,56,34,44 chr2 44546741 . T C 2800.52 PASS AC=1;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 0/1:71,78:149:99:1992,0,1839:37,34,42,36 chr2 44547131 . A G 3844.28 PASS AC=1;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 0/1:198,116:314:99:2433,0,5148:97,101,59,57 chr2 44547574 . G A 2331.79 PASS AC=1;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 0/1:48,60:108:99:1636,0,1258:22,26,28,32 chr2 44547909 . T C 3005.72 PASS AC=1;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 0/1:105,99:204:99:2297,0,2794:56,49,45,54 chr2 44548282 . T C 514.42 PASS AC=1;AF=0.818;AN=2;DP=1510;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:13,17:30:99:508,0,409:6,7,4,13 chr2 44548613 . T C 1188.75 PASS AC=1;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 0/1:32,21:53:99:533,0,824:13,19,7,14 chr2 44556298 . T C 398.92 PASS AC=1;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 0/1:13,6:19:99:172,0,425:2,11,1,5 chr2 44565447 . A T 323.09 PASS AC=1;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 0/1:9,8:17:99:228,0,287:7,2,6,2 chr2 44569474 . G A 94.47 PASS AC=1;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 0/1:9,12:21:99:298,0,279:8,1,8,4 chr2 44569700 . AAAT A 737.18 PASS AC=1;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 0/1:19,21:40:99:790,0,771:6,13,7,14 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 0/1:8,5:13:73:73,0,159:2,6,0,5 chr2 44570776 . C T 567.13 PASS AC=1;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 0/1:25,30:55:99:723,0,690:19,6,19,11 chr2 44570804 . C A 753.97 PASS AC=1;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 0/1:40,39:79:99:957,0,963:27,13,24,15 chr2 44573624 . G A 257.58 PASS AC=1;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 0/1:3,4:7:99:130,0,114:0,3,0,4 chr2 44573658 . T C 121.67 PASS AC=1;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 0/1:2,2:4:60:60,0,69:0,2,0,2 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 1/1:0,2:2:6:87,6,0:0,0,0,2 chr2 44588941 . G A 839.14 PASS AC=1;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 0/1:51,55:106:99:1367,0,1343:27,24,35,20 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 0/1:13,10:23:99:205,0,293:8,5,6,4 chr2 44942331 . CAAAAA CAAAA,CAAA,C,CAAAAAA 59.59 PASS AC=1,0,0,0;AF=0.3,0.167,0.067,0.033;AN=2;DP=214;set=variant4-variant7-variant13-variant14-variant16-variant17-variant18-variant21-variant23-variant30-variant32-variant37-variant39-variant43-variant44 GT:DP:GQ:SB 0/1:18:88:7,3,6,2 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 0/1:251:99:94,90,33,34 chr2 45170153 . G A 517.33 PASS AC=1;AF=0.571;AN=2;DP=1111;MQ=60;set=variant-variant3-variant6-variant8-variant11-variant13-variant14-variant15-variant17-variant18-variant22-variant23-variant25-variant26-variant27-variant32-variant37-variant38-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:23,34:57:99:1011,0,734:3,20,7,27 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 1/1:0,207:207:99:6000,619,0:0,0,107,100 chr2 45172485 . G A,GA 555.14 PASS AC=1,0;AF=0.5,0.071;AN=2;DP=562;set=variant-variant3-variant6-variant11-variant13-variant14-variant15-variant17-variant18-variant22-variant23-variant25-variant26-variant27-variant29-filterInvariant33-variant34-variant37-variant38-variant42-variant43 GT:DP:GQ:SB 0/1:15:79:7,1,7,0 chr2 45172556 . CT C 2062.55 PASS AC=1;AF=0.579;AN=2;DP=2871;MQ=60;set=variant-variant3-variant6-variant11-variant13-variant14-variant15-variant17-variant18-variant22-variant23-variant25-variant26-variant27-variant32-variant34-variant37-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:77,56:133:99:1291,0,1834:56,21,37,19 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 1/1:0,22:22:66:734,66,0:0,0,9,13 chr2 45236590 . TTAA T 1099.2 PASS AC=1;AF=0.5;AN=2;DP=57;FS=1.027;FractionInformativeReads=0.982;MQ=60;MQRankSum=0.869;QD=19.28;ReadPosRankSum=0.935;SOR=0.54;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:27,29:56:99:1136,0,1236:10,17,12,17 chr2 45640334 . T C 917.6 PASS AC=1;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 0/1:30,37:67:99:852,0,663:15,15,20,17 chr2 45647043 . C G 1242 PASS AC=1;AF=0.667;AN=2;DP=2659;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant33-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,30:72:99:792,0,1075:16,26,12,18 chr2 45773816 . C G 273.32 PASS AC=1;AF=0.712;AN=2;DP=1207;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant33-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,12:32:99:346,0,567:14,6,9,3 chr2 45774050 . G A 355.32 PASS AC=1;AF=0.694;AN=2;DP=1687;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant33-variant36-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,19:39:99:487,0,496:7,13,5,14 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 1/1:0,64:64:99:1972,192,0:0,0,37,27 chr2 45780962 . C G 320.4 PASS AC=1;AF=0.727;AN=2;DP=1662;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant32-variant33-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,26:56:99:568,0,686:14,16,10,16 chr2 45806963 . TA T 84.7 PASS AC=1;AF=0.5;AN=2;DP=700;MQ=60;set=variant-filterInvariant5-variant6-variant7-variant9-filterInvariant10-filterInvariant13-variant15-variant17-variant20-filterInvariant23-filterInvariant24-variant25-variant28-variant31-variant32-variant34-variant36-filterInvariant37-filterInvariant38-filterInvariant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:22,8:30:89:89,0,377:13,9,6,2 chr2 45812666 . A G 1008.09 PASS AC=1;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 0/1:25,33:58:99:865,0,662:15,10,22,11 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 1/1:0,67:67:99:2673,202,0:0,0,50,17 chr2 45879610 . A G 441.08 PASS AC=1;AF=0.864;AN=2;DP=742;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:8,9:17:99:310,0,281:0,8,1,8 chr2 46203796 . G C,A 2418.97 PASS AC=2,0;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 1/1:60:99:0,0,20,40 chr2 46211658 . G A 1135.65 PASS AC=2;AF=0.579;AN=2;DP=2771;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant10-variant14-variant16-variant18-variant23-variant25-variant26-variant29-variant30-variant34-variant36-variant38-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:4061,383,0:0,0,71,57 chr2 46231525 . T A 922.34 PASS AC=2;AF=0.579;AN=2;DP=1978;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant14-variant16-variant18-variant20-variant23-variant25-variant26-variant29-variant30-variant34-variant36-variant38-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2264,216,0:0,0,42,30 chr2 46232042 . A C 193.52 PASS AC=2;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 1/1:0,11:11:33:352,33,0:0,0,3,8 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 1/1:0,38:38:99:1510,114,0:0,0,4,34 chr2 46378419 . TACACACAC TACACACACAC,TACACAC,TACAC,TAC,TACACACACACAC,TACACACACACACAC,T,TACACACACACACACAC 491.57 PASS AC=0,0,1,0,0,0,1,0;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 7/3:15:99:0,0,4,11 chr2 46602678 . C A 202.45 PASS AC=2;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 1/1:0,9:9:27:280,27,0:0,0,6,3 chr2 46602722 . T C 410.25 PASS AC=2;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 1/1:0,19:19:57:531,57,0:0,0,11,8 chr2 46603671 . C G 2475.81 PASS AC=2;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 1/1:0,98:98:99:2874,293,0:0,0,51,47 chr2 46605659 . A G 798.43 PASS AC=2;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 1/1:0,11:11:33:456,33,0:0,0,10,1 chr2 46605954 . G C 2044.17 PASS AC=2;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 1/1:0,70:70:99:2274,209,0:0,0,22,48 chr2 46608542 . C G 199.22 PASS AC=2;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 1/1:0,22:22:66:824,66,0:0,0,19,3 chr2 46612326 . GTT G,GT 10765.4 PASS AC=1,1;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 1/2:293:99:17,3,128,145 chr2 46707808 . C CAGCGGCAGCACGAGGTGGTGATGGAGCAGCTGCAGCGGG 1967.42 PASS AC=2;AF=0.719;AN=2;DP=8832;set=variant-variant2-variant4-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,81:82:99:5579,408,0:0,1,49,32 chr2 46708129 . C G 93.22 PASS AC=2;AF=0.717;AN=2;DP=690;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:926,84,0:0,0,9,19 chr2 46738846 . T C 1422.34 PASS AC=2;AF=0.707;AN=2;DP=1178;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant24-variant25-variant27-variant31-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1739,144,0:0,0,37,11 chr2 46738891 . A G 2209.77 PASS AC=2;AF=0.707;AN=2;DP=2434;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant24-variant25-variant27-variant31-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2416,220,0:0,0,45,29 chr2 46739157 . A G 7485.27 PASS AC=2;AF=0.707;AN=2;DP=6380;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant24-variant25-variant27-variant31-variant33-variant34-variant36-variant37-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,190:190:99:5725,568,0:0,0,100,90 chr2 46739296 . A G 1891.44 PASS AC=1;AF=0.5;AN=2;DP=147;FS=2.924;FractionInformativeReads=1;MQ=60;MQRankSum=0.052;QD=12.87;ReadPosRankSum=1.509;SOR=0.487;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:75,72:147:99:1920,0,2119:32,43,35,37 chr2 46746256 . G A 700.03 PASS AC=2;AF=0.685;AN=2;DP=1010;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant24-variant25-variant27-variant31-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1152,117,0:0,0,17,22 chr2 46746675 . G A 8008.89 PASS AC=2;AF=0.685;AN=2;DP=4335;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant20-variant21-variant23-variant24-variant25-variant27-variant31-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,165:165:99:7463,509,0:0,0,99,66 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 1/1:0,176:176:99:7677,530,0:0,0,105,71 chr2 46746963 . A G 8509.41 PASS AC=2;AF=0.679;AN=2;DP=6755;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant27-variant31-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:4,221:225:99:6677,552,0:3,1,83,138 chr2 46763898 . T C 61.77 PASS AC=1;AF=0.769;AN=2;DP=87;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant8-variant11-variant12-variant16-variant20-variant23-variant24-variant27-variant29-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:3,6:9:64:162,0,64:1,2,2,4 chr2 46768543 . A C 722.33 PASS AC=1;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 0/1:36,24:60:99:518,0,871:19,17,14,10 chr2 46768650 . C T 523.77 PASS AC=1;AF=0.605;AN=2;DP=666;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant10-variant13-variant14-variant16-variant19-variant21-variant22-variant23-variant27-variant28-variant31-variant34-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,20:40:99:511,0,577:6,14,8,12 chr2 46771134 . G C 1177.9 PASS AC=1;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 0/1:14,21:35:99:668,0,380:4,10,4,17 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 1/1:0,32:32:96:1292,96,0:0,0,20,12 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 1/1:0,80:80:99:2941,241,0:0,0,42,38 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 0/1:239:99:51,61,59,68 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 0/1:79:99:17,27,3,32 chr2 46852514 . CTTTTT CT,C,CTT,CTTT,CTTTT 59.04 PASS AC=0,0,0,1,0;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 0/4:10:86:3,2,5,0 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 0/1:2,8:10:26:287,0,26:1,1,5,3 chr2 46926719 . G C 94.75 PASS AC=1;AF=0.632;AN=2;DP=377;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,2:3:37:78,0,37:0,1,1,1 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 0/1:6,2:8:66:66,0,204:1,5,0,2 chr2 46990012 . TAC T 12864.4 PASS AC=1;AF=0.5;AN=2;DP=5602;MQ=60;set=variant3-variant9-variant19-variant21-variant22-variant23-variant30 GT:AD:DP:GQ:PL:SB 0/1:349,307:656:99:9596,0,11129:162,187,143,164 chr2 47045267 . G A 1257.66 PASS AC=1;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 0/1:15,14:29:99:379,0,466:13,2,10,4 chr2 47048969 . T C 329.76 PASS AC=1;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 0/1:3,4:7:99:147,0,116:3,0,4,0 chr2 47048980 . A T 290.05 PASS AC=1;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 0/1:4,5:9:99:156,0,147:4,0,4,1 chr2 47049453 . A G 2094.06 PASS AC=1;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 0/1:43,36:79:99:901,0,1225:18,25,18,18 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 0/1:86,65:151:99:1433,0,2234:36,50,27,38 chr2 47081196 . C G 215.96 PASS AC=1;AF=0.571;AN=2;DP=587;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant8-variant11-variant12-variant15-variant16-variant17-variant19-variant21-variant23-variant26-variant28-variant29-variant32-variant33-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:324,0,418:2,11,0,9 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 0/1:4,2:6:72:72,0,394:2,2,1,1 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 0/1:9,8:17:99:215,0,248:2,7,2,6 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 0/1:84:99:30,21,19,14 chr2 47133055 . T C 3275.17 PASS AC=1;AF=0.588;AN=2;DP=4344;MQ=60;set=variant2-variant3-variant5-variant7-variant8-variant9-variant13-variant15-variant18-variant20-variant23-variant25-variant30-variant32-variant36-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:115,123:238:99:3263,0,3108:52,63,58,65 chr2 47139568 . G C 901.34 PASS AC=1;AF=0.7;AN=2;DP=94;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant23-variant30-variant41 GT:AD:DP:GQ:PL:SB 0/1:6,4:10:99:147,0,194:5,1,4,0 chr2 47142950 . GCCCCCCCCC GCCCC,G,GCCCCCC,GCCCCC,GCCCCCCC,GCCCCCCCC 171.55 PASS AC=0,2,0,0,0,0;AF=0.117,0.433,0.083,0.1,0.05,0.017;AN=2;DP=1130;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant40-variant41-variant43 GT:DP:GQ:SB 2/2:50:99:0,0,25,25 chr2 47143230 . G T 990.64 PASS AC=1;AF=0.591;AN=2;DP=989;MQ=60;set=variant2-variant3-variant7-variant8-variant15-variant18-variant20-variant23-variant30-variant32-variant41 GT:AD:DP:GQ:PL:SB 0/1:43,40:83:99:1087,0,1005:21,22,21,19 chr2 47168569 . T C 818.66 PASS AC=1;AF=0.5;AN=2;DP=179;FractionInformativeReads=1;MQ=60;set=variant4-variant14-variant23 GT:AD:DP:GQ:PL:SB 0/1:19,31:50:99:837,0,485:11,8,18,13 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 1/1:0,11:11:33:414,33,0:0,0,9,2 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 0/1:50,29:79:99:599,0,1319:31,19,20,9 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 1/1:0,40:40:99:1030,119,0:0,0,23,17 chr2 47201991 . CT C 717.83 PASS AC=2;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 1/1:0,19:19:57:734,57,0:0,0,6,13 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 0/1:3,5:8:67:160,0,67:2,1,4,1 chr2 47220341 . C T 233.01 PASS AC=1;AF=0.538;AN=2;DP=350;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant8-variant11-variant17-variant18-variant23-variant24-variant26-variant30-variant31-variant36 GT:AD:DP:GQ:PL:SB 0/1:10,14:24:99:349,0,249:8,2,9,5 chr2 47220448 . C CT 1074.68 PASS AC=1;AF=0.605;AN=2;DP=1606;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant11-variant15-variant17-variant18-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:37,23:60:99:667,0,1183:25,12,11,12 chr2 47220622 . G A 1363.32 PASS AC=1;AF=0.605;AN=2;DP=2587;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant11-variant15-variant17-variant18-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:66,62:128:99:1328,0,1654:27,39,31,31 chr2 47221693 . A G 429.54 PASS AC=1;AF=0.605;AN=2;DP=1451;MQ=60;set=variant-variant2-variant3-variant7-variant8-variant11-variant15-variant17-variant18-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:36,34:70:99:860,0,987:9,27,11,23 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 0/1:1,4:5:31:165,0,31:1,0,1,3 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 0/1:68,80:148:99:1911,0,1775:37,31,45,35 chr2 47251510 . G C 1151.44 PASS AC=1;AF=0.531;AN=2;DP=2739;MQ=60;set=variant-variant2-variant3-variant5-variant8-variant10-variant11-variant15-variant23-variant26-variant28-variant29-variant33-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:84,82:166:99:2064,0,2159:45,39,43,39 chr2 47251634 . T C 1454.14 PASS AC=2;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 1/1:0,87:87:99:2674,261,0:0,0,31,56 chr2 47251698 . T C 146.42 PASS AC=1;AF=0.529;AN=2;DP=575;MQ=60;set=variant-variant2-variant3-variant5-variant8-variant10-variant11-variant15-variant17-variant23-variant26-variant28-variant29-variant33-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,16:25:99:510,0,292:0,9,4,12 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 0/1:12,12:24:99:346,0,342:8,4,8,4 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 0/1:21,6:27:99:148,0,633:9,12,2,4 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 0/1:18,7:25:99:175,0,509:6,12,1,6 chr2 47273732 . G A 237.08 PASS AC=2;AF=0.528;AN=2;DP=259;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant7-variant8-variant10-variant15-variant17-variant23-variant26-variant28-variant29-variant33-variant34-variant37-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:173,18,0:0,0,1,5 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 0/1:13,20:33:99:582,0,417:12,1,14,6 chr2 47277207 . C A 1502.72 PASS AC=2;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 1/1:2,113:115:99:4960,247,0:1,1,50,63 chr2 47277208 . A G 1502.72 PASS AC=2;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 1/1:2,112:114:99:4960,247,0:1,1,49,63 chr2 47278901 . G A 639.44 PASS AC=1;AF=0.5;AN=2;DP=158;FractionInformativeReads=1;MQ=60;set=variant14-variant16-variant23-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:9,20:29:99:459,0,179:5,4,11,9 chr2 47301029 . A G 1418.07 PASS AC=1;AF=0.5;AN=2;DP=1519;MQ=60;set=variant7-variant14-variant17-variant23-variant28-variant29-variant34-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:57,75:132:99:2025,0,1412:25,32,33,42 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 1/1:0,92:92:99:2786,275,0:0,0,42,50 chr2 47301624 . T TTGGGGCCTC 2690.3 PASS AC=1;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 0/1:26,32:58:99:1307,0,1501:13,13,14,18 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 1/1:0,75:75:99:2364,225,0:0,0,42,33 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 1/1:0,99:99:99:2860,296,0:0,0,49,50 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 1/1:0,63:63:99:2016,189,0:0,0,24,39 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 1/1:0,22:22:66:774,66,0:0,0,16,6 chr2 47348155 . G A 424.63 PASS AC=1;AF=0.5;AN=2;DP=168;MQ=60;set=variant12-variant17-variant19-variant21-variant23-variant31-variant32-variant36 GT:AD:DP:GQ:PL:SB 0/1:7,13:20:99:525,0,466:6,1,7,6 chr2 47348156 . C A 424.63 PASS AC=1;AF=0.5;AN=2;DP=169;MQ=60;set=variant12-variant17-variant19-variant21-variant23-variant31-variant32-variant36 GT:AD:DP:GQ:PL:SB 0/1:7,13:20:99:525,0,466:6,1,7,6 chr2 47348347 . C T 3276.35 PASS AC=1;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 0/1:54,43:97:99:929,0,1341:27,27,22,21 chr2 47357458 . A G 1952.46 PASS AC=1;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 0/1:46,22:68:99:548,0,1182:18,28,7,15 chr2 47357564 . A T 297.18 PASS AC=2;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 1/1:0,11:11:33:461,33,0:0,0,0,11 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 0/1:17,21:38:99:486,0,492:6,11,9,12 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 1/1:0,57:57:99:1867,171,0:0,0,39,18 chr2 47382606 . T A 499.66 PASS AC=1;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 0/1:9,14:23:99:455,0,276:1,8,2,12 chr2 47572363 . G C 1036.29 PASS AC=1;AF=0.591;AN=2;DP=532;MQ=60;set=variant2-variant4-variant15-variant17-variant20-variant23-variant25-variant30-variant31-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,16:46:99:359,0,764:14,16,7,9 chr2 47596853 . C CG 2052.57 PASS AC=1;AF=0.5;AN=2;DP=456;MQ=60;set=variant23-variant30-variant31 GT:AD:DP:GQ:PL:SB 0/1:77,70:147:99:2090,0,2286:45,32,41,29 chr2 47601106 . T C 2991.84 PASS AC=2;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 1/1:0,130:130:99:4102,390,0:0,0,66,64 chr2 47601257 . T C 1286.27 PASS AC=2;AF=0.667;AN=2;DP=555;FractionInformativeReads=1;MQ=60;set=variant15-variant23-variant25-variant30-variant31-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2924,275,0:0,0,37,55 chr2 47601407 . A G 704.9 PASS AC=2;AF=0.643;AN=2;DP=285;FractionInformativeReads=1;MQ=60;set=variant15-variant23-variant25-variant30-variant31-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,38:40:70:1078,70,0:1,1,14,24 chr2 47604118 . A AT 677.14 PASS AC=1;AF=0.5;AN=2;DP=293;MQ=60;set=variant15-variant23-variant25-variant31-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,13:27:99:291,0,302:9,5,8,5 chr2 47604148 . T C 1507.59 PASS AC=1;AF=0.5;AN=2;DP=382;FractionInformativeReads=1;MQ=60;set=variant15-variant23-variant25-variant31-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,26:47:99:637,0,577:14,7,15,11 chr2 47604866 . C T 478.61 PASS AC=1;AF=0.5;AN=2;DP=153;FractionInformativeReads=1;MQ=60;set=variant15-variant23-variant25-variant30-variant31-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,11:27:99:252,0,460:7,9,5,6 chr2 47605107 . C T 48.22 PASS AC=1;AF=0.5;AN=2;DP=11;FS=0;MQ=60;SOR=0.693;set=variant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:44:78,0,44:0,2,0,2 chr2 47612156 . A G 109.65 PASS AC=1;AF=0.5;AN=2;DP=35;FractionInformativeReads=1;MQ=60;set=variant23-variant30-variant31 GT:AD:DP:GQ:PL:SB 0/1:11,6:17:99:138,0,307:8,3,3,3 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 0/1:53,26:79:99:475,0,1186:23,30,10,16 chr2 47641559 . TAAAAAA TAAA,TAAAAA,T,TAAAA,TA,TAA 280.44 PASS AC=0,0,1,0,0,1;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 3/6:13:86:0,1,7,5 chr2 47643274 . C T 172.69 PASS AC=2;AF=0.583;AN=2;DP=47;FS=0;FractionInformativeReads=1;MQ=60;set=variant16-variant21-variant22-variant23-variant37-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:82,6,0:0,0,2,0 chr2 47656801 . G A 97.98 PASS AC=2;AF=0.806;AN=2;DP=93;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant10-variant15-variant16-variant17-variant18-variant21-variant23-variant25-variant26-variant28-variant30-variant31-variant33-variant36-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:94,9,0:0,0,2,1 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 1/1:0,12:12:36:449,36,0:0,0,10,2 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 0/1:12,22:34:99:806,0,533:5,7,6,16 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 0/1:12,17:29:99:685,0,545:5,7,5,12 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 0/1:38,18:56:99:456,0,873:17,21,7,11 chr2 47702052 . T TAGG 179 PASS AC=1;AF=0.5;AN=2;DP=73;FS=0;MQ=60;set=variant15-variant23-variant25-variant31-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:241,0,257:5,1,5,1 chr2 47702102 . G A 311.54 PASS AC=1;AF=0.5;AN=2;DP=209;FractionInformativeReads=1;MQ=60;set=variant15-variant23-variant25-variant31-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,13:33:99:295,0,621:17,3,8,5 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 1/1:0,7:7:21:315,21,0:0,0,7,0 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 0/1:4,3:7:81:81,0,126:4,0,3,0 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 1/1:0,100:100:99:2985,299,0:0,0,45,55 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 1/1:0,32:32:96:1035,96,0:0,0,13,19 chr2 47748292 . A G 6293.49 PASS AC=1;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 0/1:82,110:192:99:2874,0,2056:40,42,56,54 chr2 47797123 . G A 384.33 PASS AC=1;AF=0.5;AN=2;DP=110;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:7,10:17:99:277,0,145:5,2,6,4 chr2 47798037 . A G 656.51 PASS AC=2;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 1/1:0,45:45:99:1490,135,0:0,0,17,28 chr2 48010145 . A G 62.99 PASS AC=2;AF=1;AN=2;DP=3;FS=0;FractionInformativeReads=1;MQ=60;QD=21;SOR=1.179;set=variant23 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:91,9,0:0,0,2,1 chr2 48010488 . G A 2407.38 PASS AC=1;AF=0.536;AN=2;DP=2760;MQ=60;set=variant-variant2-variant4-variant5-variant11-variant14-variant15-variant21-variant22-variant23-variant24-variant28-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:87,94:181:99:2081,0,2220:37,50,43,51 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 0/1:8,6:14:99:147,0,200:6,2,4,2 chr2 48022900 . A G 34.46 PASS AC=2;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 1/1:0,7:7:21:263,21,0:0,0,6,1 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 0/1:16,17:33:99:524,0,364:6,10,7,10 chr2 48025694 . C T 358.09 PASS AC=1;AF=0.556;AN=2;DP=137;MQ=60;set=variant6-variant7-variant12-variant19-variant22-variant23-variant30-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,7:17:99:210,0,276:7,3,6,1 chr2 48025764 . C T 640.76 PASS AC=1;AF=0.5;AN=2;DP=448;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant12-variant19-variant22-variant23-variant30-variant31-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,22:53:99:569,0,764:18,13,17,5 chr2 48030458 . G C 497.3 PASS AC=2;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 1/1:0,36:36:99:1302,108,0:0,0,30,6 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 0/1:34,29:63:99:773,0,910:12,22,11,18 chr2 48032874 . ACTAT A 1073.15 PASS AC=2;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 1/1:0,52:52:99:2300,157,0:0,0,22,30 chr2 48032937 . T C 410.43 PASS AC=2;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 1/1:0,23:23:69:935,69,0:0,0,2,21 chr2 48033272 . ATTTTTGTTTTAATTCCT A 452.45 PASS AC=1;AF=0.542;AN=2;DP=439;MQ=60;set=variant6-variant7-variant12-variant13-variant19-variant22-variant23-variant24-variant30-variant31-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,18:37:99:699,0,2936:11,8,17,1 chr2 48033546 . C CT 1909.81 PASS AC=1;AF=0.55;AN=2;DP=1152;MQ=60;set=variant6-variant7-variant12-variant19-variant22-variant23-variant30-variant31-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:47,38:85:99:1118,0,1417:24,23,20,18 chr2 48033551 . C G 1714.99 PASS AC=2;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 1/1:0,86:86:99:3132,258,0:0,0,45,41 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 0/1:24:99:6,5,9,4 chr2 48034806 . TA T 778.96 PASS AC=2;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 1/1:0,74:74:99:2041,222,0:0,0,27,47 chr2 48035631 . TTTATA T 247.62 PASS AC=1;AF=0.55;AN=2;DP=132;MQ=60;set=variant6-variant7-variant12-variant19-variant22-variant23-variant30-variant31-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:277,0,304:0,5,1,6 chr2 48040285 . A C 2401.09 PASS AC=1;AF=0.5;AN=2;DP=1692;MQ=60;set=variant8-variant17-variant18-variant20-variant23-variant29-variant30-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:80,68:148:99:1605,0,2266:43,37,32,36 chr2 48040564 . ATTTTT ATTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTTTTTTT,ATTTTTTTTTTT,ATTTTTTTTTT,ATTTTTTTTT,ATTT,A,ATTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTTTT,ATTTTTTT,ATTTTTTTTTTTT 34.52 PASS AC=0,0,0,0,2,0,0,0,0,0,0,0;AF=0.067,0.033,0.033,0.067,0.167,0.033,0.033,0.067,0.033,0.1,0.067,0.033;AN=2;DP=238;FS=0;set=variant2-variant7-variant9-variant15-variant16-variant17-variant21-variant23-filterInvariant24-variant27-variant28-variant29-variant36-variant38-variant41 GT:DP:GQ:SB 5/5:2:5:0,0,0,2 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 1/1:0,77:77:99:2428,237,0:0,0,45,32 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 0/1:33,15:48:99:238,0,624:21,12,10,5 chr2 48063241 . G C 37.69 PASS AC=1;AF=0.55;AN=2;DP=71;FS=0;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant12-variant19-variant22-variant23-variant30-variant31-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:63:63,0,165:0,4,0,2 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 0/1:9,11:20:99:247,0,184:5,4,6,5 chr2 48586409 . ATTTAGTT A 199.36 PASS AC=1;AF=0.542;AN=2;DP=171;MQ=60;set=variant8-variant12-variant18-variant20-variant23-variant29-variant31-variant32-variant34-variant36-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:263,0,207:0,4,1,6 chr2 48600589 . C T 124.48 PASS AC=1;AF=0.5;AN=2;DP=8;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.922;QD=15.56;ReadPosRankSum=-0.922;SOR=0.693;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:153,0,109:1,3,1,3 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 0/1:62,65:127:99:1683,0,1655:30,32,33,32 chr2 48603483 . A C 2652.52 PASS AC=1;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 0/1:94,120:214:99:2889,0,2252:43,51,55,65 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 0/1:211,198:409:99:4906,0,5537:97,114,82,116 chr2 48667883 . T C 683.17 PASS AC=1;AF=0.545;AN=2;DP=369;MQ=60;set=variant7-variant8-variant12-variant19-variant22-variant23-variant27-variant30-variant31-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,22:36:99:581,0,337:10,4,15,7 chr2 48667927 . G C 993.77 PASS AC=1;AF=0.545;AN=2;DP=679;FractionInformativeReads=1;MQ=60;set=variant7-variant8-variant12-variant19-variant22-variant23-variant27-variant30-variant31-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:34,34:68:99:810,0,850:23,11,21,13 chr2 48667951 . CGCG C,CGCGGCG,CGCGGCGGCG 49.18 PASS AC=0,1,0;AF=0.313,0.125,0.104;AN=2;DP=1618;MQ=60;set=filterInvariant3-variant7-variant8-filterInvariant9-variant10-variant12-variant14-filterInvariant15-filterInvariant16-variant18-variant19-variant22-variant23-variant24-filterInvariant26-filterInvariant28-variant30-variant31-filterInvariant32-variant37-variant39-variant41-variant42-variant43 GT:DP:GQ:SB 0/2:67:99:24,13,15,15 chr2 48687120 . A T 714.18 PASS AC=1;AF=0.5;AN=2;DP=380;MQ=60;set=variant8-variant18-variant19-variant23-variant27-variant42 GT:AD:DP:GQ:PL:SB 0/1:21,22:43:99:674,0,634:10,11,11,11 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 0/1:8,7:15:99:186,0,195:5,3,5,2 chr2 48732670 . C T 977.18 PASS AC=1;AF=0.55;AN=2;DP=1144;MQ=60;set=variant8-variant12-variant17-variant20-variant23-variant30-variant32-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,64:134:99:1562,0,1861:45,25,38,26 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 1/1:0,115:115:99:3474,345,0:0,0,46,69 chr2 48738388 . C T 441.06 PASS AC=1;AF=0.567;AN=2;DP=426;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant8-variant10-variant15-variant16-variant19-variant21-variant23-variant26-variant27-variant28-variant36 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:178,0,351:9,1,5,1 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 0/1:13,9:22:99:217,0,399:3,10,3,6 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 2/2:6:20:0,0,3,3 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 0/1:10,17:27:99:400,0,166:5,5,7,10 chr2 48757264 . C G 120.47 PASS AC=1;AF=0.5;AN=2;DP=45;set=variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:149,0,137:2,4,3,2 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 0/1:16,9:25:99:246,0,415:9,7,4,5 chr2 48807593 . GT G 69.95 PASS AC=2;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 1/1:0,11:11:33:315,33,0:0,0,10,1 chr2 48807796 . A C 2439.65 PASS AC=2;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 1/1:0,191:191:99:5570,572,0:0,0,91,100 chr2 48807976 . T C 2625.24 PASS AC=2;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 1/1:0,136:136:99:4225,408,0:0,0,74,62 chr2 48808152 . G C 2115.77 PASS AC=2;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 1/1:0,153:153:99:4847,458,0:0,0,79,74 chr2 48808594 . C T 3029.91 PASS AC=2;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 1/1:0,171:171:99:5226,511,0:0,0,84,87 chr2 48808882 . T A 1216.77 PASS AC=2;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 1/1:0,55:55:99:1908,165,0:0,0,28,27 chr2 48808898 . C T 1161.64 PASS AC=2;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 1/1:0,56:56:99:1951,168,0:0,0,29,27 chr2 48809593 . G T 1297.05 PASS AC=2;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 1/1:0,91:91:99:2845,272,0:0,0,51,40 chr2 48809756 . T C 908.43 PASS AC=2;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 1/1:2,59:61:99:1949,134,0:1,1,22,37 chr2 48809873 . T C 388.27 PASS AC=2;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 1/1:0,22:22:65:710,65,0:0,0,5,17 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 0/1:13,18:31:99:505,0,397:2,11,6,12 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 0/1:38,44:82:99:1162,0,973:21,17,27,17 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 0/1:110,114:224:99:2742,0,2824:62,48,64,50 chr2 48824650 . G A 913.59 PASS AC=1;AF=0.611;AN=2;DP=604;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant11-variant14-variant15-variant17-variant19-variant23-variant24-variant28-variant29-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,16:39:99:603,0,1180:12,11,12,4 chr2 48824652 . T C 913.59 PASS AC=1;AF=0.611;AN=2;DP=610;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant11-variant14-variant15-variant17-variant19-variant23-variant24-variant28-variant29-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,16:39:99:603,0,1180:12,11,12,4 chr2 48824698 . T C 572.71 PASS AC=1;AF=0.611;AN=2;DP=791;MQ=60;set=variant2-variant5-variant7-variant11-variant14-variant15-variant17-variant19-variant23-variant24-variant28-variant29-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,26:48:99:642,0,508:13,9,16,10 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 0/1:22,15:37:99:429,0,770:15,7,10,5 chr2 48825139 . A C 745.81 PASS AC=1;AF=0.611;AN=2;DP=1138;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant11-variant14-variant15-variant17-variant19-variant23-variant24-variant28-variant29-variant36-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,30:49:99:1004,0,534:13,6,22,8 chr2 48844968 . C G 4131.71 PASS AC=1;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 0/1:66,70:136:99:1646,0,1665:34,32,33,37 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 0/1:1,8:9:15:235,0,15:0,1,2,6 chr2 48873662 . T C 706.07 PASS AC=1;AF=0.5;AN=2;DP=453;FractionInformativeReads=1;MQ=60;set=variant5-variant20-variant23-variant25-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:38,30:68:99:718,0,867:22,16,18,12 chr2 48873925 . A G 1302.04 PASS AC=1;AF=0.5;AN=2;DP=581;FractionInformativeReads=1;MQ=60;set=variant5-variant20-variant23-variant25-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:26,57:83:99:1490,0,574:14,12,31,26 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 1/1:0,154:154:99:4159,459,0:0,0,72,82 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 1/1:0,143:143:99:4301,429,0:0,0,73,70 chr2 48914688 . A G 3290.8 PASS AC=1;AF=0.583;AN=2;DP=1649;MQ=60;set=variant5-variant20-variant23-variant25-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:154,129:283:99:3137,0,3791:78,76,69,60 chr2 48915871 . A G 4141.44 PASS AC=1;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 0/1:46,64:110:99:1494,0,904:21,25,30,34 chr2 48921375 . T C 2119.41 PASS AC=1;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 0/1:26,23:49:99:604,0,668:13,13,13,10 chr2 48921438 . T C 959.58 PASS AC=1;AF=0.5;AN=2;DP=451;FractionInformativeReads=1;MQ=60;set=variant5-variant20-variant23-variant25-variant34-variant38 GT:AD:DP:GQ:PL:SB 0/1:25,27:52:99:684,0,523:13,12,10,17 chr2 48925746 . C T 1328.99 PASS AC=2;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 1/1:0,48:48:99:1390,144,0:0,0,26,22 chr2 48925986 . ATT AT,A 102.15 PASS AC=0,2;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 2/2:2:6:0,0,1,1 chr2 48948707 . A C 4666.41 PASS AC=2;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 1/1:2,280:282:99:8697,811,0:1,1,150,130 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 1/1:0,8:8:24:282,24,0:0,0,7,1 chr2 48956417 . C T 683.42 PASS AC=1;AF=0.5;AN=2;DP=588;MQ=60;set=variant15-variant16-variant20-variant21-variant23-variant24-variant25-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:29,16:45:99:419,0,895:11,18,5,11 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 0/1:16,27:43:99:813,0,428:6,10,10,17 chr2 48960317 . A G 306.82 PASS AC=1;AF=0.55;AN=2;DP=798;FractionInformativeReads=1;MQ=60;set=variant2-variant10-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant22-variant23-variant24-variant27-variant28-variant32-variant34-variant36-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,19:38:99:522,0,517:6,13,5,14 chr2 48982755 . G GGCTGCA 1975.13 PASS AC=1;AF=0.528;AN=2;DP=1717;MQ=60;set=variant2-variant8-variant12-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant27-variant28-variant32-variant36-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,37:83:99:1524,0,2270:27,19,20,17 chr2 49003566 . C T 915.34 PASS AC=1;AF=0.5;AN=2;DP=789;MQ=60;set=variant13-variant15-variant16-variant21-variant23-variant24-variant33-variant34-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:28,27:55:99:641,0,715:10,18,10,17 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 0/1:67,63:130:99:1573,0,1659:30,37,25,38 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 0/1:32,23:55:99:523,0,933:12,20,9,14 chr2 49215977 . G A 533.84 PASS AC=1;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 0/1:19,12:31:99:325,0,538:14,5,8,4 chr2 49216284 . C T 230.15 PASS AC=1;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 0/1:12,5:17:99:166,0,430:1,11,1,4 chr2 49286879 . C A 1072.29 PASS AC=1;AF=0.537;AN=2;DP=2551;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant6-variant8-variant11-variant12-variant14-variant15-variant16-variant18-variant20-variant22-variant23-variant27-variant29-variant30-variant31-variant32-variant33-variant36-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,32:89:99:618,0,1293:30,27,15,17 chr2 49381585 . C T 151.64 PASS AC=1;AF=0.5;AN=2;DP=518;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant11-variant15-variant18-variant20-variant23-variant29-variant33-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,15:26:99:441,0,252:5,6,7,8 chr2 49381696 . CTTTT CT,CTTT,CTT,CTTTTT,C 152.26 PASS AC=1,0,0,0,0;AF=0.278,0.222,0.019,0.019,0.019;AN=2;DP=548;MQ=60;set=variant2-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-filterInvariant27-variant28-variant29-variant32-variant33-variant36-variant38-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:8:61:1,1,2,4 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 0/1:11,13:24:99:340,0,278:11,0,8,5 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 0/1:43,44:87:99:1049,0,1149:21,22,22,22 chr2 50147835 . CGTGTGTGTGTGTGTGTGT CGTGTGTGT,CGTGTGTGTGTGT,CGTGTGTGTGTGTGTGT,CGTGTGTGTGT,CGTGTGTGTGTGTGT,C,CGTGTGT,CGTGTGTGTGTGTGTGTGTGTGT,CGT 2706.54 PASS AC=0,0,1,1,0,0,0,0,0;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 4/3:62:99:0,7,25,30 chr2 50201110 . A G 865.02 PASS AC=2;AF=0.864;AN=2;DP=4277;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,90:90:99:2700,268,0:0,0,54,36 chr2 50201383 . G A 278.1 PASS AC=1;AF=0.6;AN=2;DP=798;MQ=60;set=variant-variant5-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant20-variant21-variant23-variant28-variant29-variant31-variant33-variant34-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,15:24:99:527,0,298:1,8,1,14 chr2 50280283 . T C 500.47 PASS AC=2;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 1/1:0,14:14:42:540,42,0:0,0,11,3 chr2 50280338 . G A 1185.33 PASS AC=2;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 1/1:0,41:41:99:1281,123,0:0,0,27,14 chr2 50434741 . C T 279.45 PASS AC=2;AF=0.583;AN=2;DP=869;MQ=60;set=variant6-variant9-variant11-variant14-variant16-variant19-variant21-variant23-variant26-variant27-variant28-variant31-variant32-variant36-variant37-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:1286,137,0:0,0,27,19 chr2 50434759 . C G 656.74 PASS AC=2;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 1/1:0,53:53:99:1481,159,0:0,0,29,24 chr2 50574485 . A G 2153.32 PASS AC=2;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 1/1:0,119:119:99:3844,355,0:0,0,63,56 chr2 50692459 . T A 484.96 PASS AC=1;AF=0.697;AN=2;DP=1526;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant36-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,28:48:99:772,0,577:17,3,21,7 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 0/1:101,83:184:99:1937,0,2407:59,42,48,35 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 1/1:0,30:30:90:1066,90,0:0,0,7,23 chr2 50693363 . A T 466.32 PASS AC=1;AF=0.563;AN=2;DP=166;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant8-variant11-variant17-variant19-variant23-variant24-variant25-variant27-variant37-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:250,0,146:4,0,7,0 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 0/1:42,36:78:99:1359,0,1707:23,19,19,17 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 0/1:4,8:12:99:309,0,139:4,0,8,0 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 1/1:0,44:44:99:1426,132,0:0,0,18,26 chr2 50733958 . T C 190.09 PASS AC=1;AF=0.611;AN=2;DP=320;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant10-variant12-variant13-variant15-variant16-variant18-variant20-variant22-variant23-variant24-variant26-variant28-variant30-variant32-variant33-variant34-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:192,0,199:1,5,0,5 chr2 50758657 . T C 390.13 PASS AC=2;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 1/1:0,30:30:90:1060,90,0:0,0,8,22 chr2 50858107 . T A 1313.63 PASS AC=2;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 1/1:0,44:44:99:1360,132,0:0,0,26,18 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 1/1:0,38:38:99:1166,114,0:0,0,21,17 chr2 50966283 . C T 3906.35 PASS AC=2;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 1/1:0,82:82:99:2423,246,0:0,0,48,34 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 0/1:73,77:150:99:1834,0,1859:42,31,37,40 chr2 51146150 . A AG 14735.5 PASS AC=2;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 1/1:1,315:316:99:11108,916,0:1,0,132,183 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 0/1:7,13:20:99:322,0,176:4,3,8,5 chr2 51153279 . T C 469.81 PASS AC=1;AF=0.5;AN=2;DP=44;FS=1.45;FractionInformativeReads=1;MQ=60;MQRankSum=-0.988;QD=10.68;ReadPosRankSum=-0.651;SOR=1.112;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:27,17:44:99:498,0,805:7,20,3,14 chr2 51191244 . C T 276.98 PASS AC=1;AF=0.5;AN=2;DP=193;MQ=60;set=variant9-variant15-variant16-variant18-variant20-variant22-variant23-variant26-variant27-variant31-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,4:15:77:77,0,404:1,10,1,3 chr2 51206342 . C G 626.97 PASS AC=2;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 1/1:0,64:64:99:2068,192,0:0,0,43,21 chr2 51254478 . G A 191.94 PASS AC=2;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 1/1:0,35:35:99:1008,105,0:0,0,21,14 chr2 51255692 . A G 287.5 PASS AC=2;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 1/1:0,41:41:99:1170,123,0:0,0,22,19 chr2 51255832 . T G 478.15 PASS AC=2;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 1/1:0,40:40:99:1266,120,0:0,0,23,17 chr2 51259644 . AAGAAAGAGAGAGAGAGAGAGAGAGAGAG AAGAGAGAGAGAG,AAGAGAGAGAGAGAG,A,AAGAGAGAGAGAGAGAG 241.12 PASS AC=0,1,1,0;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 3/2:8:99:0,0,2,6 chr2 53832072 . C T 1479.73 PASS AC=1;AF=0.636;AN=2;DP=855;MQ=60;set=variant3-variant6-variant12-variant19-variant20-variant23-variant24-variant28-variant29-variant30-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,35:73:99:852,0,876:15,23,12,23 chr2 53897429 . ATTTTTTTT ATTTTTTT,ATTTTTT,ATTTTT,AT,A 1302.24 PASS AC=0,0,0,1,0;AF=0.266,0.141,0.047,0.031,0.031;AN=2;DP=2877;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-filterInvariant10-filterInvariant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant23-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/4:69:99:20,15,18,16 chr2 53897525 . C G 3537.19 PASS AC=1;AF=0.583;AN=2;DP=2606;set=variant-variant4-variant10-variant18-variant20-variant23-variant34-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:104,115:219:99:2990,0,2578:55,49,63,52 chr2 53920931 . G A 399.59 PASS AC=1;AF=0.571;AN=2;DP=337;MQ=60;set=variant-variant4-variant10-variant18-variant20-variant23-variant26-variant34-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,18:28:99:588,0,277:9,1,16,2 chr2 53921270 . C T 244.62 PASS AC=1;AF=0.6;AN=2;DP=110;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant10-variant18-variant20-variant23-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:232,0,265:0,7,1,6 chr2 53955850 . C T 929.87 PASS AC=1;AF=0.577;AN=2;DP=796;MQ=60;set=variant-variant7-variant10-variant12-variant18-variant20-variant23-variant34-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,34:54:99:849,0,466:14,6,21,13 chr2 53956883 . T G 541.92 PASS AC=1;AF=0.567;AN=2;DP=648;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant7-variant10-variant12-variant18-variant20-variant23-variant34-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,15:51:99:335,0,1057:11,25,4,11 chr2 54002064 . C A 1175.44 PASS AC=1;AF=0.571;AN=2;DP=1225;MQ=60;set=variant-variant4-variant7-variant10-variant12-variant18-variant20-variant23-variant34-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,37:75:99:924,0,967:16,22,14,23 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 0/1:36,25:61:99:622,0,1001:14,22,13,12 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 0/1:8,7:15:99:149,0,180:3,5,2,5 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 0/1:25,19:44:99:478,0,538:15,10,12,7 chr2 54035374 . A G 527.02 PASS AC=1;AF=0.563;AN=2;DP=555;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant7-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant23-variant25-variant27-variant31-variant32-variant34-variant37-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,11:14:53:384,0,53:2,1,10,1 chr2 54035447 . A G 1153.03 PASS AC=1;AF=0.571;AN=2;DP=1059;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant7-variant10-variant12-variant18-variant20-variant23-variant34-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,36:52:99:1020,0,421:12,4,23,13 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 0/1:56,47:103:99:1081,0,1173:30,26,28,19 chr2 54081923 . T G 1093.39 PASS AC=1;AF=0.5;AN=2;DP=279;MQ=60;set=variant23-variant26-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,41:73:99:1122,0,724:14,18,14,27 chr2 54115845 . T A 493.27 PASS AC=1;AF=0.5;AN=2;DP=247;MQ=60;set=variant22-variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:28,38:66:99:798,0,792:21,7,26,12 chr2 54120185 . G A 184.46 PASS AC=1;AF=0.5;AN=2;DP=33;FractionInformativeReads=1;MQ=60;set=variant22-variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:121,0,138:0,4,0,4 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 0/1:41,51:92:99:1201,0,886:18,23,25,26 chr2 54122956 . A G 419.99 PASS AC=1;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 0/1:13,12:25:99:340,0,432:2,11,3,9 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 0/1:50,51:101:99:1069,0,1162:23,27,27,24 chr2 54131154 . C T 638.52 PASS AC=1;AF=0.5;AN=2;DP=136;FractionInformativeReads=1;MQ=60;set=variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:36,28:64:99:667,0,938:24,12,17,11 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 0/1:6,5:11:99:151,0,199:1,5,1,4 chr2 54150237 . A G 1003.31 PASS AC=1;AF=0.5;AN=2;DP=241;FractionInformativeReads=1;MQ=60;set=variant22-variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:39,27:66:99:605,0,931:18,21,14,13 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 0/1:15,15:30:99:396,0,388:3,12,4,11 chr2 54160059 . T C 88.29 PASS AC=1;AF=0.5;AN=2;DP=21;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:76:117,0,76:0,2,0,3 chr2 54197829 . C A 1450.14 PASS AC=1;AF=0.5;AN=2;DP=336;FractionInformativeReads=1;MQ=60;set=variant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:80,71:151:99:1533,0,1699:37,43,31,40 chr2 54343012 . C A 351.52 PASS AC=2;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 1/1:0,28:28:84:948,84,0:0,0,10,18 chr2 54369588 . A G 448.06 PASS AC=2;AF=0.567;AN=2;DP=413;FractionInformativeReads=1;MQ=60;set=variant4-variant9-variant13-variant16-variant22-variant23-variant26-variant27-variant34-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:62:643,62,0:0,0,5,16 chr2 54370348 . C T 4530.48 PASS AC=2;AF=0.563;AN=2;DP=2836;MQ=60;set=variant4-variant9-variant13-variant16-variant17-variant22-variant23-variant26-variant27-variant34-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,165:165:99:7169,499,0:0,0,71,94 chr2 54370356 . A G 4404.43 PASS AC=2;AF=0.563;AN=2;DP=2597;FractionInformativeReads=1;MQ=60;set=variant4-variant9-variant13-variant16-variant17-variant22-variant23-variant26-variant27-variant34-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,153:153:99:6998,476,0:0,0,62,91 chr2 54480245 . G A 183.95 PASS AC=1;AF=0.583;AN=2;DP=93;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant16-variant23-variant29-variant41 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:177,0,199:5,0,5,0 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 0/1:34,38:72:99:980,0,1370:23,11,26,12 chr2 54480336 . A T 1058.56 PASS AC=1;AF=0.583;AN=2;DP=577;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant16-variant23-variant29-variant41 GT:AD:DP:GQ:PL:SB 0/1:41,41:82:99:1035,0,1563:28,13,27,14 chr2 54480369 . C A 2099.61 PASS AC=2;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 1/1:0,124:124:99:3708,371,0:0,0,76,48 chr2 54481076 . CTTT C 2157.08 PASS AC=1;AF=0.571;AN=2;DP=645;MQ=60;set=variant6-variant10-variant16-variant23-variant29-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:42,44:86:99:1685,0,1972:23,19,23,21 chr2 54481592 . C G 808.66 PASS AC=2;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 1/1:0,55:55:99:1910,165,0:0,0,28,27 chr2 54481636 . T C 876.06 PASS AC=1;AF=0.571;AN=2;DP=309;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant16-variant23-variant29-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,27:47:99:710,0,451:12,8,12,15 chr2 54482703 . GGGGCCC G 3578.05 PASS AC=1;AF=0.556;AN=2;DP=1949;MQ=60;set=variant6-variant10-variant16-variant22-variant23-variant29-variant37-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:71,105:176:99:4032,0,3656:29,42,44,61 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 0/1:80,95:175:99:2512,0,1960:44,36,50,45 chr2 54482989 . C T 3254.47 PASS AC=1;AF=0.5;AN=2;DP=1625;MQ=60;set=variant6-variant16-variant22-variant23-variant29-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:102,99:201:99:2498,0,2509:58,44,54,45 chr2 54483443 . T C 720.17 PASS AC=2;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 1/1:0,46:46:99:1464,138,0:0,0,15,31 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 1/1:0,20:20:60:691,60,0:0,0,16,4 chr2 54494448 . G A 679.12 PASS AC=1;AF=0.556;AN=2;DP=764;FractionInformativeReads=1;MQ=60;set=variant6-variant10-variant16-variant22-variant23-variant29-variant33-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:30,46:76:99:1031,0,675:20,10,26,20 chr2 54587596 . C T 4000.05 PASS AC=1;AF=0.711;AN=2;DP=4204;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-variant33-variant34-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,49:102:99:1275,0,1403:27,26,25,24 chr2 54587659 . G C 1950.42 PASS AC=1;AF=0.5;AN=2;DP=2201;MQ=60;set=variant4-variant6-variant7-variant8-variant9-variant10-variant12-variant16-variant22-variant23-variant29-variant31-variant33 GT:AD:DP:GQ:PL:SB 0/1:82,68:150:99:1712,0,2152:47,35,38,30 chr2 54588046 . G C 8070.42 PASS AC=1;AF=0.711;AN=2;DP=9282;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-variant33-variant34-variant36-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:96,111:207:99:2742,0,2470:42,54,45,66 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 1/1:0,102:102:99:2854,306,0:0,0,50,52 chr2 54785493 . A G 334.21 PASS AC=2;AF=0.577;AN=2;DP=253;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant8-variant10-variant13-variant14-variant23-variant29-variant31-variant33-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:652,69,0:0,0,14,9 chr2 54785705 . T C 1800.83 PASS AC=2;AF=0.6;AN=2;DP=1099;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant8-variant10-variant13-variant14-variant23-variant28-variant29-variant31-variant33-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,69:70:99:2185,164,0:0,1,33,36 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 1/1:0,284:284:99:8367,851,0:0,0,134,150 chr2 54844926 . T G 768.96 PASS AC=2;AF=0.563;AN=2;DP=392;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant8-variant10-variant13-variant14-variant18-variant23-variant29-variant31-variant33-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:669,66,0:0,0,7,15 chr2 54848494 . A ACC 1288.52 PASS AC=1;AF=0.5;AN=2;DP=411;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant10-variant13-variant23-variant29-variant31-variant33 GT:AD:DP:GQ:PL:SB 0/1:26,20:46:99:804,0,1929:15,11,12,8 chr2 54848495 . G C 1297.53 PASS AC=1;AF=0.5;AN=2;DP=419;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant10-variant13-variant23-variant29-variant31-variant33 GT:AD:DP:GQ:PL:SB 0/1:26,21:47:99:803,0,1929:15,11,13,8 chr2 54848728 . A G 1039.51 PASS AC=2;AF=0.611;AN=2;DP=496;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant8-variant10-variant13-variant14-variant18-variant19-variant23-variant28-variant29-variant31-variant33-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:457,39,0:0,0,3,10 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 1/1:0,69:69:99:2338,207,0:0,0,51,18 chr2 54855454 . G A 869.86 PASS AC=2;AF=0.571;AN=2;DP=402;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant8-variant10-variant13-variant14-variant23-variant29-variant31-variant33-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:1134,84,0:0,0,3,25 chr2 54858214 . A G 1359.24 PASS AC=1;AF=0.5;AN=2;DP=1441;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant10-variant13-variant23-variant29-variant31-variant33 GT:AD:DP:GQ:PL:SB 0/1:90,88:178:99:2310,0,2233:47,43,41,47 chr2 54858664 . C T 2193.06 PASS AC=2;AF=0.6;AN=2;DP=1845;MQ=60;set=variant-variant2-variant6-variant8-variant10-variant13-variant14-variant23-variant28-variant29-variant31-variant33-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,118:118:99:3684,353,0:0,0,44,74 chr2 54877146 . A G 817.78 PASS AC=2;AF=0.607;AN=2;DP=399;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant8-variant10-variant13-variant23-variant28-variant29-variant31-variant33-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,34:34:99:1180,102,0:0,0,10,24 chr2 54882381 . G A 4093.1 PASS AC=2;AF=0.607;AN=2;DP=1632;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant8-variant10-variant13-variant23-variant28-variant29-variant31-variant33-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,107:107:99:3476,320,0:0,0,39,68 chr2 54884870 . C T 697.76 PASS AC=2;AF=0.65;AN=2;DP=660;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant18-variant19-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:819,72,0:0,0,18,6 chr2 54888075 . G A 1586.33 PASS AC=2;AF=0.6;AN=2;DP=689;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant8-variant10-variant13-variant19-variant23-variant28-variant29-variant31-variant33-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:1,38:39:99:1183,106,0:1,0,20,18 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 1/1:0,307:307:99:9600,919,0:0,0,149,158 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 1/1:0,290:290:99:9529,869,0:0,0,142,148 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 1/1:0,201:201:99:6231,602,0:0,0,105,96 chr2 54889149 . T C 9231.82 PASS AC=2;AF=0.615;AN=2;DP=3051;MQ=60;set=variant-variant2-variant6-variant8-variant10-variant13-variant23-variant28-variant29-variant31-variant33-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,210:210:99:6618,630,0:0,0,108,102 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 1/1:0,42:42:99:1413,126,0:0,0,11,31 chr2 54895925 . AT A 1079.15 PASS AC=2;AF=0.6;AN=2;DP=830;MQ=60;set=variant-variant2-variant6-variant8-variant10-variant13-variant23-variant28-variant29-variant31-variant33-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,47:47:99:1320,139,0:0,0,25,22 chr2 54896377 . A AT,ATTTT,ATT,ATTT,ATTTTT 3316.09 PASS AC=2,0,0,0,0;AF=0.364,0.205,0.125,0.284,0.011;AN=2;DP=6478;set=Intersection GT:DP:GQ:SB 1/1:118:99:5,3,61,49 chr2 55040426 . A G 6406.02 PASS AC=2;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 1/1:0,161:161:99:4874,482,0:0,0,76,85 chr2 55071101 . TTGTG TTGTGTGTGTGTGTG,TTGTGTGTGTGTG,TTG,TTGTGTGTGTGTGTGTGTG,T,TTGTGTGTGTG,TTGTGTGTGTGTGTGTG,TTGTGTGTGTGTGTGTGTGTG,TTGTGTG,TTGTGTGTG 1208.79 PASS AC=0,1,0,0,0,0,1,0,0,0;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 2/7:19:99:1,0,14,4 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 0/1:5,2:7:69:69,0,200:4,1,2,0 chr2 55074875 . A AGG 477.36 PASS AC=1;AF=0.563;AN=2;DP=253;set=variant6-variant17-variant23-variant24-variant28-variant34-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,17:30:99:619,0,3314:6,7,5,12 chr2 55074878 . A ATCGTAG 477.36 PASS AC=1;AF=0.563;AN=2;DP=216;FractionInformativeReads=1;set=variant6-variant17-variant23-variant24-variant28-variant34-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:619,0,3314:6,7,3,12 chr2 55074880 . TA T 385.49 PASS AC=1;AF=0.563;AN=2;DP=191;FractionInformativeReads=1;set=variant6-variant17-variant23-variant24-variant28-variant34-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:12,13:25:99:591,0,3319:6,6,1,12 chr2 55074887 . G GT 304.52 PASS AC=1;AF=0.563;AN=2;DP=171;FractionInformativeReads=1;set=variant6-variant17-variant23-variant24-variant28-variant34-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:468,0,3282:5,6,1,11 chr2 55074889 . TC T 262.53 PASS AC=1;AF=0.563;AN=2;DP=165;FractionInformativeReads=1;set=variant6-variant17-variant23-variant24-variant28-variant34-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:471,0,3185:5,6,1,11 chr2 55074891 . TACGATCC T 223.55 PASS AC=1;AF=0.563;AN=2;DP=158;FractionInformativeReads=1;set=variant6-variant17-variant23-variant24-variant28-variant34-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:471,0,3185:5,6,1,10 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 0/1:15,8:23:99:283,0,549:14,1,8,0 chr2 55093842 . G A 837.36 PASS AC=1;AF=0.667;AN=2;DP=1152;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant9-variant11-variant13-variant15-variant17-variant19-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant33-variant34-variant36-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,19:44:99:433,0,597:14,11,12,7 chr2 55093859 . C G 688.26 PASS AC=1;AF=0.643;AN=2;DP=397;MQ=60;set=variant6-variant17-variant23-variant24-variant28-variant34-variant41 GT:AD:DP:GQ:PL:SB 0/1:35,25:60:99:534,0,818:20,15,15,10 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 0/1:43,26:69:99:622,0,1077:19,24,11,15 chr2 55138272 . G A 554.2 PASS AC=2;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 1/1:0,13:13:39:541,39,0:0,0,1,12 chr2 55155551 . C T 1439.63 PASS AC=1;AF=0.7;AN=2;DP=636;MQ=60;set=variant6-variant17-variant23-variant24-variant28 GT:AD:DP:GQ:PL:SB 0/1:74,50:124:99:1011,0,1730:40,34,28,22 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 0/1:48,76:124:99:1987,0,1155:30,18,35,41 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 0/1:47,34:81:99:823,0,1305:17,30,14,20 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 0/1:54,56:110:99:1307,0,1291:30,24,30,26 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 1/1:0,9:9:27:361,27,0:0,0,8,1 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 0/1:45:99:23,10,9,3 chr2 55186229 . T C 2627.07 PASS AC=1;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 0/1:65,46:111:99:1032,0,1497:32,33,25,21 chr2 55186394 . A C 2143.67 PASS AC=1;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 0/1:28,34:62:99:898,0,648:13,15,13,21 chr2 55187295 . G A 752.35 PASS AC=1;AF=0.625;AN=2;DP=1583;MQ=60;set=variant-variant6-variant10-variant11-variant13-variant14-variant17-variant23-variant24-variant26-variant28-variant36-variant38-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:43,55:98:99:1323,0,991:24,19,32,23 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 1/1:0,100:100:99:3888,300,0:0,0,58,42 chr2 55191321 . G A 1087.56 PASS AC=1;AF=0.75;AN=2;DP=195;FractionInformativeReads=1;MQ=60;MQRankSum=-0.106;ReadPosRankSum=0.145;set=variant23-variant24 GT:AD:DP:GQ:PL:SB 0/1:48,44:92:99:1116,0,1268:19,29,14,30 chr2 55197967 . A G 1313.92 PASS AC=1;AF=0.6;AN=2;DP=457;FractionInformativeReads=1;MQ=60;set=variant6-variant11-variant23-variant24-variant28 GT:AD:DP:GQ:PL:SB 0/1:36,37:73:99:1002,0,1068:25,11,24,13 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 0/1:97,79:176:99:1701,0,2350:50,47,41,38 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 0/1:101,75:176:99:1727,0,2425:51,50,35,40 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 0/1:78,53:131:99:1223,0,1800:40,38,24,29 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 0/1:28,41:69:99:1210,0,844:10,18,15,26 chr2 55199170 . CTT C 1792.23 PASS AC=1;AF=0.625;AN=2;DP=256;MQ=60;set=variant6-variant23-variant24-variant28 GT:AD:DP:GQ:PL:SB 0/1:25,24:49:99:933,0,967:12,13,14,10 chr2 55199931 . CT C,CTT 550.76 PASS AC=0,1;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 0/2:209:99:67,82,25,35 chr2 55201038 . C T 787.03 PASS AC=1;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 0/1:20,35:55:99:924,0,445:8,12,14,21 chr2 55214618 . A C 162.77 PASS AC=1;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 0/1:13,18:31:99:508,0,330:9,4,11,7 chr2 55258704 . C G 1111.02 PASS AC=1;AF=0.525;AN=2;DP=1645;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant16-variant20-variant23-variant27-variant30-variant32-variant33-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,34:70:99:938,0,878:23,13,24,10 chr2 55277226 . C T 1204.44 PASS AC=1;AF=0.625;AN=2;DP=386;FractionInformativeReads=1;MQ=60;set=variant6-variant23-variant24-variant28 GT:AD:DP:GQ:PL:SB 0/1:49,60:109:99:1457,0,1240:28,21,34,26 chr2 55277641 . C G 5117.59 PASS AC=1;AF=0.63;AN=2;DP=2884;MQ=60;set=variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant16-variant18-variant20-variant21-variant23-variant27-variant30-variant32-variant33-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:79,67:146:99:1551,0,1874:43,36,34,33 chr2 55277712 . C T 1414.57 PASS AC=1;AF=0.625;AN=2;DP=446;FractionInformativeReads=1;MQ=60;set=variant6-variant23-variant24-variant28 GT:AD:DP:GQ:PL:SB 0/1:61,69:130:99:1692,0,1487:30,31,34,35 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 1/1:0,66:66:99:2949,199,0:0,0,35,31 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 1/1:0,65:65:99:2949,199,0:0,0,34,31 chr2 55404925 . C T 646.99 PASS AC=1;AF=0.556;AN=2;DP=1108;MQ=60;set=variant3-variant4-variant7-variant9-variant11-variant12-variant14-variant18-variant20-variant23-variant26-variant27-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,29:55:99:723,0,722:8,18,9,20 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 1/1:0,113:113:99:3303,337,0:0,0,58,55 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 1/1:0,19:19:57:773,57,0:0,0,1,18 chr2 55436001 . CTTT CT,C,CTT 112.87 PASS AC=0,0,1;AF=0.464,0.179,0.107;AN=2;DP=127;set=variant2-variant4-variant8-variant12-variant16-variant21-variant23-variant29-variant31-variant34-variant36-variant39-variant42-variant44 GT:DP:GQ:SB 0/3:7:5:0,1,1,5 chr2 55436003 . T C 77.39 PASS AC=1;AF=0.5;AN=2;DP=19;FS=0;FractionInformativeReads=1;MQ=60;set=variant12-variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:1,6:7:5:163,0,5:0,1,1,5 chr2 55436488 . GA G 273.38 PASS AC=2;AF=0.694;AN=2;DP=195;MQ=60;set=variant4-variant7-variant9-variant12-variant14-variant18-variant20-variant23-variant24-variant26-variant27-variant28-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:206,21,0:0,0,6,1 chr2 55436934 . G A 1528.35 PASS AC=1;AF=0.556;AN=2;DP=1650;MQ=60;set=variant3-variant4-variant7-variant9-variant11-variant12-variant14-variant18-variant20-variant23-variant26-variant27-variant37-variant38-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:45,32:77:99:837,0,1124:20,25,15,17 chr2 55437014 . C T 489.92 PASS AC=1;AF=0.583;AN=2;DP=326;FractionInformativeReads=1;MQ=60;set=variant4-variant14-variant23-variant24-variant28-variant29 GT:AD:DP:GQ:PL:SB 0/1:22,30:52:99:889,0,482:8,14,10,20 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 1/1:0,60:60:99:1926,180,0:0,0,20,40 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 1/1:0,30:30:90:1133,90,0:0,0,19,11 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 0/1:27,34:61:99:860,0,800:9,18,16,18 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 0/1:1,3:4:34:123,0,34:1,0,3,0 chr2 55461823 . T A 1797.88 PASS AC=2;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 1/1:0,43:43:99:1275,129,0:0,0,25,18 chr2 55464785 . CTTT CTTTTT,CT,C 71.82 PASS AC=1,0,0;AF=0.214,0.286,0.071;AN=2;DP=76;FS=0;set=variant4-variant5-variant11-variant23-variant24-variant26-variant34 GT:DP:GQ:SB 0/1:4:19:0,1,0,3 chr2 55470115 . C T 590.27 PASS AC=2;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 1/1:1,40:41:81:1170,81,0:1,0,24,16 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 1/1:0,60:60:99:1947,180,0:0,0,24,36 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 0/1:8,10:18:99:271,0,294:7,1,7,3 chr2 55473386 . CAT C 679.99 PASS AC=2;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 1/1:0,26:26:78:1170,78,0:0,0,18,8 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 1/1:0,12:12:36:515,36,0:0,0,2,10 chr2 55481322 . T A 1052.28 PASS AC=1;AF=0.583;AN=2;DP=373;FractionInformativeReads=1;MQ=60;set=variant4-variant14-variant23-variant24-variant28-variant29 GT:AD:DP:GQ:PL:SB 0/1:31,27:58:99:716,0,887:12,19,8,19 chr2 55489629 . T C 145.21 PASS AC=2;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 1/1:0,7:7:21:291,21,0:0,0,0,7 chr2 55490819 . G T 782.41 PASS AC=2;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 1/1:0,85:85:99:2411,254,0:0,0,49,36 chr2 55491007 . G GA 484.01 PASS AC=1;AF=0.583;AN=2;DP=339;MQ=60;set=variant4-variant14-variant23-variant24-variant28-variant29 GT:AD:DP:GQ:PL:SB 0/1:17,25:42:99:575,0,336:6,11,13,12 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 1/1:0,95:95:99:3265,285,0:0,0,42,53 chr2 55516588 . G C 15550.4 PASS AC=2;AF=0.966;AN=2;DP=21528;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,399:400:99:12472,1187,0:1,0,205,194 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 1/1:0,358:358:99:11584,1074,0:0,0,166,192 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 1/1:96:99:0,0,44,52 chr2 55517491 . G A 4122.87 PASS AC=2;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 1/1:0,285:285:99:8262,853,0:0,0,162,123 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 1/1:0,32:32:96:944,96,0:0,0,20,12 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 1/1:0,56:56:99:1856,168,0:0,0,26,30 chr2 55523308 . C CAA,CA,CAAA 503.29 PASS AC=2,0,0;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 1/1:10:36:0,0,7,3 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 1/1:0,12:12:36:503,36,0:0,0,9,3 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 1/1:0,90:90:99:2841,270,0:0,0,35,55 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 1/1:0,48:48:99:1531,144,0:0,0,30,18 chr2 55528514 . A G 151.77 PASS AC=2;AF=1;AN=2;DP=112;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant31-variant32-variant34-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,0,2 chr2 55599655 . G A 286.99 PASS AC=2;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 1/1:0,55:55:99:1578,164,0:0,0,27,28 chr2 55646761 . T C 1455.28 PASS AC=2;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 1/1:0,65:65:99:2041,195,0:0,0,32,33 chr2 55749193 . A G 578.5 PASS AC=1;AF=0.5;AN=2;DP=196;FractionInformativeReads=1;MQ=60;set=variant7-variant11-variant23-variant37 GT:AD:DP:GQ:PL:SB 0/1:23,23:46:99:474,0,527:14,9,11,12 chr2 55760940 . G T 1915.33 PASS AC=2;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 1/1:0,51:51:99:1672,153,0:0,0,36,15 chr2 55762832 . T C 1239.8 PASS AC=1;AF=0.5;AN=2;DP=462;FractionInformativeReads=1;MQ=60;set=variant4-variant15-variant19-variant23-variant24-variant29 GT:AD:DP:GQ:PL:SB 0/1:29,37:66:99:892,0,700:19,10,19,18 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 0/1:35,35:70:99:813,0,831:15,20,16,19 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 0/1:19,19:38:99:734,0,2109:7,12,8,11 chr2 55771050 . C G 789.51 PASS AC=2;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 1/1:0,27:27:81:884,81,0:0,0,18,9 chr2 55771161 . A G 1772.9 PASS AC=2;AF=0.932;AN=2;DP=3054;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:1921,189,0:0,0,33,30 chr2 55772688 . G C 1575.35 PASS AC=1;AF=0.5;AN=2;DP=856;MQ=60;set=variant4-variant15-variant19-variant23-variant24-variant29 GT:AD:DP:GQ:PL:SB 0/1:63,51:114:99:1067,0,1497:29,34,22,29 chr2 55774356 . C G 194.86 PASS AC=1;AF=0.5;AN=2;DP=14;FS=2.363;FractionInformativeReads=1;MQ=60;MQRankSum=-1.733;QD=13.92;ReadPosRankSum=-1.867;SOR=0.207;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:5,9:14:99:223,0,145:4,1,5,4 chr2 55776641 . A G 124.46 PASS AC=1;AF=0.5;AN=2;DP=57;FractionInformativeReads=1;MQ=60;set=variant4-variant15-variant19-variant23-variant24-variant29 GT:AD:DP:GQ:PL:SB 0/1:7,3:10:97:97,0,206:5,2,3,0 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 0/1:52,46:98:99:1163,0,1311:33,19,31,15 chr2 55785828 . A G 649.25 PASS AC=1;AF=0.5;AN=2;DP=386;FractionInformativeReads=1;MQ=60;set=variant4-variant15-variant19-variant23-variant24 GT:AD:DP:GQ:PL:SB 0/1:30,41:71:99:1002,0,759:21,9,25,16 chr2 55791688 . T C 184.64 PASS AC=1;AF=0.5;AN=2;DP=102;FractionInformativeReads=1;MQ=60;set=variant4-variant15-variant19-variant23-variant24 GT:AD:DP:GQ:PL:SB 0/1:6,11:17:99:351,0,159:1,5,2,9 chr2 55805440 . T C 1093.85 PASS AC=2;AF=0.977;AN=2;DP=1863;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1037,110,0:0,0,15,22 chr2 55808969 . C T 406.41 PASS AC=2;AF=0.932;AN=2;DP=600;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:415,36,0:0,0,3,9 chr2 55812061 . A G 616.34 PASS AC=1;AF=0.586;AN=2;DP=1183;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant8-variant11-variant12-variant13-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant29-variant30-variant31-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,17:37:99:458,0,542:14,6,12,5 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 0/1:20,23:43:99:656,0,573:14,6,16,7 chr2 55815997 . T C 1320.45 PASS AC=1;AF=0.536;AN=2;DP=1485;MQ=60;set=variant4-variant12-variant15-variant19-variant23-variant24-variant26-variant29-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:57,34:91:99:755,0,1278:28,29,19,15 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 0/1:51,54:105:99:1627,0,1606:18,33,28,26 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 1/1:0,184:184:99:6769,554,0:0,0,93,91 chr2 55862440 . T C 3302.94 PASS AC=2;AF=0.932;AN=2;DP=4452;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,82:82:99:2602,245,0:0,0,33,49 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 0/1:58:22:5,3,16,34 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 0/1:71,69:140:99:1563,0,1571:35,36,37,32 chr2 55862804 . T TTTGGTAA 2256.38 PASS AC=1;AF=0.559;AN=2;DP=1957;MQ=60;set=variant6-variant8-variant11-variant13-variant18-variant20-variant21-variant22-variant23-variant30-variant31-variant33-variant34-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,58:123:99:2218,0,2535:32,33,26,32 chr2 55863066 . TTCTA T 409.57 PASS AC=1;AF=0.559;AN=2;DP=281;MQ=60;set=variant6-variant8-variant11-variant13-variant18-variant20-variant21-variant22-variant23-variant30-variant31-variant33-variant34-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,3:13:96:96,0,501:3,7,1,2 chr2 55863110 . CTA C 124.67 PASS AC=1;AF=0.567;AN=2;DP=147;MQ=60;set=variant6-variant8-variant13-variant18-variant20-variant21-variant22-variant23-variant30-variant31-variant33-variant34-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,2:7:69:69,0,216:1,4,1,1 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 0/1:9,8:17:99:187,0,196:7,2,7,1 chr2 55867938 . A G 103.69 PASS AC=1;AF=0.567;AN=2;DP=193;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant13-variant18-variant20-variant21-variant22-variant23-variant31-variant33-variant34-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:131,0,149:2,5,1,4 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 0/1:16,3:19:75:75,0,503:12,4,3,0 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 0/1:13,19:32:99:454,0,289:7,6,12,7 chr2 55889062 . G A 616.36 PASS AC=2;AF=0.932;AN=2;DP=831;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:567,54,0:0,0,12,6 chr2 55894090 . A G 371.27 PASS AC=1;AF=0.5;AN=2;DP=151;FractionInformativeReads=1;MQ=60;set=variant8-variant18-variant21-variant23-variant31-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,10:24:99:305,0,430:12,2,9,1 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 0/1:45,48:93:99:1195,0,1062:19,26,21,27 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 0/1:11,7:18:99:172,0,305:8,3,5,2 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 0/1:38,27:65:99:575,0,757:19,19,16,11 chr2 55898929 . A G 511.77 PASS AC=2;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 1/1:0,10:10:30:450,30,0:0,0,9,1 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 0/1:4,6:10:99:233,0,150:3,1,6,0 chr2 55899228 . A T 705.24 PASS AC=2;AF=0.932;AN=2;DP=1026;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:830,75,0:0,0,8,17 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 0/1:18,17:35:99:417,0,466:7,11,7,10 chr2 55900459 . A G 403.89 PASS AC=1;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 0/1:3,4:7:99:115,0,112:0,3,2,2 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 0/1:31,34:65:99:827,0,721:13,18,17,17 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 0/1:10,18:28:99:493,0,265:7,3,13,5 chr2 55915155 . T A 196.77 PASS AC=2;AF=0.932;AN=2;DP=359;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:87,6,0:0,0,0,2 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 0/1:26,13:39:99:320,0,718:10,16,3,10 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 1/1:0,104:104:99:2972,311,0:0,0,57,47 chr2 56411157 . T C 432.81 PASS AC=2;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 1/1:0,15:15:45:496,45,0:0,0,11,4 chr2 56411363 . G A 5865.67 PASS AC=2;AF=0.92;AN=2;DP=7659;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:4257,423,0:0,0,79,63 chr2 56411817 . C T 3332.95 PASS AC=2;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 1/1:1,130:131:99:3817,379,0:1,0,69,61 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 1/1:0,119:119:99:3707,357,0:0,0,44,75 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 0/1:42,41:83:99:1565,0,1795:17,25,16,25 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 0/1:82,59:141:99:1474,0,2270:47,35,38,21 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 0/1:152,75:227:99:1873,0,4396:72,80,33,42 chr2 58260250 . T C 296.7 PASS AC=1;AF=0.5;AN=2;DP=45;FS=1.526;FractionInformativeReads=1;MQ=60;MQRankSum=0.013;QD=6.59;ReadPosRankSum=-0.163;SOR=0.411;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:32,13:45:99:325,0,1045:26,6,10,3 chr2 58275666 . G A 770.53 PASS AC=1;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 0/1:46,45:91:99:942,0,1064:24,22,23,22 chr2 58316814 . A G 1066.7 PASS AC=1;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 0/1:52,45:97:99:998,0,1262:27,25,26,19 chr2 58362161 . G A 715.64 PASS AC=1;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 0/1:12,16:28:99:499,0,389:11,1,11,5 chr2 58381785 . T C 695.91 PASS AC=1;AF=0.625;AN=2;DP=727;MQ=60;set=variant-variant5-variant6-variant7-variant13-variant16-variant17-variant19-variant20-variant23-variant26-variant28-variant30-variant31-variant34-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,19:41:99:450,0,606:16,6,12,7 chr2 58388696 . A G 1454.87 PASS AC=1;AF=0.684;AN=2;DP=4057;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,41:110:99:842,0,1683:36,33,22,19 chr2 58392789 . T C 470.04 PASS AC=1;AF=0.625;AN=2;DP=703;MQ=60;set=variant-variant5-variant6-variant7-variant13-variant16-variant17-variant19-variant20-variant23-variant26-variant28-variant30-variant31-variant34-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,11:20:99:313,0,226:6,3,7,4 chr2 58392797 . TTTA T 634.46 PASS AC=1;AF=0.6;AN=2;DP=798;MQ=60;set=variant-variant5-variant6-variant7-variant13-variant16-variant17-variant19-variant20-variant23-variant26-variant28-variant30-variant31-variant34-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,14:26:99:538,0,551:8,4,10,4 chr2 58453843 . G GA 318.04 PASS AC=1;AF=0.575;AN=2;DP=936;MQ=60;set=variant-variant5-variant6-variant7-variant13-variant16-variant17-variant19-variant20-variant23-variant26-variant28-variant30-variant31-variant34-variant36-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,22:40:99:430,0,327:11,7,14,8 chr2 58468569 . G C 397.22 PASS AC=1;AF=0.5;AN=2;DP=97;FractionInformativeReads=1;MQ=60;set=variant8-variant23 GT:AD:DP:GQ:PL:SB 0/1:19,41:60:99:1023,0,395:7,12,18,23 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 0/1:7,5:12:99:142,0,192:5,2,5,0 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 0/1:69,49:118:99:1158,0,1661:36,33,30,19 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 0/1:11,6:17:99:213,0,538:2,9,1,5 chr2 59246730 . CT CTT,C,CTTT 34.63 PASS AC=1,0,0;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 0/1:29:79:14,8,3,4 chr2 59249956 . A G 301.71 PASS AC=1;AF=0.5;AN=2;DP=283;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant8-variant19-variant20-variant22-variant23-variant24-variant31-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,8:20:99:259,0,405:10,2,7,1 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 0/1:62,97:159:99:2342,0,1568:30,32,50,47 chr2 60679226 . G A 1819.03 PASS AC=1;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 0/1:87,84:171:99:2340,0,2112:47,40,51,33 chr2 60679831 . GA G 1342.31 PASS AC=1;AF=0.5;AN=2;DP=98;FS=0.79;FractionInformativeReads=0.959;MQ=60;MQRankSum=-1.267;QD=13.7;ReadPosRankSum=0.867;SOR=0.676;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:38,56:94:99:1380,0,807:18,20,29,27 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 0/1:24,29:53:99:683,0,584:9,15,13,16 chr2 60684805 . GT G,GTT 184.32 PASS AC=1,0;AF=0.474,0.053;AN=2;DP=498;set=variant2-variant4-variant8-variant9-variant12-variant13-variant15-variant17-variant19-variant22-variant23-variant26-variant28-variant31-variant33-variant34-variant37-variant40-variant44 GT:DP:GQ:SB 0/1:11:66:2,2,2,5 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 0/1:18:99:3,4,3,8 chr2 60687400 . C CTGTT 522.83 PASS AC=1;AF=0.5;AN=2;DP=22;FS=0;FractionInformativeReads=0.955;MQ=60;MQRankSum=0.616;QD=23.76;ReadPosRankSum=1.919;SOR=0.693;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:8,13:21:99:560,0,367:5,3,8,5 chr2 60687959 . A G 5902.68 PASS AC=1;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 0/1:114,71:185:99:1897,0,3152:49,65,30,41 chr2 60689748 . A G 319.82 PASS AC=1;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 0/1:15,11:26:99:328,0,586:1,14,1,10 chr2 60768978 . G A 786.99 PASS AC=1;AF=0.743;AN=2;DP=714;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:222,0,139:4,2,6,2 chr2 60769160 . T C 287.79 PASS AC=1;AF=0.5;AN=2;DP=21;FS=4.359;FractionInformativeReads=1;MQ=60;MQRankSum=0.616;QD=13.7;ReadPosRankSum=0.616;SOR=0.399;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:8,13:21:99:316,0,215:2,6,7,6 chr2 60780650 . G GGAGA 156.67 PASS AC=2;AF=1;AN=2;DP=44;FS=0;set=variant3-variant6-variant11-variant13-variant17-variant21-variant22-variant23-variant26-variant27-variant28-variant34-variant37-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,1,1 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 0/1:47,35:82:99:830,0,1192:29,18,22,13 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 1/1:0,34:34:99:1365,102,0:0,0,4,30 chr2 61009788 . CTT CT,C,CTTTT,CTTTTT,CTTT 144.25 PASS AC=1,0,0,0,0;AF=0.321,0.071,0.036,0.036,0.071;AN=2;DP=279;set=variant3-variant5-variant6-filterInvariant7-variant9-variant13-variant16-variant19-variant23-variant27-variant28-filterInvariant29-variant39-variant42 GT:DP:GQ:SB 0/1:18:65:4,3,7,4 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 0/1:3,6:9:32:162,0,32:1,2,2,4 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 1/1:0,17:17:51:620,51,0:0,0,13,4 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 0/1:9:51:1,2,1,5 chr2 61145498 . AT A 101.3 PASS AC=1;AF=0.5;AN=2;DP=944;MQ=60;set=filterInvariant3-filterInvariant10-filterInvariant15-filterInvariant17-filterInvariant20-filterInvariant23-filterInvariant27-filterInvariant34-variant36-filterInvariant37-filterInvariant40-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:50,16:66:99:173,0,1091:29,21,7,9 chr2 61187478 . CAA CAAA,CA,C 149.62 PASS AC=0,1,0;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 0/2:29:99:14,3,10,2 chr2 61238871 . GA G 68.04 PASS AC=1;AF=0.5;AN=2;DP=17;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.055;QD=4;ReadPosRankSum=1.156;SOR=1.022;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:11,6:17:99:105,0,210:8,3,5,1 chr2 61246145 . G A 2240.22 PASS AC=1;AF=0.643;AN=2;DP=5085;FractionInformativeReads=1;set=variant-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant14-variant15-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,71:142:99:1951,0,1895:29,42,26,45 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 1/1:0,277:277:99:8451,827,0:0,0,122,155 chr2 61304002 . A G 537.6 PASS AC=1;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 0/1:13,13:26:99:329,0,375:10,3,9,4 chr2 61304377 . A T 357.98 PASS AC=1;AF=0.559;AN=2;DP=315;FractionInformativeReads=1;MQ=60;set=variant4-variant9-variant10-variant14-variant15-variant19-variant20-variant21-variant23-variant25-variant26-variant29-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,11:19:99:344,0,255:1,7,2,9 chr2 61308517 . A G 271.56 PASS AC=1;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 0/1:14,6:20:99:129,0,365:8,6,4,2 chr2 61349446 . G A 2279.35 PASS AC=1;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 0/1:43,34:77:99:995,0,1121:23,20,23,11 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 0/1:137,108:245:99:2576,0,3435:55,82,42,66 chr2 61351187 . T C 115.64 PASS AC=1;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 0/1:2,8:10:99:321,0,322:1,1,6,2 chr2 61351188 . T C 115.64 PASS AC=1;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 0/1:4,8:12:99:321,0,322:2,2,6,2 chr2 61351189 . T A 115.64 PASS AC=1;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 0/1:5,8:13:99:321,0,322:3,2,6,2 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 0/1:8,11:19:99:313,0,221:6,2,8,3 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 0/1:31,31:62:99:1181,0,1621:17,14,13,18 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 0/1:31,30:61:99:1184,0,1598:16,15,13,17 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 0/1:33,30:63:99:780,0,850:16,17,16,14 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 0/1:21,18:39:99:520,0,638:5,16,2,16 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 0/1:6,6:12:99:202,0,196:1,5,1,5 chr2 61404452 . GCGCGTCCC GCGCGTCCCCGCGTCCC,G 78.98 PASS AC=1,0;AF=0.591,0.023;AN=2;DP=201;FS=0;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant16-variant19-variant22-variant23-variant25-variant27-variant28-variant32-variant36-variant39-variant41 GT:DP:GQ:SB 0/1:6:72:2,0,4,0 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 0/1:6,5:11:99:117,0,121:4,2,3,2 chr2 61404917 . G A 926.62 PASS AC=1;AF=0.5;AN=2;DP=37;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.016;QD=25.04;ReadPosRankSum=-1.738;SOR=0.776;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:14,23:37:99:955,0,869:7,7,12,11 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 0/1:15,25:40:99:987,0,887:7,8,15,10 chr2 61405795 . G T 1404.06 PASS AC=1;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 0/1:39,26:65:99:595,0,988:20,19,16,10 chr2 61413723 . A G 3806.65 PASS AC=1;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 0/1:38,52:90:99:1317,0,943:17,21,27,25 chr2 61414639 . GCAAT G,GCAATCAAT 4038.64 PASS AC=1,0;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 0/1:87:99:21,21,21,24 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 0/1:26,26:52:99:631,0,666:16,10,16,10 chr2 61417617 . A G 1504.48 PASS AC=1;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 0/1:46,61:107:99:1407,0,1115:24,22,30,31 chr2 61439206 . C T 855.17 PASS AC=1;AF=0.719;AN=2;DP=531;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,4:15:99:132,0,361:2,9,0,4 chr2 61448776 . A C 680.57 PASS AC=1;AF=0.6;AN=2;DP=1623;MQ=60;set=variant7-variant12-variant13-variant14-variant18-variant19-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant37-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,36:72:99:826,0,834:13,23,16,20 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 0/1:30,21:51:99:476,0,845:8,22,8,13 chr2 61454059 . T A 457.68 PASS AC=1;AF=0.741;AN=2;DP=477;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant19-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant37-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,4:16:73:73,0,399:5,7,2,2 chr2 61456611 . C A,CAA 517.08 PASS AC=0,1;AF=0.5,0.313;AN=2;DP=99;set=variant12-variant22-variant23-variant24-variant30-variant34-variant37-variant43 GT:DP:GQ:SB 0/2:10:99:5,1,3,1 chr2 61483715 . A T 279.77 PASS AC=1;AF=0.815;AN=2;DP=293;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,3:8:69:69,0,228:1,4,1,2 chr2 61483725 . T A 330.38 PASS AC=1;AF=0.804;AN=2;DP=247;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:77:77,0,200:1,2,1,2 chr2 61484556 . T C 397.01 PASS AC=1;AF=0.726;AN=2;DP=345;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant31-variant33-variant34-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:228,0,149:0,4,0,6 chr2 61522047 . T C 64.71 PASS AC=1;AF=0.654;AN=2;DP=368;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant12-variant13-variant14-variant15-variant18-variant19-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant37-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,11:15:94:366,0,94:3,1,8,3 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 1/1:0,65:65:99:1861,195,0:0,0,38,27 chr2 61528299 . T TA 442.66 PASS AC=1;AF=0.654;AN=2;DP=1088;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-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:382,0,321:4,9,6,9 chr2 61538602 . G GAAAAGAGAAAGAAAAAGAAAA,GAAAAGAGAAAGAAAAAGAAAAA 186.37 PASS AC=2,0;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 1/1:5:18:0,0,3,2 chr2 61544759 . T C 357.78 PASS AC=1;AF=0.5;AN=2;DP=52;FS=0;FractionInformativeReads=0.981;MQ=60;MQRankSum=0.579;QD=6.88;ReadPosRankSum=-0.903;SOR=0.776;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:35,16:51:99:386,0,869:23,12,11,5 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 0/1:16,10:26:99:237,0,383:10,6,7,3 chr2 61566824 . GA G,GAA 141.02 PASS AC=1,0;AF=0.464,0.036;AN=2;DP=620;MQ=60;set=variant3-filterInvariant7-filterInvariant10-filterInvariant14-variant15-filterInvariant17-variant18-filterInvariant23-filterInvariant27-filterInvariant30-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant40 GT:DP:GQ:SB 0/1:38:99:9,18,4,7 chr2 61570886 . AAAGT A 1072.07 PASS AC=1;AF=0.635;AN=2;DP=1121;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-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,13:33:99:486,0,1098:18,2,11,2 chr2 61575308 . A G 5083.97 PASS AC=2;AF=0.977;AN=2;DP=6666;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,133:133:99:4177,397,0:0,0,63,70 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 1/1:0,84:84:99:2647,252,0:0,0,30,54 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 0/1:31,21:52:99:461,0,758:14,17,9,12 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 0/1:13,7:20:99:198,0,429:6,7,5,2 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 0/1:34,33:67:99:929,0,732:15,19,9,24 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 0/1:11:35:2,0,5,4 chr2 61648932 . A G,ACG,ACACG 533.78 PASS AC=1,0,0;AF=0.345,0.241,0.069;AN=2;DP=471;set=variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant33-variant34-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:17:99:5,3,5,4 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 0/1:4,15:19:99:598,0,572:0,4,2,13 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 0/1:3,14:17:99:598,0,572:0,3,1,13 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 0/1:3,14:17:99:579,0,480:0,3,1,13 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 0/1:29,26:55:99:659,0,758:18,11,16,10 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 0/1:37,33:70:99:1335,0,2052:20,17,20,13 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 0/1:38,38:76:99:1426,0,2086:20,18,24,14 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 0/1:22,12:34:99:307,0,592:12,10,8,4 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 0/1:28,14:42:99:415,0,801:15,13,10,4 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 1/1:0,60:60:99:2063,180,0:0,0,40,20 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 0/1:31,38:69:99:1010,0,787:15,16,14,24 chr2 61764887 . AACACACAC AACACACACACAC,AACACACACACACACAC,AACACACACACACAC,AACACACACACACACACACACAC,AACACACACAC,AACACACACACACACACACAC,AACACACACACACACACAC,AACACAC,A,AACAC 169.91 PASS AC=0,0,0,0,0,1,0,1,0,0;AF=0.181,0.028,0.236,0.014,0.125,0.028,0.083,0.028,0.083,0.014;AN=2;DP=449;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:DP:GQ:SB 8/6:11:96:0,0,8,3 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 0/1:20,14:34:99:362,0,487:9,11,8,6 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 0/1:21:99:7,7,0,7 chr2 61765187 . C G 237.21 PASS AC=1;AF=0.5;AN=2;DP=83;MQ=60;set=variant23-variant27-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,8:20:99:265,0,508:5,7,0,8 chr2 62052380 . A G 2629.88 PASS AC=2;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 1/1:0,132:132:99:4316,395,0:0,0,79,53 chr2 62053290 . A G 1702.71 PASS AC=2;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 1/1:1,74:75:99:2570,180,0:1,0,43,31 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 0/1:59,66:125:99:2594,0,2893:23,36,30,36 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 1/1:0,7:7:21:249,21,0:0,0,1,6 chr2 62063093 . TA T 721.45 PASS AC=2;AF=0.614;AN=2;DP=2245;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:4,30:34:8:546,8,0:2,2,19,11 chr2 62065759 . C T 3794.79 PASS AC=1;AF=0.542;AN=2;DP=1417;FractionInformativeReads=1;MQ=60;set=variant7-variant11-variant12-variant17-variant18-variant20-variant23-variant25-variant26-variant31-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,51:112:99:1183,0,1520:31,30,24,27 chr2 62066417 . ATATAT A 171.57 PASS AC=2;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 1/1:0,6:6:18:270,18,0:0,0,4,2 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 1/1:0,95:95:99:2851,284,0:0,0,49,46 chr2 62067788 . T A 246.22 PASS AC=1;AF=0.5;AN=2;DP=8;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.747;QD=30.78;ReadPosRankSum=0.747;SOR=2.833;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:1,7:8:18:274,0,18:0,1,0,7 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 0/1:19,24:43:99:644,0,511:5,14,8,16 chr2 62074140 . A AAC 661.08 PASS AC=2;AF=0.955;AN=2;DP=861;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:566,39,0:0,0,0,13 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 1/1:1,227:228:99:6857,672,0:1,0,124,103 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 1/1:0,105:105:99:3169,315,0:0,0,36,69 chr2 62095994 . A G 599.79 PASS AC=2;AF=0.955;AN=2;DP=1001;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:490,42,0:0,0,4,10 chr2 62098993 . C T 470.9 PASS AC=2;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 1/1:0,43:43:99:1280,129,0:0,0,26,17 chr2 62099156 . T C 489.67 PASS AC=2;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 1/1:0,43:43:99:1290,128,0:0,0,16,27 chr2 62104660 . TA T,TAA 228.24 PASS AC=2,0;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 1/1:25:22:1,1,8,15 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 1/1:0,45:45:99:1846,144,0:0,0,30,15 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 0/3:8:28:3,0,4,1 chr2 62112246 . C CT 357.68 PASS AC=2;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 1/1:1,29:30:63:722,63,0:0,1,10,19 chr2 62727363 . A C 493.46 PASS AC=1;AF=0.5;AN=2;DP=212;FractionInformativeReads=1;MQ=60;set=variant6-variant11-variant21-variant23-variant24-variant25-variant26-variant33-variant36 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:231,0,209:6,2,6,2 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 1/1:1,103:104:99:2648,301,0:1,0,55,48 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 0/1:24,20:44:99:552,0,688:18,6,14,6 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 0/1:102,69:171:99:1842,0,2634:63,39,46,23 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 0/1:159,133:292:99:3418,0,4019:94,65,82,51 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 0/1:214,190:404:99:4571,0,5420:116,98,99,91 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 0/1:204,195:399:99:4753,0,5008:111,93,103,92 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 0/1:32,28:60:99:751,0,872:17,15,15,13 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 0/1:26,31:57:99:795,0,641:15,11,16,15 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 0/1:100,84:184:99:2151,0,2754:35,65,33,51 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 0/1:27,19:46:99:452,0,650:16,11,13,6 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 0/1:39,30:69:99:650,0,996:23,16,17,13 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 0/1:5,9:14:99:347,0,145:1,4,0,9 chr2 62998485 . G A 2761.7 PASS AC=1;AF=0.75;AN=2;DP=160;FractionInformativeReads=1;MQ=60;MQRankSum=0.566;ReadPosRankSum=-3.731;set=variant14-variant23 GT:AD:DP:GQ:PL:SB 0/1:33,23:56:99:570,0,959:19,14,15,8 chr2 63220661 . T C 1264.77 PASS AC=1;AF=0.5;AN=2;DP=118;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.004;QD=10.72;ReadPosRankSum=0.573;SOR=0.7;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:60,58:118:99:1293,0,1415:33,27,32,26 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 0/1:2,5:7:70:163,0,70:2,0,4,1 chr2 63283178 . C G 3975.09 PASS AC=1;AF=0.5;AN=2;DP=4238;MQ=60;set=variant9-variant11-variant17-variant18-variant19-variant23-variant24-variant25-variant26-variant33-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:123,141:264:99:3287,0,3142:66,57,66,75 chr2 63380809 . G A 61.77 PASS AC=2;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 1/1:0,3:3:9:132,9,0:0,0,0,3 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 0/1:20,27:47:99:660,0,515:8,12,11,16 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 0/1:41,38:79:99:916,0,1024:23,18,24,14 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 0/1:3,10:13:60:278,0,60:0,3,3,7 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 0/1:19,12:31:99:307,0,555:5,14,4,8 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 0/1:22,9:31:99:204,0,563:13,9,7,2 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 0/1:7,18:25:99:448,0,159:2,5,7,11 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 0/1:3,7:10:65:244,0,65:1,2,1,6 chr2 63669625 . T C 6557.85 PASS AC=2;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 1/1:0,200:200:99:6535,600,0:0,0,92,108 chr2 63669666 . G A 2679.36 PASS AC=1;AF=0.531;AN=2;DP=3334;MQ=60;set=variant-variant3-variant4-variant7-variant13-variant15-variant16-variant22-variant23-variant30-variant31-variant32-variant34-variant36-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:102,120:222:99:3243,0,2655:56,46,61,59 chr2 63670274 . T A 269.03 PASS AC=1;AF=0.5;AN=2;DP=365;MQ=60;set=variant2-variant4-variant5-variant8-variant9-variant10-variant12-variant15-variant16-variant21-variant23-variant24-variant29-variant32-variant34-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,9:12:59:243,0,59:1,2,4,5 chr2 63719887 . T C 108.67 PASS AC=2;AF=0.577;AN=2;DP=216;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant13-variant15-variant22-variant23-variant31-variant32-variant34-variant36-variant37-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:463,39,0:0,0,10,3 chr2 63720210 . A G 154.82 PASS AC=2;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 1/1:0,4:4:12:177,12,0:0,0,0,4 chr2 63798333 . C T 1982.59 PASS AC=2;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 1/1:0,44:44:99:1232,131,0:0,0,25,19 chr2 63815206 . A G 117.36 PASS AC=2;AF=0.536;AN=2;DP=260;MQ=60;set=variant-variant7-variant13-variant15-variant16-variant22-variant23-variant30-variant31-variant32-variant34-variant36-variant37-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,19:19:57:543,57,0:0,0,11,8 chr2 63815801 . A C 884.34 PASS AC=2;AF=0.567;AN=2;DP=1012;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant13-variant15-variant16-variant22-variant23-variant30-variant31-variant32-variant34-variant36-variant37-variant38 GT:AD:DP:GQ:PL:SB 1/1:2,57:59:99:1814,121,0:1,1,32,25 chr2 63816672 . C G 912.56 PASS AC=2;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 1/1:0,22:22:66:832,66,0:0,0,3,19 chr2 63821117 . G A 142.98 PASS AC=2;AF=0.625;AN=2;DP=29;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant23-variant37 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:173,15,0:0,0,4,1 chr2 63822785 . T C 2099.61 PASS AC=2;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 1/1:0,75:75:99:2338,225,0:0,0,36,39 chr2 63826528 . T G 151.77 PASS AC=2;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 1/1:0,6:6:18:250,18,0:0,0,0,6 chr2 63849916 . TG T 1536.3 PASS AC=1;AF=0.5;AN=2;DP=558;set=variant-variant7-variant23-variant37 GT:AD:DP:GQ:PL:SB 0/1:67,71:138:99:2240,0,2078:36,31,34,37 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 1/1:0,17:17:51:591,51,0:0,0,13,4 chr2 64069311 . G C 1296.7 PASS AC=1;AF=0.5;AN=2;DP=716;MQ=60;set=variant4-variant10-variant15-variant16-variant22-variant23-variant32-variant36-variant38 GT:AD:DP:GQ:PL:SB 0/1:30,28:58:99:787,0,741:18,12,20,8 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 1/1:0,62:62:99:1821,185,0:0,0,24,38 chr2 64082619 . G C 194.27 PASS AC=2;AF=0.538;AN=2;DP=502;MQ=60;set=variant-variant4-variant7-variant10-variant15-variant16-variant22-variant23-variant30-variant32-variant36-variant37-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1179,120,0:0,0,16,24 chr2 64082654 . GTTTTT GTTT,GTTTTTTT,GTTTTTT,GTTTT,GT,GTTTTTTTT,GTT,G 74.11 PASS AC=2,0,0,0,0,0,0,0;AF=0.111,0.093,0.093,0.056,0.111,0.019,0.093,0.019;AN=2;DP=660;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant29-variant32-variant33-variant37-variant41-filterInvariant42-filterInvariant43 GT:DP:GQ:SB 1/1:10:11:1,0,2,7 chr2 64082721 . G A 88.49 PASS AC=2;AF=0.563;AN=2;DP=42;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant10-variant16-variant23-variant32-variant36-variant37 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:94,9,0:0,0,1,2 chr2 64083600 . G C 239.2 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=575;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:39,11:50:78:78,0,1992:3,36,11,0 chr2 64083605 . T C 191.93 PASS AC=1;AF=0.5;AN=2;DP=394;MQ=60;set=filterInvariant3-filterInvariant9-filterInvariant12-variant13-filterInvariant21-filterInvariant23-filterInvariant26-filterInvariant39 GT:AD:DP:GQ:PL:SB 0/1:36,9:45:90:90,0,1873:3,33,9,0 chr2 64084005 . G A 865.1 PASS AC=2;AF=0.538;AN=2;DP=661;MQ=60;set=variant-variant4-variant7-variant10-variant15-variant16-variant22-variant23-variant30-variant32-variant36-variant37-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1437,129,0:0,0,11,32 chr2 64084098 . T C 85.48 PASS AC=2;AF=0.6;AN=2;DP=71;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant10-variant15-variant16-variant22-variant23-variant30-variant32-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:126,9,0:0,0,0,3 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 1/1:0,81:81:99:2564,243,0:0,0,36,45 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 1/1:0,21:21:63:776,63,0:0,0,17,4 chr2 64117423 . G A 304.68 PASS AC=2;AF=0.545;AN=2;DP=120;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant10-variant15-variant16-variant22-variant23-variant30-variant32-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:405,27,0:0,0,0,9 chr2 64117425 . G T 304.68 PASS AC=2;AF=0.545;AN=2;DP=117;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant10-variant15-variant16-variant22-variant23-variant30-variant32-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:405,27,0:0,0,0,9 chr2 64117426 . C A 304.68 PASS AC=2;AF=0.545;AN=2;DP=114;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant10-variant15-variant16-variant22-variant23-variant30-variant32-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:27:405,27,0:0,0,0,8 chr2 64117428 . AC A 295.64 PASS AC=2;AF=0.55;AN=2;DP=101;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant15-variant16-variant22-variant23-variant30-variant32-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:360,24,0:0,0,0,8 chr2 64117431 . T TAG 253.65 PASS AC=2;AF=0.55;AN=2;DP=96;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant15-variant16-variant22-variant23-variant30-variant32-variant37-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:315,21,0:0,0,0,7 chr2 64124440 . TAA T 307.53 PASS AC=2;AF=0.545;AN=2;DP=203;MQ=60;set=variant-variant7-variant15-variant16-variant22-variant23-variant30-variant32-variant36-variant37-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:865,60,0:0,0,14,6 chr2 64126765 . A G 771.17 PASS AC=2;AF=0.542;AN=2;DP=603;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant10-variant15-variant16-variant22-variant23-variant30-variant32-variant36-variant37-variant38 GT:AD:DP:GQ:PL:SB 1/1:2,50:52:99:1457,107,0:1,1,21,29 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 1/1:0,11:11:33:392,33,0:0,0,2,9 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 1/1:0,33:33:99:1031,99,0:0,0,22,11 chr2 64195997 . CAA CAAA,CA,C 410.82 PASS AC=1,0,0;AF=0.406,0.078,0.016;AN=2;DP=1138;MQ=60;set=variant-filterInvariant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant15-variant16-variant17-variant18-variant19-variant20-filterInvariant21-variant22-variant23-variant24-variant26-variant29-variant30-variant31-variant32-filterInvariant34-variant36-variant37-variant38-filterInvariant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:15:95:4,3,3,5 chr2 64210875 . C A 123.45 PASS AC=2;AF=0.545;AN=2;DP=117;FractionInformativeReads=1;MQ=60;set=variant-variant7-variant10-variant15-variant16-variant22-variant23-variant30-variant32-variant37-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:229,18,0:0,0,5,1 chr2 64320669 . G A 1292.4 PASS AC=1;AF=0.5;AN=2;DP=90;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.533;QD=14.36;ReadPosRankSum=-2.641;SOR=0.618;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:47,43:90:99:1321,0,1401:25,22,22,21 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 0/1:32:99:11,7,10,4 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 1/1:0,16:16:51:605,51,0:0,0,12,4 chr2 64371615 . C G 1790.87 PASS AC=2;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 1/1:0,52:52:99:1463,155,0:0,0,23,29 chr2 64567680 . T G 139.7 PASS AC=1;AF=0.679;AN=2;DP=293;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant7-variant12-variant15-variant17-variant21-variant23-variant26-variant29-variant31-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:306,0,382:10,0,8,2 chr2 64567916 . C G 706.62 PASS AC=1;AF=0.679;AN=2;DP=1129;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant7-variant12-variant15-variant17-variant21-variant23-variant26-variant29-variant31-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,28:63:99:600,0,906:13,22,12,16 chr2 64687147 . GT GTT,G 86.95 PASS AC=1,0;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 0/1:70:99:29,21,12,8 chr2 64687777 . G T 2568.11 PASS AC=1;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 0/1:72,65:137:99:1544,0,1805:39,33,36,29 chr2 64800239 . G A 345.41 PASS AC=1;AF=0.5;AN=2;DP=216;FractionInformativeReads=1;MQ=60;set=variant11-variant23-variant29-variant30-variant31-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:13,14:27:99:424,0,295:5,8,4,10 chr2 64819249 . TA T,TAAAA,TAAA,TAA 95.51 PASS AC=1,0,0,0;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 0/1:45:99:14,15,7,9 chr2 64859377 . CTTT CT,CTT,C 2176.63 PASS AC=1,1,0;AF=0.227,0.489,0.011;AN=2;DP=8271;set=Intersection GT:DP:GQ:SB 1/2:136:99:9,9,51,67 chr2 64859679 . T C 2968.94 PASS AC=2;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 1/1:0,85:85:99:2612,255,0:0,0,46,39 chr2 64860029 . CTTCAAA C 6081 PASS AC=2;AF=0.794;AN=2;DP=3751;set=variant2-variant3-variant8-variant10-variant14-variant19-variant20-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant34-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:2,192:194:99:8481,495,0:1,1,97,95 chr2 64861511 . TG T 711.46 PASS AC=2;AF=0.85;AN=2;DP=696;MQ=60;set=variant2-variant3-variant8-variant10-variant13-variant14-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant30-variant31-variant34-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:839,84,0:0,0,26,2 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 1/1:0,19:19:57:855,57,0:0,0,8,11 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 1/1:0,19:19:57:855,57,0:0,0,8,11 chr2 65215487 . C G 346.78 PASS AC=2;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 1/1:0,12:12:36:491,36,0:0,0,10,2 chr2 65215789 . G A 583.11 PASS AC=2;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 1/1:0,64:64:99:2102,192,0:0,0,26,38 chr2 65216487 . T C 345.37 PASS AC=2;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 1/1:0,32:32:96:1046,96,0:0,0,18,14 chr2 65216647 . C G 2521.91 PASS AC=2;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 1/1:0,165:165:99:7375,503,0:0,0,103,62 chr2 65216648 . G C 2521.91 PASS AC=2;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 1/1:0,165:165:99:7375,503,0:0,0,102,63 chr2 65217089 . G C 2337.24 PASS AC=2;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 1/1:0,139:139:99:4403,417,0:0,0,73,66 chr2 65249702 . T TGGAGAAAGGACTG 874.12 PASS AC=1;AF=0.565;AN=2;DP=966;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant11-variant13-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant28-variant30-variant34-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,15:47:99:576,0,7413:16,16,7,8 chr2 65249705 . C CTGTG 790.18 PASS AC=1;AF=0.565;AN=2;DP=966;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant11-variant13-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant28-variant30-variant34-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,15:47:99:534,0,7419:16,16,7,8 chr2 65249706 . C G 799.22 PASS AC=1;AF=0.565;AN=2;DP=966;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant11-variant13-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant28-variant30-variant34-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,14:46:99:533,0,7420:16,16,7,7 chr2 65249707 . A AG 789.95 PASS AC=1;AF=0.565;AN=2;DP=964;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant11-variant13-variant16-variant17-variant21-variant22-variant23-variant24-variant25-variant28-variant30-variant34-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,14:46:99:532,0,7421:16,16,7,7 chr2 65250027 . A C 944.41 PASS AC=1;AF=0.5;AN=2;DP=69;FS=3.248;FractionInformativeReads=1;MQ=60;MQRankSum=-1.506;QD=13.69;ReadPosRankSum=1.062;SOR=0.705;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:34,35:69:99:973,0,930:15,19,19,16 chr2 65250436 . T C 1462.12 PASS AC=1;AF=0.5;AN=2;DP=138;FS=3.188;FractionInformativeReads=1;MQ=60;MQRankSum=-1.335;QD=10.6;ReadPosRankSum=1.65;SOR=1.004;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:80,58:138:99:1490,0,2065:33,47,20,38 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 1/1:0,26:26:80:893,80,0:0,0,7,19 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 1/1:0,12:12:36:397,36,0:0,0,2,10 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 0/1:71,75:146:99:2038,0,1719:34,37,33,42 chr2 65299766 . T C 2287.45 PASS AC=1;AF=0.5;AN=2;DP=1069;MQ=60;set=variant2-variant13-variant17-variant23-variant28-variant42 GT:AD:DP:GQ:PL:SB 0/1:105,86:191:99:2004,0,2427:49,56,40,46 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 0/1:3,5:8:99:174,0,113:0,3,0,5 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 0/1:13,10:23:99:331,0,354:7,6,7,3 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 0/1:66,61:127:99:1616,0,1778:38,28,34,27 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 0/1:155:99:39,42,41,33 chr2 65311929 . G A 2597.45 PASS AC=1;AF=0.5;AN=2;DP=1245;MQ=60;set=variant2-variant13-variant17-variant23-variant28 GT:AD:DP:GQ:PL:SB 0/1:114,113:227:99:2952,0,3211:61,53,59,54 chr2 65312217 . C T 4777.8 PASS AC=2;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 1/1:0,291:291:99:8495,870,0:0,0,156,135 chr2 65313215 . C CAG 664.41 PASS AC=2;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 1/1:0,51:51:99:2248,156,0:0,0,30,21 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 0/1:13,15:28:99:471,0,320:4,9,4,11 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 0/1:8,11:19:99:374,0,225:2,6,1,10 chr2 65473930 . AAAATTTTC A 1249.53 PASS AC=2;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 1/1:0,45:45:99:1981,136,0:0,0,15,30 chr2 65478371 . T A 103.61 PASS AC=2;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 1/1:0,15:15:45:571,45,0:0,0,3,12 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 1/1:0,90:90:99:2654,269,0:0,0,38,52 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 1/1:0,70:70:99:2026,210,0:0,0,30,40 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 1/1:0,36:36:99:1657,111,0:0,0,28,8 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 1/1:0,36:36:99:1695,114,0:0,0,28,8 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 1/1:0,38:38:99:1695,114,0:0,0,30,8 chr2 65495887 . G A 5184.3 PASS AC=2;AF=0.898;AN=2;DP=8146;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,162:162:99:4802,485,0:0,0,72,90 chr2 65496144 . A G 8818.26 PASS AC=2;AF=0.864;AN=2;DP=10210;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,201:201:99:6021,602,0:0,0,111,90 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 1/1:0,46:46:99:1202,137,0:0,0,25,21 chr2 65538467 . C T 521.93 PASS AC=1;AF=0.5;AN=2;DP=82;MQ=60;set=variant23-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,18:35:99:550,0,439:7,10,5,13 chr2 65559027 . A G 3115.51 PASS AC=1;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 0/1:56,61:117:99:1372,0,1339:31,25,29,32 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 0/1:47,40:87:99:1040,0,1120:22,25,22,18 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 0/1:7,12:19:99:536,0,294:6,1,10,2 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 0/1:8,14:22:99:588,0,310:7,1,11,3 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 0/1:10,17:27:99:612,0,331:8,2,12,5 chr2 65571366 . T A 1460.49 PASS AC=1;AF=0.5;AN=2;DP=278;MQ=60;set=variant23-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,65:141:99:1489,0,1900:46,30,37,28 chr2 65593439 . A AAAC,AAACAACAACAAC,AAACAACAAC 257.51 PASS AC=0,1,0;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 0/2:5:99:3,0,2,0 chr2 65604914 . A G 993.11 PASS AC=2;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 1/1:0,38:38:99:1311,114,0:0,0,12,26 chr2 66666588 . G A 819.29 PASS AC=1;AF=0.5;AN=2;DP=154;MQ=60;set=variant17-variant23 GT:AD:DP:GQ:PL:SB 0/1:36,35:71:99:881,0,1152:9,27,11,24 chr2 66667200 . A AACACACACACAC,AACACACAC,AAC,AACACACACACACAC,AACAC,AACACACACACACACAC,AACACACACAC,AACACACACACACACACAC 64.04 PASS AC=1,0,0,0,0,0,0,0;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 0/1:13:99:2,6,3,2 chr2 66668642 . AAC A 337.48 PASS AC=1;AF=0.5;AN=2;DP=78;MQ=60;set=variant23-variant33 GT:AD:DP:GQ:PL:SB 0/1:20,11:31:99:375,0,738:8,12,2,9 chr2 66794923 . A AT 3959.97 PASS AC=2;AF=0.977;AN=2;DP=7234;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,154:155:99:4425,435,0:0,1,79,75 chr2 66795237 . CT C,CTT 1641.32 PASS AC=1,0;AF=0.2,0.4;AN=2;DP=1696;MQ=60;set=variant12-variant17-variant22-variant23-variant25-variant27-variant30-variant31-variant34-variant43 GT:DP:GQ:SB 0/1:118:99:24,33,22,39 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 1/1:0,19:19:57:561,57,0:0,0,12,7 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 1/1:0,42:42:99:1342,126,0:0,0,14,28 chr2 67630980 . G A 3779.42 PASS AC=2;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 1/1:0,126:126:99:4072,378,0:0,0,59,67 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 0/1:52,37:89:99:1025,0,1409:24,28,17,20 chr2 67632125 . C T 3945.89 PASS AC=2;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 1/1:0,98:98:99:3167,294,0:0,0,50,48 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 1/1:0,195:195:99:5965,584,0:0,0,97,98 chr2 68273094 . A G 575.62 PASS AC=1;AF=0.5;AN=2;DP=145;FractionInformativeReads=1;MQ=60;set=variant23-variant27-variant40 GT:AD:DP:GQ:PL:SB 0/1:14,26:40:99:604,0,268:7,7,11,15 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 0/1:102,95:197:99:2354,0,2705:46,56,38,57 chr2 68357236 . TGAGAGAGA T,TGA,TGAGA 273.91 PASS AC=1,0,0;AF=0.563,0.063,0.083;AN=2;DP=685;set=variant-variant2-variant3-variant6-variant7-variant9-variant10-variant11-variant14-variant15-variant17-variant18-variant20-variant22-variant23-variant28-variant30-variant32-variant33-variant34-variant37-variant38-variant39-variant44 GT:DP:GQ:SB 0/1:20:99:2,14,0,4 chr2 68358341 . T C 787.66 PASS AC=1;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 0/1:27,31:58:99:952,0,601:16,11,24,7 chr2 68358653 . T C 211.57 PASS AC=1;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 0/1:20,15:35:99:445,0,539:5,15,3,12 chr2 68385097 . A G 1729.64 PASS AC=1;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 0/1:82,75:157:99:2044,0,2091:43,39,35,40 chr2 68388823 . A G 1604.94 PASS AC=1;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 0/1:53,63:116:99:1492,0,1303:27,26,34,29 chr2 68389276 . G GA 282.62 PASS AC=1;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 0/1:20,18:38:99:390,0,410:14,6,13,5 chr2 68389481 . CTT C 3293.3 PASS AC=1;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 0/1:69,60:129:99:2219,0,2941:28,41,24,36 chr2 68402153 . TA T 3242.12 PASS AC=1;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 0/1:34,40:74:99:1272,0,982:15,19,20,20 chr2 68402786 . TTTGCAGTTTC T 8212.68 PASS AC=1;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 0/1:85,57:142:99:2065,0,3984:50,35,37,20 chr2 68402830 . G C 11419.3 PASS AC=1;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 0/1:107,82:189:99:3191,0,4679:64,43,52,30 chr2 68402835 . A G 11597.5 PASS AC=1;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 0/1:111,90:201:99:3267,0,4684:67,44,56,34 chr2 68405934 . G GA 411.49 PASS AC=1;AF=0.5;AN=2;DP=46;FS=1.719;FractionInformativeReads=0.957;MQ=60;MQRankSum=-1.002;QD=8.95;ReadPosRankSum=0.695;SOR=1.186;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:24,20:44:99:449,0,589:20,4,18,2 chr2 68407926 . A G 7655.39 PASS AC=1;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 0/1:128,117:245:99:2588,0,2894:66,62,60,57 chr2 68415767 . G A 3767.93 PASS AC=1;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 0/1:59,66:125:99:1628,0,1316:28,31,29,37 chr2 68444171 . C G,CGCAG,CACGCAG,CACACGCAG 3275.22 PASS AC=0,0,1,0;AF=0.317,0.083,0.317,0.017;AN=2;DP=1969;set=variant7-variant8-variant11-variant14-variant15-variant3-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant28-variant30-variant31-variant32-variant33-variant34-variant6-variant37-variant38-variant39-variant40-variant12-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/3:38:99:18,11,6,3 chr2 68479576 . G A 1375.2 PASS AC=1;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 0/1:41,27:68:99:685,0,1080:23,18,17,10 chr2 68479671 . A G 924.42 PASS AC=1;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 0/1:36,21:57:99:495,0,919:19,17,9,12 chr2 68479717 . G GGGCGGAGGCGGGGGCGCGCGCGGGCCGGC 567.21 PASS AC=1;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 0/1:28,12:40:99:361,0,1581:12,16,4,8 chr2 68483396 . A T 834.7 PASS AC=1;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 0/1:9,6:15:99:158,0,279:3,6,1,5 chr2 68511506 . GA G,GAA 1874.76 PASS AC=2,0;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 1/1:64:99:0,3,29,32 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 0/1:22,34:56:99:898,0,535:8,14,13,21 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 0/1:26,20:46:99:532,0,727:19,7,15,5 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 0/1:7,6:13:99:150,0,195:4,3,4,2 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 0/1:6,9:15:99:198,0,149:3,3,5,4 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 0/1:6,13:19:99:366,0,132:2,4,7,6 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 0/1:31,48:79:99:1111,0,734:17,14,29,19 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 1/1:0,81:81:99:2416,243,0:0,0,35,46 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 0/1:18,12:30:99:406,0,467:8,10,1,11 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 0/1:52,48:100:99:1263,0,1248:23,29,23,25 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 0/1:63,61:124:99:1685,0,1679:26,37,30,31 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 0/1:12,6:18:99:210,0,418:11,1,6,0 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 0/1:22,24:46:99:643,0,571:14,8,17,7 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 0/1:55,54:109:99:1295,0,1528:24,31,24,30 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 0/1:3,4:7:98:102,0,98:3,0,4,0 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 0/1:33,43:76:99:1139,0,882:10,23,18,25 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 0/1:21,12:33:99:279,0,724:3,18,4,8 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 0/1:37,34:71:99:744,0,879:16,21,18,16 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 0/1:14,16:30:99:482,0,437:4,10,4,12 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 0/1:5,17:22:99:600,0,121:4,1,14,3 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 1/1:1,163:164:99:5160,480,0:1,0,63,100 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 0/1:60,76:136:99:2008,0,1397:27,33,30,46 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 0/1:12,13:25:99:490,0,507:6,6,6,7 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 0/1:13,12:25:99:457,0,510:7,6,6,6 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 2/1:24:99:0,0,12,12 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 0/1:21,10:31:99:396,0,714:12,9,6,4 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 1/1:0,39:39:99:1220,117,0:0,0,18,21 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 0/1:8,8:16:99:181,0,175:6,2,5,3 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 0/1:29,19:48:99:424,0,717:18,11,10,9 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 0/1:86,101:187:99:2343,0,1854:43,43,47,54 chr2 68694364 . C T 1080.71 PASS AC=1;AF=0.5;AN=2;DP=238;FractionInformativeReads=1;MQ=60;set=variant23-variant40 GT:AD:DP:GQ:PL:SB 0/1:56,50:106:99:1109,0,1349:29,27,22,28 chr2 68772281 . AT A 658.95 PASS AC=1;AF=0.5;AN=2;DP=760;MQ=60;set=variant5-variant12-variant22-variant23-variant24-variant27-variant28-variant30-variant32-variant33-variant34-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,37:55:99:876,0,348:10,8,22,15 chr2 68881938 . CAA CAAA,C,CA,CAAAA 146.83 PASS AC=0,0,1,0;AF=0.088,0.025,0.375,0.075;AN=2;DP=1760;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-variant28-variant30-filterInvariant31-variant32-variant33-variant36-variant37-variant38-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/3:32:97:18,6,6,2 chr2 69002760 . C T 1545.29 PASS AC=2;AF=0.538;AN=2;DP=2552;MQ=60;set=variant3-variant5-variant7-variant9-variant10-variant12-variant15-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant37-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:2957,286,0:0,0,59,37 chr2 69040500 . G A 1419.13 PASS AC=1;AF=0.6;AN=2;DP=1526;MQ=60;set=variant5-variant8-variant12-variant15-variant16-variant17-variant19-variant20-variant23-variant24-variant29-variant30-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:55,42:97:99:966,0,1331:26,29,23,19 chr2 69043264 . CT C 1151.17 PASS AC=1;AF=0.636;AN=2;DP=1820;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,24:58:99:500,0,1627:20,14,15,9 chr2 69043266 . T A 578.21 PASS AC=1;AF=0.636;AN=2;DP=1835;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant29-variant30-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,24:58:99:500,0,1627:20,14,15,9 chr2 69044064 . A C 1359.9 PASS AC=1;AF=0.6;AN=2;DP=2150;MQ=60;set=variant5-variant8-variant12-variant15-variant16-variant17-variant19-variant20-variant23-variant24-variant29-variant30-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:85,88:173:99:1869,0,1842:43,42,46,42 chr2 69049939 . G T 1561.61 PASS AC=1;AF=0.6;AN=2;DP=1574;MQ=60;set=variant5-variant8-variant12-variant15-variant16-variant17-variant19-variant20-variant23-variant24-variant29-variant30-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:55,42:97:99:1108,0,1524:27,28,20,22 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 0/1:32,47:79:99:1245,0,835:20,12,26,21 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 0/1:26,29:55:99:644,0,688:16,10,17,12 chr2 69180161 . T A 1054 PASS AC=2;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 1/1:0,20:20:60:697,60,0:0,0,5,15 chr2 69201501 . G A 332.98 PASS AC=2;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 1/1:0,28:28:84:1027,84,0:0,0,23,5 chr2 69201894 . C T 833.8 PASS AC=2;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 1/1:0,37:37:99:1357,111,0:0,0,6,31 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 1/1:0,58:58:99:1726,174,0:0,0,32,26 chr2 69317925 . G A 6041.88 PASS AC=2;AF=0.864;AN=2;DP=7209;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,132:132:99:4140,395,0:0,0,57,75 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 1/1:0,21:21:63:692,63,0:0,0,5,16 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 1/1:0,10:10:30:366,30,0:0,0,2,8 chr2 69351621 . T A 427.8 PASS AC=1;AF=0.553;AN=2;DP=410;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant9-variant10-variant13-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant29-variant30-variant31-variant32-variant34-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,9:21:99:249,0,459:11,1,7,2 chr2 69351963 . G A 112.64 PASS AC=1;AF=0.6;AN=2;DP=138;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant9-variant19-variant20-variant22-variant23-variant29-variant30-variant32 GT:AD:DP:GQ:PL:SB 0/1:7,4:11:99:106,0,240:1,6,1,3 chr2 69362161 . C T 1849.65 PASS AC=1;AF=0.567;AN=2;DP=2772;MQ=60;set=variant4-variant7-variant9-variant13-variant15-variant18-variant19-variant20-variant22-variant23-variant29-variant30-variant32-variant34-variant43 GT:AD:DP:GQ:PL:SB 0/1:125,80:205:99:1630,0,2921:70,55,45,35 chr2 69362262 . C G 2084.76 PASS AC=1;AF=0.567;AN=2;DP=3609;MQ=60;set=variant4-variant7-variant9-variant13-variant15-variant18-variant19-variant20-variant22-variant23-variant29-variant30-variant32-variant34-variant43 GT:AD:DP:GQ:PL:SB 0/1:149,92:241:99:1866,0,3478:72,77,42,50 chr2 69362407 . C A 541.5 PASS AC=1;AF=0.567;AN=2;DP=362;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant9-variant13-variant15-variant18-variant19-variant20-variant22-variant23-variant29-variant30-variant32-variant34-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,8:25:99:245,0,541:4,13,1,7 chr2 69362431 . T G 406.75 PASS AC=1;AF=0.667;AN=2;DP=146;MQ=60;set=variant4-variant7-variant9-variant20-variant22-variant23-variant29-variant30-variant32 GT:AD:DP:GQ:PL:SB 0/1:7,5:12:99:129,0,284:0,7,1,4 chr2 69398263 . G A 959.91 PASS AC=2;AF=0.677;AN=2;DP=1745;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant9-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1667,150,0:0,0,31,19 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 1/1:0,102:102:99:3312,306,0:0,0,38,64 chr2 69420591 . T TCTCA,TCACA,TCTCACA,TCACACA 614.72 PASS AC=1,0,0,0;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 0/1:21:1:0,2,3,16 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 1/1:0,32:32:97:1409,97,0:0,0,6,26 chr2 69552521 . C A 9954.42 PASS AC=1;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 0/1:127,176:303:99:4196,0,3025:76,51,102,74 chr2 69553375 . GA G 996.2 PASS AC=1;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 0/1:16,25:41:99:476,0,280:7,9,13,12 chr2 69573029 . T C 2047.23 PASS AC=1;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 0/1:34,31:65:99:763,0,814:17,17,16,15 chr2 69586293 . A C 1418.34 PASS AC=1;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 0/1:10,12:22:99:345,0,272:8,2,8,4 chr2 69586370 . A G 1301.89 PASS AC=1;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 0/1:25,16:41:99:395,0,551:13,12,9,7 chr2 69614161 . A G 2851.93 PASS AC=1;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 0/1:59,79:138:99:2013,0,1250:29,30,46,33 chr2 69623136 . A G 6459.13 PASS AC=1;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 0/1:122,116:238:99:2618,0,2715:59,63,59,57 chr2 69626342 . CA C 64.08 PASS AC=1;AF=0.5;AN=2;DP=1146;set=filterInvariant-variant2-variant3-variant4-variant6-variant7-filterInvariant8-filterInvariant9-variant11-filterInvariant13-variant14-variant15-variant16-variant17-filterInvariant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-filterInvariant30-variant31-variant34-variant36-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:200,0,175:9,3,9,2 chr2 69633382 . A T 170.22 PASS AC=1;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 0/1:3,3:6:99:105,0,119:0,3,0,3 chr2 69642572 . T C 337.45 PASS AC=1;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 0/1:9,4:13:60:60,0,331:1,8,2,2 chr2 69657349 . CTT CT,C 281.15 PASS AC=1,0;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 0/1:6:35:0,2,0,4 chr2 69659126 . A T 2617.5 PASS AC=1;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 0/1:50,34:84:99:752,0,1262:21,29,13,21 chr2 69688631 . CA CAA,C 1682.52 PASS AC=1,0;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 0/1:247:99:88,81,40,38 chr2 69688727 . AT A,ATT 630.49 PASS AC=1,0;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 0/1:190:99:56,82,21,31 chr2 69693006 . C T 4386.24 PASS AC=1;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 0/1:74,79:153:99:1954,0,2025:31,43,40,39 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 0/1:49,48:97:99:1143,0,1164:22,27,29,19 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 0/1:39,42:81:99:1557,0,1630:17,22,20,22 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 1/1:0,79:79:99:2480,237,0:0,0,32,47 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 0/1:20,25:45:99:666,0,515:14,6,16,9 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 0/1:12,14:26:99:418,0,323:3,9,4,10 chr2 69769884 . A T 239.18 PASS AC=1;AF=0.5;AN=2;DP=12;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.831;QD=19.93;ReadPosRankSum=1.309;SOR=1.022;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:5,7:12:99:267,0,183:0,5,0,7 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 0/1:51,57:108:99:1501,0,1380:35,16,37,20 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 0/1:14,15:29:99:564,0,825:2,12,3,12 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 0/1:10,12:22:99:516,0,732:0,10,2,10 chr2 70107979 . CAAA CA,CAA,C,CAAAA 439.63 PASS AC=0,1,0,0;AF=0.274,0.145,0.081,0.048;AN=2;DP=1210;set=variant-variant2-variant4-variant6-variant7-variant8-filterInvariant9-variant11-variant15-variant16-filterInvariant17-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant40-variant41-variant44 GT:DP:GQ:SB 0/2:30:99:8,6,13,3 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 0/1:26,17:43:99:354,0,614:16,10,11,6 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 0/1:56,61:117:99:1696,0,1559:32,24,32,29 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 0/1:44,48:92:99:699,0,629:27,17,28,20 chr2 70187727 . A AC 1278.05 PASS AC=1;AF=0.5;AN=2;DP=201;MQ=60;set=variant23-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,55:104:99:1315,0,1142:24,25,34,21 chr2 70188676 . T C 1517.65 PASS AC=1;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 0/1:56,63:119:99:1549,0,1414:20,36,30,33 chr2 70189141 . G A 494.15 PASS AC=1;AF=0.5;AN=2;DP=350;FractionInformativeReads=1;MQ=60;set=variant3-variant11-variant14-variant17-variant21-variant23-variant33-variant38 GT:AD:DP:GQ:PL:SB 0/1:13,19:32:99:580,0,289:5,8,8,11 chr2 70189331 . GACACACACACACAC GACACACACAC,GACACACACACAC,GACACAC,GACACACAC,G 299.81 PASS AC=0,2,0,0,0;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 2/2:4:12:0,0,1,3 chr2 70475933 . T G 305.87 PASS AC=1;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 0/1:3,8:11:96:191,0,96:2,1,3,5 chr2 70504926 . A G 543.45 PASS AC=2;AF=0.716;AN=2;DP=1109;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:518,42,0:0,0,6,8 chr2 70504972 . G C 622.14 PASS AC=2;AF=0.786;AN=2;DP=1568;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:793,69,0:0,0,13,10 chr2 70506223 . TA T 36.21 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=61;FS=1.501;FractionInformativeReads=0.967;MQ=60;MQRankSum=1.697;QD=0.59;ReadPosRankSum=-1.55;SOR=0.339;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:50,9:59:73:73,0,1159:33,17,5,4 chr2 70506331 . ACTT A 5798.08 PASS AC=2;AF=0.716;AN=2;DP=10810;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,257:257:99:11459,774,0:0,0,150,107 chr2 70508379 . G A 1142.04 PASS AC=2;AF=0.786;AN=2;DP=2233;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1966,149,0:0,0,0,50 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 0/1:33,17:50:99:608,0,1398:22,11,14,3 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 0/1:37,17:54:99:593,0,1628:26,11,14,3 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 0/1:40,20:60:99:710,0,1745:28,12,16,4 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 0/1:51,19:70:99:725,0,2120:35,16,16,3 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 0/1:54,22:76:99:864,0,2234:37,17,16,6 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 0/1:53,24:77:99:825,0,2195:36,17,16,8 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 0/1:88,15:103:99:149,0,3546:58,30,10,5 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 0/1:76,29:105:99:839,0,2155:49,27,19,10 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 0/1:104,32:136:99:1067,0,4331:62,42,21,11 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 0/1:114,33:147:99:1043,0,4626:67,47,22,11 chr2 70524576 . C G 561.01 PASS AC=1;AF=0.5;AN=2;DP=1778;set=variant3-variant5-variant14-filterInvariant15-filterInvariant20-filterInvariant23-filterInvariant26-variant41 GT:AD:DP:GQ:PL:SB 0/1:163,28:191:99:224,0,4196:86,77,18,10 chr2 70529205 . C CCCGCCCCCTCA 336.29 PASS AC=1;AF=0.5;AN=2;DP=33;FS=13.931;FractionInformativeReads=0.758;MQ=60;MQRankSum=-1.692;QD=10.19;ReadPosRankSum=0.471;SOR=3.25;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:15,10:25:99:374,0,1036:8,7,1,9 chr2 70674749 . G C 2105.81 PASS AC=1;AF=0.694;AN=2;DP=4370;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant36-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:61,64:125:99:1659,0,1644:42,19,42,22 chr2 70675581 . C G 109.9 PASS AC=1;AF=0.7;AN=2;DP=702;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant36-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:203,0,304:6,7,5,4 chr2 70676098 . G A 3189.7 PASS AC=1;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 0/1:34,28:62:99:748,0,936:17,17,13,15 chr2 70676318 . T TA 3060.63 PASS AC=1;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 0/1:37,24:61:99:501,0,874:17,20,12,12 chr2 70676639 . A G 922.11 PASS AC=1;AF=0.7;AN=2;DP=2341;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant34-variant36-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:34,21:55:99:522,0,928:22,12,12,9 chr2 70676769 . GA G 10663.5 PASS AC=1;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 0/1:86,109:195:99:2662,0,1884:58,28,65,44 chr2 70677463 . G A 4705.27 PASS AC=1;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 0/1:25,61:86:99:1545,0,513:11,14,28,33 chr2 70677994 . G A 6005.18 PASS AC=1;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 0/1:54,75:129:99:1862,0,1298:27,27,40,35 chr2 70678173 . C A 1801.13 PASS AC=1;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 0/1:16,17:33:99:666,0,912:6,10,5,12 chr2 70678176 . G A 1765.47 PASS AC=1;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 0/1:12,17:29:99:666,0,912:4,8,5,12 chr2 70678265 . C T 72.4 PASS AC=1;AF=0.7;AN=2;DP=36;FS=0;MQ=60;set=variant15-variant19-variant23-variant32-variant35 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:66:70,0,66:1,2,2,2 chr2 70679067 . G A 3940.34 PASS AC=1;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 0/1:41,43:84:99:992,0,1073:13,28,15,28 chr2 70680211 . CT C 2826.76 PASS AC=1;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 0/1:46,29:75:99:899,0,1605:29,17,18,11 chr2 70683753 . T C 682.07 PASS AC=1;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 0/1:3,14:17:68:409,0,68:0,3,3,11 chr2 70692557 . C T 675.03 PASS AC=1;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 0/1:4,6:10:99:147,0,102:2,2,4,2 chr2 70888203 . C A 426 PASS AC=1;AF=0.533;AN=2;DP=658;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant9-variant10-variant11-variant13-variant14-variant15-variant22-variant23-variant26-variant36-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,21:37:99:547,0,524:9,7,10,11 chr2 70900403 . G A 1793.18 PASS AC=1;AF=0.536;AN=2;DP=1654;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant9-variant10-variant11-variant14-variant15-variant22-variant23-variant26-variant36-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:63,54:117:99:1265,0,1622:27,36,27,27 chr2 70901785 . A G 1374.87 PASS AC=1;AF=0.536;AN=2;DP=919;MQ=60;set=variant-variant3-variant5-variant9-variant10-variant11-variant14-variant15-variant22-variant23-variant26-variant36-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:39,20:59:99:761,0,1736:26,13,12,8 chr2 70901788 . GGT G 1393.61 PASS AC=1;AF=0.536;AN=2;DP=972;MQ=60;set=variant-variant3-variant5-variant9-variant10-variant11-variant14-variant15-variant22-variant23-variant26-variant36-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:44,21:65:99:749,0,1875:29,15,13,8 chr2 70902120 . T A 247.44 PASS AC=1;AF=0.536;AN=2;DP=235;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant5-variant9-variant10-variant11-variant14-variant15-variant22-variant23-variant26-variant36-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:192,0,192:1,4,1,5 chr2 70902502 . C T 818.08 PASS AC=1;AF=0.5;AN=2;DP=670;MQ=60;set=variant3-variant5-variant9-variant11-variant14-variant15-variant22-variant23-variant26-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:32,29:61:99:729,0,744:15,17,13,16 chr2 70902672 . C A 1342.82 PASS AC=1;AF=0.5;AN=2;DP=671;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant9-variant11-variant14-variant15-variant22-variant23-variant26-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:24,38:62:99:988,0,599:10,14,19,19 chr2 70902823 . C T 566.58 PASS AC=1;AF=0.5;AN=2;DP=415;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant9-variant11-variant14-variant15-variant22-variant23-variant26-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:21,23:44:99:582,0,573:11,10,12,11 chr2 70903664 . G A 1679.54 PASS AC=1;AF=0.5;AN=2;DP=1049;MQ=60;set=variant3-variant5-variant9-variant11-variant15-variant22-variant23-variant26-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:33,52:85:99:1319,0,873:12,21,25,27 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 0/1:23,18:41:99:533,0,773:2,21,3,15 chr2 70917812 . C T 2476.49 PASS AC=1;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 0/1:45,43:88:99:821,0,1109:28,17,26,17 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 0/1:6,6:12:99:193,0,864:2,4,6,0 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 0/1:8,5:13:99:193,0,864:3,5,5,0 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 0/1:9,5:14:99:180,0,1088:4,5,5,0 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 0/1:12,5:17:99:171,0,1295:6,6,5,0 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 0/1:13,3:16:99:165,0,1338:7,6,3,0 chr2 70931420 . T C 49.57 PASS AC=1;AF=0.5;AN=2;DP=397;set=variant2-variant4-variant6-variant9-variant12-variant13-variant17-variant23-variant24-variant31-variant33-variant36-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,3:19:78:78,0,1366:8,8,3,0 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 0/1:78,75:153:99:1946,0,1875:38,40,35,40 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 0/1:64,55:119:99:1133,0,2311:33,31,27,28 chr2 70995233 . G A 1513.17 PASS AC=1;AF=0.556;AN=2;DP=969;MQ=60;set=variant17-variant18-variant19-variant20-variant23-variant29-variant34-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,63:112:99:1604,0,1795:24,25,32,31 chr2 71004368 . A G 228.53 PASS AC=2;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 1/1:0,5:5:15:169,15,0:0,0,3,2 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 0/1:7:28:2,0,3,2 chr2 71004492 . T C 492.85 PASS AC=1;AF=0.577;AN=2;DP=355;FractionInformativeReads=1;MQ=60;set=variant8-variant17-variant18-variant19-variant20-variant23-variant27-variant29-variant34-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,18:27:99:729,0,324:4,5,9,9 chr2 71004494 . A T 492.85 PASS AC=1;AF=0.577;AN=2;DP=358;FractionInformativeReads=1;MQ=60;set=variant8-variant17-variant18-variant19-variant20-variant23-variant27-variant29-variant34-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,18:27:99:729,0,324:4,5,9,9 chr2 71012604 . G A 869.59 PASS AC=2;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 1/1:0,105:105:99:3251,314,0:0,0,58,47 chr2 71012734 . C G 714.46 PASS AC=2;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 1/1:0,55:55:99:1897,165,0:0,0,17,38 chr2 71017516 . A G 985.3 PASS AC=1;AF=0.556;AN=2;DP=1969;MQ=60;set=variant-variant8-variant10-variant16-variant17-variant18-variant19-variant20-variant23-variant26-variant27-variant29-variant33-variant34-variant37-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,57:121:99:1359,0,1611:36,28,35,22 chr2 71043461 . C T 1330.89 PASS AC=1;AF=0.56;AN=2;DP=2590;FractionInformativeReads=1;MQ=60;set=variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-variant23-variant25-variant29-variant30-variant31-variant32-variant34-variant36-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,44:98:99:1133,0,1364:25,29,17,27 chr2 71044211 . C T 1054.13 PASS AC=1;AF=0.56;AN=2;DP=2236;MQ=60;set=variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant20-variant23-variant24-variant25-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,43:87:99:984,0,1114:18,26,17,26 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 0/1:24,32:56:99:724,0,556:15,9,18,14 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 1/1:0,55:55:99:1509,164,0:0,0,28,27 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 0/1:32,25:57:99:679,0,791:19,13,14,11 chr2 71058835 . A G 1083.72 PASS AC=1;AF=0.6;AN=2;DP=3618;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,45:105:99:1213,0,1592:42,18,32,13 chr2 71061108 . G A 1233.45 PASS AC=1;AF=0.5;AN=2;DP=1509;MQ=60;set=variant-variant2-variant3-variant4-variant12-variant13-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant33-variant37-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:34,26:60:99:607,0,846:11,23,10,16 chr2 71062648 . G A 1192.05 PASS AC=1;AF=0.558;AN=2;DP=2381;MQ=60;set=variant2-variant3-variant5-variant7-variant11-variant12-variant14-variant15-variant16-variant17-variant20-variant21-variant22-variant23-variant27-variant28-variant29-variant30-variant32-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,38:83:99:1020,0,1245:29,16,27,11 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 1/1:0,119:119:99:4446,364,0:0,0,50,69 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 0/1:10,11:21:99:331,0,287:6,4,7,4 chr2 71148045 . C T 782.27 PASS AC=2;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 1/1:0,21:21:63:660,63,0:0,0,14,7 chr2 71160421 . G C 885.97 PASS AC=1;AF=0.55;AN=2;DP=1644;FractionInformativeReads=1;MQ=60;set=variant8-variant9-variant10-variant11-variant12-variant15-variant19-variant21-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant33-variant34-variant36-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,28:57:99:728,0,747:9,20,9,19 chr2 71170807 . C T 946.57 PASS AC=1;AF=0.5;AN=2;DP=1485;set=variant-variant10-variant13-variant16-variant17-variant19-variant23-variant26-variant27-variant33-variant36-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,45:99:99:1173,0,1304:24,30,14,31 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 0/1:20,17:37:99:411,0,487:8,12,6,11 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 0/1:6,4:10:99:142,0,235:0,6,2,2 chr2 71206626 . G T 857.71 PASS AC=1;AF=0.5;AN=2;DP=863;MQ=60;set=variant4-variant5-variant6-variant11-variant20-variant23-variant25-variant31-variant34-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,26:67:99:569,0,1081:19,22,13,13 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 0/1:17,12:29:99:357,0,417:11,6,8,4 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 0/1:38,40:78:99:964,0,879:16,22,16,24 chr2 71304738 . G A 1512 PASS AC=1;AF=0.533;AN=2;DP=1880;MQ=60;set=variant5-variant7-variant9-variant16-variant19-variant21-variant23-variant25-variant29-variant30-variant32-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,40:91:99:1131,0,1313:21,30,15,25 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 0/1:39,47:86:99:1173,0,1023:22,17,25,22 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 1/1:0,135:135:99:3766,402,0:0,0,63,72 chr2 71351487 . G A 877.93 PASS AC=2;AF=0.571;AN=2;DP=1980;MQ=60;set=variant-variant2-variant5-variant7-variant8-variant9-variant11-variant12-variant14-variant16-variant19-variant21-variant23-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1651,150,0:0,0,19,31 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 1/1:0,177:177:99:4806,520,0:0,0,80,97 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 1/1:0,154:154:99:4883,461,0:0,0,93,61 chr2 71360723 . A G 805.17 PASS AC=2;AF=0.875;AN=2;DP=1592;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:1170,78,0:0,0,9,17 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 1/1:0,26:26:78:1170,78,0:0,0,9,17 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 1/1:0,80:80:99:2445,240,0:0,0,45,35 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 1/1:0,66:66:99:1967,198,0:0,0,29,37 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 1/1:0,18:18:54:586,54,0:0,0,15,3 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 1/1:0,182:182:99:5211,543,0:0,0,96,86 chr2 71559107 . T G 924.56 PASS AC=1;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 0/1:12,17:29:99:555,0,362:0,12,6,11 chr2 71607539 . G A 509.49 PASS AC=1;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 0/1:11,8:19:99:255,0,358:5,6,4,4 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 1/1:0,30:30:90:1158,90,0:0,0,25,5 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 1/1:0,61:61:99:1761,182,0:0,0,24,37 chr2 71622318 . T C 758.55 PASS AC=1;AF=0.5;AN=2;DP=123;FractionInformativeReads=1;MQ=60;set=variant10-variant13-variant23-variant39 GT:AD:DP:GQ:PL:SB 0/1:16,11:27:99:244,0,357:8,8,7,4 chr2 71626679 . CT C 2104.66 PASS AC=1;AF=0.667;AN=2;DP=1886;MQ=60;set=variant5-variant7-variant10-variant11-variant13-variant15-variant17-variant18-variant23-variant24-variant27-variant32-variant33-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:62,52:114:99:1449,0,1738:36,26,31,21 chr2 71627539 . C T 1744.56 PASS AC=1;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 0/1:18,16:34:99:399,0,446:10,8,11,5 chr2 71633275 . T C 4431.48 PASS AC=1;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 0/1:78,63:141:99:1324,0,1616:41,37,35,28 chr2 71633389 . C T 2840.28 PASS AC=1;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 0/1:41,40:81:99:979,0,1088:13,28,15,25 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 1/1:0,143:143:99:4721,427,0:0,0,50,93 chr2 71635431 . A G 3160.3 PASS AC=1;AF=0.5;AN=2;DP=235;FS=3.631;FractionInformativeReads=1;MQ=60;MQRankSum=0.821;QD=13.45;ReadPosRankSum=4.102;SOR=0.716;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:108,127:235:99:3189,0,2629:51,57,67,60 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 1/1:0,61:61:99:1879,183,0:0,0,23,38 chr2 71636036 . A G 149.59 PASS AC=1;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 0/1:4,8:12:99:283,0,147:0,4,1,7 chr2 71645828 . G A 1883.94 PASS AC=1;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 0/1:24,19:43:99:539,0,708:7,17,6,13 chr2 71645890 . G C 675.3 PASS AC=1;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 0/1:8,6:14:99:181,0,319:0,8,1,5 chr2 71645946 . G A 323.54 PASS AC=1;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 0/1:2,2:4:78:78,0,79:0,2,0,2 chr2 71651939 . T A 1290.99 PASS AC=1;AF=0.717;AN=2;DP=2609;MQ=60;set=variant3-variant5-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant27-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:33,48:81:99:1241,0,857:15,18,22,26 chr2 71680950 . C A 1537.71 PASS AC=1;AF=0.5;AN=2;DP=894;FractionInformativeReads=1;MQ=60;set=variant10-variant11-variant13-variant20-variant23-variant25-variant34-variant36-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:47,34:81:99:976,0,1339:33,14,22,12 chr2 71708201 . T C 272.19 PASS AC=1;AF=0.5;AN=2;DP=50;FractionInformativeReads=1;MQ=60;set=variant23-variant40 GT:AD:DP:GQ:PL:SB 0/1:15,11:26:99:300,0,376:6,9,2,9 chr2 71708825 . T TATCCATCC,TATCC,TATCCATCCATCC,TATCCATCCATCCATCC,TCC 160.48 PASS AC=0,1,0,0,0;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 0/2:19:99:4,2,11,2 chr2 71730149 . C T 163.69 PASS AC=1;AF=0.5;AN=2;DP=62;FractionInformativeReads=1;MQ=60;set=variant9-variant21-variant23-variant40 GT:AD:DP:GQ:PL:SB 0/1:7,3:10:70:70,0,245:6,1,3,0 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 1/1:0,91:91:99:2927,272,0:0,0,60,31 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 1/1:0,60:60:99:2030,179,0:0,0,14,46 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 1/1:0,31:31:93:1072,93,0:0,0,23,8 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 1/1:0,52:52:99:1638,155,0:0,0,34,18 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 1/1:0,98:98:99:3009,294,0:0,0,60,38 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 1/1:0,96:96:99:2809,286,0:0,0,39,57 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 1/1:0,53:53:99:1871,159,0:0,0,26,27 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 1/1:0,77:77:99:2615,229,0:0,0,25,52 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 1/1:0,33:33:99:1485,99,0:0,0,24,9 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 1/1:0,33:33:99:1485,99,0:0,0,24,9 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 0/1:78,77:155:99:1608,0,1833:32,46,40,37 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 0/1:9,12:21:99:371,0,307:7,2,8,4 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 0/1:34,23:57:99:627,0,986:17,17,7,16 chr2 71801564 . G A 954.38 PASS AC=1;AF=0.583;AN=2;DP=1335;MQ=60;set=variant2-variant3-variant4-variant6-variant10-variant13-variant16-variant17-variant18-variant21-variant23-variant24-variant25-variant27-variant30-variant38-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,42:69:99:1154,0,762:7,20,13,29 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 0/1:7,8:15:99:315,0,267:3,4,0,8 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 1/1:0,19:19:56:668,56,0:0,0,16,3 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 1/1:0,99:99:99:2980,296,0:0,0,61,38 chr2 71838597 . C A 1397.38 PASS AC=1;AF=0.636;AN=2;DP=3491;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,47:101:99:1330,0,1367:24,30,21,26 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 1/1:0,38:38:99:1148,114,0:0,0,16,22 chr2 71848076 . G A 128.18 PASS AC=1;AF=0.69;AN=2;DP=140;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant10-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant36-variant37-variant38-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,2:8:66:66,0,200:1,5,0,2 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 1/1:0,52:52:99:1600,156,0:0,0,32,20 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 1/1:0,21:21:63:742,63,0:0,0,4,17 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 1/1:0,71:71:99:2076,212,0:0,0,46,25 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 1/1:0,21:21:63:806,63,0:0,0,14,7 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 1/1:0,67:67:99:2215,201,0:0,0,46,21 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 0/1:81,72:153:99:1851,0,1925:42,39,34,38 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 1/1:0,11:11:33:442,33,0:0,0,9,2 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 0/1:31,28:59:99:769,0,949:8,23,6,22 chr2 72356351 . C G 466.74 PASS AC=1;AF=0.545;AN=2;DP=691;MQ=60;set=variant-variant4-variant5-variant10-variant12-variant13-variant14-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant33-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,11:31:99:311,0,662:16,4,9,2 chr2 72356370 . G A 991.13 PASS AC=1;AF=0.5;AN=2;DP=368;FractionInformativeReads=1;MQ=60;set=variant5-variant10-variant14-variant16-variant20-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:27,16:43:99:369,0,870:22,5,11,5 chr2 72356449 . G T 1983.7 PASS AC=1;AF=0.607;AN=2;DP=1990;MQ=60;set=variant-variant5-variant9-variant10-variant13-variant14-variant16-variant18-variant20-variant23-variant27-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:70,62:132:99:1478,0,1677:41,29,34,28 chr2 72356627 . T G 922.81 PASS AC=1;AF=0.591;AN=2;DP=1055;set=variant-variant4-variant5-variant6-variant9-variant10-variant12-variant13-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant33-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,24:42:99:726,0,510:5,13,6,18 chr2 72356745 . T TG 146.92 PASS AC=1;AF=0.615;AN=2;DP=116;MQ=60;set=variant5-variant9-variant16-variant20-variant21-variant23-variant26-variant27-variant28-variant33-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,6:11:99:188,0,152:3,2,3,3 chr2 72356965 . A ACACACG 805.93 PASS AC=1;AF=0.575;AN=2;DP=1426;set=variant4-variant5-variant6-variant10-variant12-variant13-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant33-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,31:60:99:1257,0,1962:16,13,19,12 chr2 72357336 . C T 849.37 PASS AC=1;AF=0.563;AN=2;DP=996;MQ=60;set=variant4-variant5-variant12-variant13-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant33-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:33,40:73:99:965,0,757:19,14,21,19 chr2 72357455 . G C 963.69 PASS AC=1;AF=0.563;AN=2;DP=964;MQ=60;set=variant4-variant5-variant12-variant13-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant33-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,32:56:99:848,0,708:11,13,14,18 chr2 72358959 . C A 704.66 PASS AC=1;AF=0.563;AN=2;DP=815;MQ=60;set=variant4-variant5-variant12-variant13-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant33-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,18:40:99:421,0,604:14,8,10,8 chr2 72359312 . A G 1453.53 PASS AC=1;AF=0.563;AN=2;DP=2202;MQ=60;set=variant4-variant5-variant12-variant13-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant33-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:66,62:128:99:1595,0,1654:38,28,35,27 chr2 72359518 . A G 3366.43 PASS AC=1;AF=0.5;AN=2;DP=881;FractionInformativeReads=1;MQ=60;set=variant5-variant16-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:94,99:193:99:2798,0,2405:54,40,61,38 chr2 72361865 . C A 688.73 PASS AC=1;AF=0.563;AN=2;DP=849;MQ=60;set=variant4-variant5-variant12-variant13-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant33-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,18:36:99:385,0,531:11,7,11,7 chr2 72361960 . A G 1754.6 PASS AC=1;AF=0.563;AN=2;DP=1552;MQ=60;set=variant4-variant5-variant12-variant13-variant16-variant20-variant21-variant23-variant25-variant26-variant27-variant28-variant30-variant33-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,27:64:99:669,0,974:19,18,12,15 chr2 72403387 . CA CAA,C 138.75 PASS AC=1,0;AF=0.425,0.075;AN=2;DP=717;set=variant3-variant4-variant7-filterInvariant10-variant11-variant12-variant13-variant14-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant32-variant34-variant36-variant38-variant41 GT:DP:GQ:SB 0/1:23:46:2,5,6,10 chr2 72403408 . GGAA G 641.05 PASS AC=2;AF=0.536;AN=2;DP=520;set=variant3-variant7-variant11-variant19-variant20-variant21-variant23-variant24-variant27-variant32-variant34-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:979,69,0:0,0,11,12 chr2 72403848 . T C 506.12 PASS AC=2;AF=0.536;AN=2;DP=754;MQ=60;set=variant3-variant7-variant11-variant19-variant20-variant21-variant23-variant24-variant27-variant32-variant34-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1283,117,0:0,0,23,16 chr2 72405008 . C G 826.75 PASS AC=2;AF=0.536;AN=2;DP=855;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant11-variant19-variant20-variant21-variant23-variant24-variant27-variant32-variant34-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1082,105,0:0,0,17,18 chr2 72405098 . C A 870.23 PASS AC=2;AF=0.536;AN=2;DP=714;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant11-variant19-variant20-variant21-variant23-variant24-variant27-variant32-variant34-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1324,143,0:0,0,24,24 chr2 72405641 . G GTA 1653.62 PASS AC=2;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 1/1:0,42:42:99:1882,126,0:0,0,20,22 chr2 72405827 . A T 1372.44 PASS AC=2;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 1/1:0,41:41:99:1780,123,0:0,0,26,15 chr2 72405833 . A G 1443.66 PASS AC=2;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 1/1:0,39:39:99:1765,123,0:0,0,24,15 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 1/1:0,105:105:99:4882,330,0:0,0,58,47 chr2 72742083 . GACAC GAC,G,GACACAC,GACACACAC 1455.95 PASS AC=2,0,0,0;AF=0.693,0.17,0.011,0.011;AN=2;DP=2385;set=Intersection GT:DP:GQ:SB 1/1:38:99:0,0,28,10 chr2 73114352 . A C 139.16 PASS AC=1;AF=0.769;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-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,11:20:99:369,0,169:5,4,7,4 chr2 73151231 . C T 7557.27 PASS AC=2;AF=0.955;AN=2;DP=9336;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,204:205:99:5525,590,0:1,0,117,87 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 0/1:6,8:14:99:283,0,301:1,5,3,5 chr2 73215562 . T C 652.74 PASS AC=1;AF=0.587;AN=2;DP=1181;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant13-variant22-variant23-variant24-variant26-variant27-variant30-variant33-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,25:46:99:727,0,479:8,13,6,19 chr2 73226090 . G A 854.07 PASS AC=1;AF=0.6;AN=2;DP=1577;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant22-variant23-variant24-variant26-variant27-variant33-variant36-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:50,37:87:99:791,0,1353:28,22,22,15 chr2 73226259 . A G 196.29 PASS AC=1;AF=0.591;AN=2;DP=725;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant13-variant22-variant23-variant24-variant26-variant27-variant33-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,12:31:99:272,0,534:5,14,4,8 chr2 73226282 . T C 188.87 PASS AC=1;AF=0.591;AN=2;DP=453;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant13-variant22-variant23-variant24-variant26-variant27-variant33-variant36-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:10,6:16:99:181,0,357:1,9,1,5 chr2 73268663 . A G 123.94 PASS AC=1;AF=0.5;AN=2;DP=53;FractionInformativeReads=1;MQ=60;set=variant22-variant23-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:15,7:22:99:168,0,468:11,4,4,3 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 0/1:2,4:6:34:84,0,34:2,0,2,2 chr2 73285752 . T A 1397.21 PASS AC=1;AF=0.55;AN=2;DP=2881;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant22-variant23-variant24-variant26-variant27-variant33-variant36-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:81,50:131:99:1117,0,1796:38,43,22,28 chr2 73300661 . A C 824.35 PASS AC=1;AF=0.536;AN=2;DP=589;MQ=60;set=variant3-variant8-variant11-variant16-variant19-variant20-variant23-variant24-variant28-variant30-variant31-variant34-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,14:28:99:325,0,346:7,7,9,5 chr2 73301618 . T C 567.93 PASS AC=1;AF=0.571;AN=2;DP=1256;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant22-variant23-variant24-variant26-variant27-variant31-variant33-variant36-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,26:54:99:628,0,648:14,14,15,11 chr2 73301687 . G A 669.94 PASS AC=1;AF=0.571;AN=2;DP=1241;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant22-variant23-variant24-variant26-variant27-variant31-variant33-variant36-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,27:47:99:634,0,511:10,10,15,12 chr2 73301817 . T C 764.92 PASS AC=1;AF=0.536;AN=2;DP=849;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant9-variant22-variant23-variant24-variant26-variant31-variant33-variant36-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,31:55:99:695,0,616:13,11,14,17 chr2 73302891 . G GGCCT 425.39 PASS AC=1;AF=0.571;AN=2;DP=1300;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant22-variant23-variant24-variant26-variant27-variant31-variant33-variant36-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,23:41:99:883,0,904:8,10,9,14 chr2 73316540 . A T 1441.95 PASS AC=1;AF=0.571;AN=2;DP=3671;MQ=60;set=variant-variant2-variant3-variant6-variant8-variant9-variant10-variant11-variant22-variant23-variant24-variant26-variant27-variant31-variant33-variant36-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:69,75:144:99:1872,0,1770:35,34,35,40 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 1/1:0,155:155:99:4380,462,0:0,0,86,69 chr2 73339708 . G A 2255.88 PASS AC=1;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 0/1:155,127:282:99:2920,0,3836:83,72,66,61 chr2 73430234 . T C 1149.12 PASS AC=1;AF=0.742;AN=2;DP=1325;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,16:41:99:394,0,611:12,13,6,10 chr2 73430416 . G A 255.13 PASS AC=1;AF=0.643;AN=2;DP=183;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant9-variant10-variant12-variant13-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,4:7:74:112,0,74:1,2,1,3 chr2 73435786 . C A 899.91 PASS AC=1;AF=0.62;AN=2;DP=849;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant9-variant10-variant12-variant13-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,10:21:99:262,0,352:2,9,3,7 chr2 73438442 . GA GAA,G 243.52 PASS AC=1,0;AF=0.71,0.048;AN=2;DP=684;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant33-variant36-variant37-variant38-filterInvariant39-variant40-variant41-variant42-variant43 GT:DP:GQ:SB 0/1:33:99:9,7,11,6 chr2 73441717 . C T 1438.44 PASS AC=1;AF=0.5;AN=2;DP=680;MQ=60;set=variant-variant22-variant23-variant27-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:52,45:97:99:1057,0,1273:27,25,26,19 chr2 73449981 . G A 547.15 PASS AC=1;AF=0.5;AN=2;DP=331;FractionInformativeReads=1;MQ=60;set=variant-variant22-variant23-variant27-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:34,42:76:99:983,0,847:18,16,23,19 chr2 73454403 . G A 174.16 PASS AC=1;AF=0.5;AN=2;DP=86;FractionInformativeReads=1;MQ=60;set=variant-variant22-variant23-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:6,2:8:66:66,0,191:2,4,0,2 chr2 73457424 . G A 507.42 PASS AC=1;AF=0.5;AN=2;DP=396;FractionInformativeReads=1;MQ=60;set=variant-variant10-variant13-variant22-variant23-variant27-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:26,13:39:99:349,0,644:10,16,5,8 chr2 73460293 . AGGGCC A 1751.3 PASS AC=1;AF=0.726;AN=2;DP=1391;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:28,31:59:99:1198,0,1718:9,19,13,18 chr2 73460517 . T G 44.15 PASS AC=1;AF=0.5;AN=2;DP=38;FractionInformativeReads=1;MQ=60;set=variant-variant23-variant27-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:5,2:7:69:69,0,124:2,3,0,2 chr2 73461553 . C T 1410.6 PASS AC=1;AF=0.5;AN=2;DP=733;MQ=60;set=variant-variant22-variant23-variant27-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:80,57:137:99:1203,0,1838:36,44,24,33 chr2 73462880 . A G 1479.43 PASS AC=1;AF=0.5;AN=2;DP=740;MQ=60;set=variant-variant10-variant13-variant22-variant23-variant27-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:52,45:97:99:1031,0,1290:23,29,18,27 chr2 73471193 . GT G,GTT 130.77 PASS AC=1,0;AF=0.457,0.043;AN=2;DP=2427;set=filterInvariant-filterInvariant2-variant3-filterInvariant5-variant6-variant7-variant8-filterInvariant9-filterInvariant10-filterInvariant11-variant13-variant14-filterInvariant15-variant16-filterInvariant17-filterInvariant18-variant20-variant21-filterInvariant23-filterInvariant24-variant25-variant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant31-filterInvariant32-variant33-variant34-variant36-variant39-variant40-filterInvariant41-filterInvariant42-variant44 GT:DP:GQ:SB 0/1:47:99:10,24,4,9 chr2 73472012 . G A 1618.86 PASS AC=1;AF=0.742;AN=2;DP=1460;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,12:28:99:353,0,476:5,11,2,10 chr2 73476417 . GT G,GTT 251.36 PASS AC=0,1;AF=0.25,0.25;AN=2;DP=66;MQ=60;set=variant10-variant23 GT:DP:GQ:SB 0/2:26:99:3,7,4,12 chr2 73476857 . T C 45.21 PASS AC=1;AF=0.5;AN=2;DP=317;FractionInformativeReads=1;MQ=60;set=variant-variant10-variant13-variant22-variant23-variant27-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:16,32:48:99:817,0,439:10,6,20,12 chr2 73477527 . C T 909.51 PASS AC=1;AF=0.5;AN=2;DP=725;MQ=60;set=variant-variant10-variant13-variant22-variant23-variant27-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:42,37:79:99:992,0,1018:19,23,12,25 chr2 73480204 . A G 845.81 PASS AC=1;AF=0.563;AN=2;DP=737;MQ=60;set=variant-variant10-variant13-variant22-variant23-variant27-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:37,39:76:99:954,0,1033:10,27,14,25 chr2 73483057 . T C 1224.76 PASS AC=1;AF=0.742;AN=2;DP=1533;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,21:39:99:546,0,458:7,11,10,11 chr2 73483186 . C G 516.23 PASS AC=1;AF=0.563;AN=2;DP=414;FractionInformativeReads=1;MQ=60;set=variant-variant10-variant13-variant22-variant23-variant27-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:26,18:44:99:356,0,624:15,11,8,10 chr2 73484751 . A T 447.34 PASS AC=1;AF=0.563;AN=2;DP=244;MQ=60;set=variant-variant10-variant13-variant22-variant23-variant27-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:10,12:22:99:318,0,247:4,6,6,6 chr2 73488189 . C CT 98.4 PASS AC=2;AF=0.667;AN=2;DP=60;MQ=60;set=variant10-variant13-variant23-variant27-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:129,15,0:0,0,2,3 chr2 73490125 . A G 332.45 PASS AC=1;AF=0.708;AN=2;DP=438;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant9-variant12-variant13-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant33-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:11,5:16:99:160,0,278:7,4,4,1 chr2 73490412 . A G 847.65 PASS AC=1;AF=0.719;AN=2;DP=1760;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:30,24:54:99:655,0,757:13,17,10,14 chr2 73491683 . G A 1214.74 PASS AC=1;AF=0.568;AN=2;DP=914;MQ=60;set=variant2-variant4-variant5-variant6-variant8-variant11-variant14-variant15-variant19-variant22-variant23-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,10:37:99:201,0,818:7,20,3,7 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 0/1:108,93:201:99:2171,0,2754:49,59,36,57 chr2 73493303 . T C 553.98 PASS AC=1;AF=0.679;AN=2;DP=868;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant18-variant19-variant20-variant23-variant24-variant25-variant27-variant31-variant32-variant34-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,17:27:99:478,0,288:2,8,7,10 chr2 73511468 . A G 525.11 PASS AC=1;AF=0.643;AN=2;DP=176;MQ=60;set=variant-variant10-variant17-variant23-variant30-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:7,14:21:99:382,0,136:6,1,6,8 chr2 73518533 . G A 3939.73 PASS AC=1;AF=0.643;AN=2;DP=1006;MQ=60;set=variant-variant17-variant23-variant30-variant34-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:66,80:146:99:2080,0,1493:34,32,43,37 chr2 73518867 . G A 6523.2 PASS AC=1;AF=0.643;AN=2;DP=1735;MQ=60;set=variant-variant17-variant23-variant30-variant34-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:141,145:286:99:3307,0,3448:73,68,75,70 chr2 73613031 . TGGAGGAGGA TGGA,TGGAGGAGGAGGA,TGGAGGA,TGGAGGAGGAGGAGGA,T 601.68 PASS AC=1,1,0,0,0;AF=0.318,0.42,0.045,0.034,0.011;AN=2;DP=2483;set=Intersection GT:DP:GQ:SB 1/2:53:99:1,0,39,13 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 0/1:39,25:64:99:554,0,1142:13,26,7,18 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 0/1:33,24:57:99:641,0,999:25,8,17,7 chr2 73650122 . T A 811.79 PASS AC=1;AF=0.716;AN=2;DP=2295;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,25:54:99:627,0,935:4,25,7,18 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 0/1:37,36:73:99:829,0,877:14,23,18,18 chr2 73675227 . T TCTC 2725.07 PASS AC=1;AF=0.737;AN=2;DP=5569;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,76:154:99:2979,0,3382:42,36,39,37 chr2 73675669 . T G 1353.97 PASS AC=2;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 1/1:0,96:96:99:3207,288,0:0,0,52,44 chr2 73675844 . C T 1611.65 PASS AC=1;AF=0.716;AN=2;DP=7457;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:102,92:194:99:2202,0,2714:52,50,51,41 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 0/1:156,143:299:99:3573,0,3966:82,74,78,65 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 0/1:147,144:291:99:3601,0,3656:79,68,76,68 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 0/1:68,68:136:99:1760,0,1810:30,38,33,35 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 0/1:49,36:85:99:826,0,1341:23,26,15,21 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 0/1:41,27:68:99:669,0,1052:19,22,14,13 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 0/1:46,54:100:99:1373,0,1255:23,23,25,29 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 0/1:47,24:71:99:542,0,1215:23,24,14,10 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 0/1:60,41:101:99:879,0,1528:29,31,19,22 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 0/1:20,14:34:99:290,0,505:12,8,8,6 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 0/1:14,12:26:99:366,0,518:14,0,10,2 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 0/1:8,7:15:99:240,0,266:1,7,0,7 chr2 73828310 . T C 1387.08 PASS AC=1;AF=0.724;AN=2;DP=5499;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:52,73:125:99:2172,0,1539:40,12,56,17 chr2 73828538 . G A 2577.55 PASS AC=1;AF=0.737;AN=2;DP=8418;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:117,105:222:99:2515,0,3204:40,77,40,65 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 0/1:93,56:149:99:1287,0,2338:56,37,33,23 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 0/1:15:46:1,3,2,9 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 0/1:72,65:137:99:1712,0,2037:18,54,19,46 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 0/1:8,6:14:99:171,0,237:5,3,5,1 chr2 73867897 . A G 270.12 PASS AC=2;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 1/1:0,20:20:60:643,60,0:0,0,13,7 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 0/1:103,91:194:99:2046,0,2610:58,45,54,37 chr2 73898118 . C T 396.83 PASS AC=1;AF=0.73;AN=2;DP=1149;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,11:27:99:367,0,432:11,5,10,1 chr2 73898359 . G A 686.91 PASS AC=1;AF=0.73;AN=2;DP=2040;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,29:53:99:799,0,677:6,18,7,22 chr2 73898420 . A G 323.76 PASS AC=1;AF=0.73;AN=2;DP=694;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,10:16:99:361,0,211:0,6,1,9 chr2 73899955 . G T 3007.29 PASS AC=2;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 1/1:0,268:268:99:7801,798,0:0,0,171,97 chr2 73900210 . A G 938.26 PASS AC=2;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 1/1:0,49:49:99:1973,147,0:0,0,6,43 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 0/1:10,10:20:99:383,0,242:8,2,10,0 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 0/1:34:99:7,6,18,3 chr2 73927931 . A G 1248.66 PASS AC=1;AF=0.789;AN=2;DP=4756;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,56:107:99:1554,0,1445:24,27,34,22 chr2 73928043 . G T 2227.74 PASS AC=1;AF=0.5;AN=2;DP=240;FS=1.001;FractionInformativeReads=0.996;MQ=60;MQRankSum=-0.22;QD=9.28;ReadPosRankSum=-1.159;SOR=0.617;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:136,103:239:99:2256,0,3279:74,62,54,49 chr2 73928098 . C G 1476.79 PASS AC=1;AF=0.716;AN=2;DP=11028;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:121,162:283:99:4056,0,2833:65,56,76,86 chr2 73928366 . G C 2446.4 PASS AC=1;AF=0.708;AN=2;DP=9527;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:146,129:275:99:3095,0,3683:76,70,64,65 chr2 73956940 . CTT CT,C 247.98 PASS AC=1,0;AF=0.588,0.013;AN=2;DP=1286;set=variant-variant2-variant3-variant4-variant5-filterInvariant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:19:91:6,0,8,5 chr2 73957124 . A G 1396.92 PASS AC=1;AF=0.716;AN=2;DP=4382;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:56,63:119:99:1333,0,1303:23,33,29,34 chr2 73957227 . T A 460.72 PASS AC=1;AF=0.716;AN=2;DP=1241;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,10:23:99:326,0,386:3,10,1,9 chr2 73959935 . T A 504.77 PASS AC=1;AF=0.743;AN=2;DP=561;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:189,0,265:3,3,2,3 chr2 73959960 . G T 471.79 PASS AC=1;AF=0.743;AN=2;DP=439;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,5:13:99:186,0,272:3,5,2,3 chr2 73964631 . C T 46.15 PASS AC=1;AF=0.689;AN=2;DP=537;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:159,0,111:1,3,2,4 chr2 73994074 . G A 2540.04 PASS AC=2;AF=0.943;AN=2;DP=2506;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1209,111,0:0,0,12,25 chr2 73995810 . G A 827.28 PASS AC=1;AF=0.5;AN=2;DP=64;FS=1.056;FractionInformativeReads=1;MQ=60;MQRankSum=1.115;QD=12.93;ReadPosRankSum=1.222;SOR=0.914;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:33,31:64:99:856,0,863:10,23,8,23 chr2 74000701 . C T 113.67 PASS AC=1;AF=0.773;AN=2;DP=286;FS=0;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:68:182,0,68:0,2,2,4 chr2 74007136 . T C 492.02 PASS AC=1;AF=0.73;AN=2;DP=3198;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,41:99:99:1058,0,1454:29,29,20,21 chr2 74007345 . A G 591.17 PASS AC=1;AF=0.724;AN=2;DP=1867;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,25:38:99:647,0,303:3,10,12,13 chr2 74035880 . A G 218.73 PASS AC=1;AF=0.989;AN=2;DP=461;FS=0;MQRankSum=-1.221;ReadPosRankSum=-0.322;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:3,5:8:71:117,0,71:1,2,2,3 chr2 74044406 . T A 68.08 PASS AC=1;AF=0.5;AN=2;DP=26;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.065;QD=2.62;ReadPosRankSum=-1.041;SOR=0.394;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:21,5:26:96:96,0,678:4,17,1,4 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 1/1:0,41:41:99:1242,123,0:0,0,16,25 chr2 74074501 . T C 577.86 PASS AC=1;AF=0.5;AN=2;DP=45;FS=2.54;FractionInformativeReads=1;MQ=60;MQRankSum=-0.811;QD=12.84;ReadPosRankSum=-2.136;SOR=1.136;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:20,25:45:99:606,0,471:10,10,15,10 chr2 74087298 . A G 756.18 PASS AC=1;AF=0.5;AN=2;DP=345;FractionInformativeReads=1;MQ=60;set=variant13-variant21-variant23-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:48,22:70:99:516,0,1280:18,30,9,13 chr2 74090063 . TA T 3444.3 PASS AC=2;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 1/1:0,194:194:99:5893,583,0:0,0,106,88 chr2 74091097 . T C 4470.46 PASS AC=1;AF=0.5;AN=2;DP=2574;MQ=60;set=variant-variant6-variant15-variant17-variant22-variant23-variant36-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:109,142:251:99:3291,0,2641:56,53,70,72 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 1/1:0,56:56:99:1709,168,0:0,0,26,30 chr2 74091650 . G A 164.06 PASS AC=1;AF=0.5;AN=2;DP=159;FractionInformativeReads=1;MQ=60;set=variant-variant17-variant23-variant36 GT:AD:DP:GQ:PL:SB 0/1:22,22:44:99:571,0,513:11,11,11,11 chr2 74091805 . C T 682.57 PASS AC=2;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 1/1:0,74:74:99:2069,221,0:0,0,37,37 chr2 74092119 . C T 569.63 PASS AC=1;AF=0.5;AN=2;DP=435;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant15-variant17-variant22-variant23-variant36-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,19:46:99:374,0,589:15,12,10,9 chr2 74092829 . G A 3576.06 PASS AC=1;AF=0.5;AN=2;DP=1074;FractionInformativeReads=1;MQ=60;set=variant-variant17-variant23-variant36 GT:AD:DP:GQ:PL:SB 0/1:119,127:246:99:2943,0,2724:59,60,60,67 chr2 74093652 . T C 1180.11 PASS AC=1;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 0/1:50,50:100:99:1325,0,1256:25,25,24,26 chr2 74093682 . T A 1210.94 PASS AC=1;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 0/1:43,43:86:99:1114,0,1043:21,22,20,23 chr2 74100830 . G GT 200.83 PASS AC=1;AF=0.5;AN=2;DP=215;MQ=60;set=variant13-variant21-variant23-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:17,11:28:99:246,0,435:3,14,3,8 chr2 74120181 . A G 976.83 PASS AC=1;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 0/1:23,21:44:99:509,0,546:11,12,8,13 chr2 74120275 . G A 181.63 PASS AC=1;AF=0.5;AN=2;DP=16;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.059;QD=11.35;ReadPosRankSum=-0.635;SOR=0.473;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:210,0,322:1,8,1,6 chr2 74128659 . ATGTG A,ATGTGTG,ATGTGTGTG 92.55 PASS AC=0,0,1;AF=0.056,0.278,0.222;AN=2;DP=374;set=variant-filterInvariant3-filterInvariant16-variant18-filterInvariant21-filterInvariant22-variant23-filterInvariant28-variant42 GT:DP:GQ:SB 0/3:8:10:0,1,0,7 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 0/1:16,11:27:99:308,0,437:6,10,4,7 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 1/1:0,146:146:99:4430,434,0:0,0,92,54 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 0/1:7,6:13:99:150,0,155:3,4,2,4 chr2 74273383 . T TC 1149.23 PASS AC=1;AF=0.586;AN=2;DP=2733;MQ=60;set=variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,32:85:99:781,0,1384:31,22,18,14 chr2 74300717 . T C 1210.73 PASS AC=1;AF=0.583;AN=2;DP=2958;MQ=60;set=variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,35:69:99:812,0,799:13,21,17,18 chr2 74320262 . C G 217.59 PASS AC=1;AF=0.583;AN=2;DP=1015;MQ=60;set=variant4-variant6-variant7-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant31-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,16:31:99:531,0,425:4,11,3,13 chr2 74326902 . C T 77.95 PASS AC=2;AF=0.677;AN=2;DP=522;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant29-variant31-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,20:21:53:675,53,0:1,0,7,13 chr2 74327453 . C T 256.38 PASS AC=2;AF=0.556;AN=2;DP=395;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant13-variant14-variant15-variant18-variant19-variant21-variant22-variant23-variant26-variant31-variant33-variant34-variant36-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,29:29:87:981,87,0:0,0,20,9 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 1/1:0,58:58:99:2555,174,0:0,0,29,29 chr2 74333220 . C CT 6402.99 PASS AC=2;AF=0.977;AN=2;DP=12538;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:17,184:201:99:4521,134,0:7,10,74,110 chr2 74334462 . G A 1112.29 PASS AC=1;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 0/1:53,44:97:99:1082,0,1481:31,22,21,23 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 0/1:4,5:9:69:158,0,69:3,1,4,1 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 1/1:0,20:20:60:726,60,0:0,0,4,16 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 0/1:13,4:17:81:81,0,319:5,8,1,3 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 0/1:18,14:32:99:288,0,419:10,8,8,6 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 0/1:4,3:7:99:114,0,433:2,2,1,2 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 0/1:1,2:3:37:81,0,37:0,1,0,2 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 0/1:8:34:0,3,0,5 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 0/1:11,13:24:99:332,0,302:4,7,5,8 chr2 74441799 . A G 700.28 PASS AC=1;AF=0.525;AN=2;DP=731;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant10-variant11-variant12-variant17-variant20-variant21-variant23-variant25-variant29-variant32-variant33-variant34-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,15:25:99:540,0,326:7,3,13,2 chr2 74442353 . G C 460.63 PASS AC=1;AF=0.5;AN=2;DP=80;FractionInformativeReads=1;MQ=60;set=variant23-variant33 GT:AD:DP:GQ:PL:SB 0/1:26,18:44:99:489,0,621:14,12,16,2 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 0/1:52,43:95:99:1712,0,2077:28,24,25,18 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 0/1:54,56:110:99:1939,0,2085:23,31,28,28 chr2 74443542 . C T 1241.88 PASS AC=1;AF=0.5;AN=2;DP=204;FractionInformativeReads=1;MQ=60;set=variant23-variant33 GT:AD:DP:GQ:PL:SB 0/1:50,43:93:99:1270,0,1459:27,23,24,19 chr2 74444431 . A T 4369.21 PASS AC=1;AF=0.526;AN=2;DP=7162;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant10-variant11-variant12-variant17-variant20-variant21-variant23-variant25-variant29-variant32-variant33-variant34-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:172,178:350:99:4371,0,4479:87,85,102,76 chr2 74445416 . TTGA T 1894.57 PASS AC=1;AF=0.526;AN=2;DP=1827;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant10-variant11-variant12-variant17-variant20-variant21-variant23-variant25-variant29-variant32-variant33-variant34-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:32,31:63:99:1206,0,1586:9,23,10,21 chr2 74452259 . C T 565.7 PASS AC=1;AF=0.5;AN=2;DP=307;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant11-variant13-variant21-variant23-variant27-variant33 GT:AD:DP:GQ:PL:SB 0/1:9,20:29:99:589,0,274:2,7,7,13 chr2 74489490 . CTTT CTT,CT,CTTTTT,C 168.93 PASS AC=1,0,0,0;AF=0.426,0.074,0.037,0.019;AN=2;DP=854;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant13-filterInvariant15-variant16-filterInvariant19-variant22-variant23-variant24-variant25-variant27-variant28-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:24:99:4,10,3,7 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 0/1:51,12:63:75:75,0,1250:33,18,8,4 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 0/1:51,18:69:99:150,0,1075:33,18,11,7 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 0/1:111,44:155:81:81,0,1418:28,83,44,0 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 0/1:109,40:149:99:241,0,3429:21,88,40,0 chr2 74720002 . C G 1754.44 PASS AC=1;AF=0.977;AN=2;DP=3163;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:55,43:98:99:994,0,1325:28,27,21,22 chr2 74725144 . T C 7133.06 PASS AC=1;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 0/1:119,117:236:99:2905,0,2836:65,54,64,53 chr2 74732957 . GCCAT G 2336.79 PASS AC=1;AF=0.5;AN=2;DP=90;FS=0.844;FractionInformativeReads=1;MQ=60;MQRankSum=0.195;QD=25.96;ReadPosRankSum=2.055;SOR=0.569;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:31,59:90:99:2374,0,1503:12,19,25,34 chr2 74732962 . GAT G 2336.71 PASS AC=1;AF=0.5;AN=2;DP=89;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.48;QD=26.26;ReadPosRankSum=1.966;SOR=0.614;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:30,59:89:99:2374,0,1503:12,18,25,34 chr2 74780250 . T C 248.86 PASS AC=1;AF=0.5;AN=2;DP=25;FS=0;FractionInformativeReads=1;MQ=60;set=variant5-variant23 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:153,0,111:1,4,1,3 chr2 74803013 . G T 65.5 PASS AC=1;AF=0.75;AN=2;DP=13;FractionInformativeReads=1;MQ=60;MQRankSum=1.106;ReadPosRankSum=0.715;set=variant23-variant33 GT:AD:DP:GQ:PL:SB 0/1:8,3:11:94:94,0,257:1,7,1,2 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 1/1:0,137:137:99:4572,411,0:0,0,41,96 chr2 75095103 . G GTA 1087.07 PASS AC=2;AF=0.729;AN=2;DP=664;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant10-variant11-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant26-variant27-variant29-variant34-variant36-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:1079,72,0:0,0,4,20 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 0/1:37,34:71:99:887,0,1048:27,10,22,12 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 0/1:65,64:129:99:1528,0,1550:41,24,39,25 chr2 75104570 . A G 656.09 PASS AC=1;AF=0.528;AN=2;DP=567;FractionInformativeReads=1;MQ=60;set=variant11-variant12-variant14-variant15-variant16-variant18-variant20-variant21-variant23-variant26-variant28-variant31-variant34-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,9:29:99:310,0,982:6,14,1,8 chr2 75104575 . G A 631.41 PASS AC=1;AF=0.528;AN=2;DP=501;FractionInformativeReads=1;MQ=60;set=variant11-variant12-variant14-variant15-variant16-variant18-variant20-variant21-variant23-variant26-variant28-variant31-variant34-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,8:22:99:285,0,935:4,10,1,7 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 1/1:0,102:102:99:3071,306,0:0,0,47,55 chr2 75107201 . G A 454.11 PASS AC=1;AF=0.5;AN=2;DP=36;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.353;QD=12.61;ReadPosRankSum=-2.31;SOR=0.818;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:21,15:36:99:482,0,735:19,2,14,1 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 0/1:44,33:77:99:852,0,1190:33,11,23,10 chr2 75107367 . T G 3640.08 PASS AC=1;AF=0.5;AN=2;DP=4593;MQ=60;set=variant11-variant12-variant14-variant15-variant16-variant18-variant21-variant23-variant26-variant28-variant31-variant34-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:138,118:256:99:2791,0,3209:68,70,58,60 chr2 75113572 . G A 762.98 PASS AC=2;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 1/1:0,117:117:99:3370,350,0:0,0,54,63 chr2 75113789 . C G 981.05 PASS AC=2;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 1/1:0,150:150:99:4224,450,0:0,0,75,75 chr2 75113903 . A G 877.2 PASS AC=2;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 1/1:0,50:50:99:1622,150,0:0,0,15,35 chr2 75115108 . A G 1335.27 PASS AC=2;AF=0.725;AN=2;DP=2172;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-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:2035,183,0:0,0,40,21 chr2 75116627 . C T 169.32 PASS AC=2;AF=0.695;AN=2;DP=2680;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-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1218,126,0:0,0,16,26 chr2 75118330 . T G 4410.86 PASS AC=2;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 1/1:0,329:329:99:10061,985,0:0,0,141,188 chr2 75118737 . C T 621.58 PASS AC=2;AF=0.659;AN=2;DP=2740;set=variant-variant2-variant3-variant4-variant5-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-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,57:57:99:1747,171,0:0,0,24,33 chr2 75118856 . T C 476.77 PASS AC=2;AF=0.667;AN=2;DP=1429;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant13-filterInvariant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:530,45,0:0,0,4,11 chr2 75118884 . G GA 246.54 PASS AC=2;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 1/1:0,16:16:48:597,48,0:0,0,8,8 chr2 75118913 . TAATG T 451.45 PASS AC=2;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 1/1:0,12:12:36:540,36,0:0,0,6,6 chr2 75119989 . C T 1044.97 PASS AC=1;AF=0.5;AN=2;DP=73;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.927;QD=14.31;ReadPosRankSum=1.75;SOR=0.708;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:35,38:73:99:1073,0,1051:13,22,14,24 chr2 75120159 . CT CTTT,CTT,C 1372.33 PASS AC=1,0,0;AF=0.4,0.113,0.075;AN=2;DP=7515;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant9-variant10-filterInvariant11-filterInvariant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant36-filterInvariant37-variant39-filterInvariant40-variant41-variant42-variant43-filterInvariant44 GT:DP:GQ:SB 0/1:162:99:49,25,47,41 chr2 75120525 . C A 453.48 PASS AC=1;AF=0.5;AN=2;DP=398;FractionInformativeReads=1;MQ=60;set=variant11-variant12-variant14-variant18-variant21-variant23-variant26-variant31-variant34-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,19:28:99:447,0,236:4,5,10,9 chr2 75185667 . C G 1998.59 PASS AC=1;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 0/1:43,32:75:99:804,0,992:22,21,14,18 chr2 75186337 . A G 563.66 PASS AC=1;AF=0.5;AN=2;DP=896;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant9-variant12-variant14-variant22-variant23-variant26-variant30-variant32-variant34-variant36-variant37-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,25:49:99:560,0,593:15,9,14,11 chr2 75187573 . G A 2690.39 PASS AC=1;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 0/1:37,27:64:99:565,0,1021:22,15,14,13 chr2 75187793 . A T 848.09 PASS AC=1;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 0/1:9,10:19:99:286,0,290:3,6,2,8 chr2 75196731 . A G 872.38 PASS AC=1;AF=0.5;AN=2;DP=1344;MQ=60;set=variant-variant2-variant4-variant9-variant12-variant14-variant22-variant23-variant26-variant30-variant32-variant34-variant36-variant37-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,33:66:99:895,0,823:12,21,12,21 chr2 75276429 . C G 1026.92 PASS AC=1;AF=0.5;AN=2;DP=1122;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant10-variant12-variant14-variant20-variant22-variant23-variant30-variant34-variant37-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,44:87:99:1178,0,1058:24,19,27,17 chr2 75719537 . T TAA,TA,TTA,TTAA,TAAA 548.19 PASS AC=0,1,0,0,0;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 0/2:73:99:9,9,16,39 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 0/1:45,39:84:99:833,0,1165:29,16,23,16 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 1/1:0,19:19:57:620,57,0:0,0,13,6 chr2 75787972 . G C 447.81 PASS AC=1;AF=0.617;AN=2;DP=1412;MQ=60;set=variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,36:64:99:772,0,603:14,14,16,20 chr2 75788287 . C T 328.29 PASS AC=2;AF=0.645;AN=2;DP=637;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:668,60,0:0,0,13,7 chr2 75788500 . CTT C,CT 95.69 PASS AC=0,1;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 0/2:17:39:1,3,4,9 chr2 75796950 . C T 173.66 PASS AC=2;AF=0.673;AN=2;DP=243;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant7-variant10-variant11-variant14-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant33-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:240,24,0:0,0,3,5 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 1/1:0,20:20:60:803,60,0:0,0,18,2 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 0/1:80,64:144:99:1448,0,1885:33,47,28,36 chr2 75916925 . C T 240.67 PASS AC=1;AF=0.5;AN=2;DP=16;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.473;QD=15.04;ReadPosRankSum=0.578;SOR=1.802;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:269,0,260:7,1,8,0 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 0/1:41,29:70:99:640,0,903:21,20,13,16 chr2 75929080 . C T 2655.48 PASS AC=1;AF=0.5;AN=2;DP=241;FS=1.001;FractionInformativeReads=0.988;MQ=60;MQRankSum=-0.188;QD=11.02;ReadPosRankSum=0.488;SOR=0.781;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:123,115:238:99:2684,0,2981:68,55,66,49 chr2 76975383 . A G 607.17 PASS AC=1;AF=0.628;AN=2;DP=2277;MQ=60;set=variant-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-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,28:53:99:762,0,520:12,13,11,17 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 0/2:54:99:10,16,11,17 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 0/1:212:99:77,89,19,27 chr2 77748604 . TA T 359.49 PASS AC=1;AF=0.545;AN=2;DP=622;MQ=60;set=variant6-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant23-variant28-variant29-variant31-variant33-variant34-variant36-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,15:32:99:325,0,390:15,2,11,4 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 0/1:20,11:31:99:274,0,477:12,8,7,4 chr2 79252950 . A G 144.28 PASS AC=1;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 0/1:13,11:24:99:407,0,384:5,8,5,6 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 0/1:31,25:56:99:746,0,876:23,8,21,4 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 0/1:116,88:204:99:2180,0,2843:65,51,52,36 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 0/1:38,31:69:99:887,0,1196:9,29,9,22 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 0/1:32,22:54:99:627,0,860:19,13,13,9 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 0/1:84,14:98:99:332,0,3921:42,42,5,9 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 0/1:80,14:94:99:347,0,3712:40,40,5,9 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 0/1:77,13:90:99:254,0,2823:42,35,8,5 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 0/1:81,31:112:99:719,0,2097:38,43,25,6 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 0/1:85,57:142:99:1311,0,2226:44,41,38,19 chr2 79254261 . T C 270.18 PASS AC=1;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 0/1:67,68:135:99:1730,0,1666:25,42,24,44 chr2 79255426 . G C 963.91 PASS AC=1;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 0/1:43,45:88:99:1192,0,1131:22,21,25,20 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 0/1:38,38:76:99:1006,0,895:15,23,13,25 chr2 79255629 . G T 619.67 PASS AC=1;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 0/1:20,20:40:99:571,0,573:5,15,6,14 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 1/1:0,65:65:99:2098,194,0:0,0,29,36 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 1/1:0,84:84:99:2568,252,0:0,0,47,37 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 0/1:36,24:60:99:568,0,915:13,23,8,16 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 1/1:0,50:50:99:1508,149,0:0,0,16,34 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 1/1:0,51:51:99:1820,153,0:0,0,17,34 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 1/1:0,26:26:78:834,78,0:0,0,16,10 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 0/1:19,25:44:99:604,0,482:8,11,14,11 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 0/1:14,5:19:99:160,0,387:6,8,1,4 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 2/2:81:99:0,0,25,56 chr2 79349372 . C G 984.28 PASS AC=1;AF=0.641;AN=2;DP=2119;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant33-variant36-variant37-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,31:72:99:751,0,968:17,24,11,20 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 0/1:77,68:145:99:1645,0,1873:35,42,32,36 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 1/1:0,106:106:99:3364,318,0:0,0,54,52 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 0/1:40,33:73:99:806,0,1031:14,26,13,20 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 0/1:130,49:179:99:811,0,3412:75,55,22,27 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 0/1:137,40:177:99:1244,0,5898:78,59,16,24 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 0/1:136,39:175:99:1244,0,5898:76,60,15,24 chr2 79539988 . G C 893.85 PASS AC=2;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 1/1:0,51:51:99:1554,153,0:0,0,22,29 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 0/1:4,7:11:97:191,0,97:3,1,4,3 chr2 79600948 . A C 63.56 PASS AC=1;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 0/1:5,7:12:99:157,0,150:3,2,4,3 chr2 79601000 . G C 75.16 PASS AC=1;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 0/1:9,7:16:99:145,0,274:6,3,4,3 chr2 79601273 . A T 51.23 PASS AC=1;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 0/1:11,7:18:99:139,0,295:6,5,3,4 chr2 79750282 . A G 757.02 PASS AC=1;AF=0.595;AN=2;DP=711;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant8-variant11-variant13-variant18-variant20-variant23-variant25-variant26-variant27-variant28-variant29-variant33-variant36-variant37-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,19:44:99:477,0,678:18,7,13,6 chr2 79750543 . C T 235.31 PASS AC=2;AF=0.878;AN=2;DP=254;FractionInformativeReads=1;MQ=60;set=variant-variant3-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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:87,6,0:0,0,0,2 chr2 79914539 . G A 493.52 PASS AC=1;AF=0.5;AN=2;DP=287;FractionInformativeReads=1;MQ=60;set=variant4-variant9-variant16-variant22-variant23-variant24-variant25-variant36-variant37-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,16:24:99:464,0,289:8,0,12,4 chr2 79914570 . C CT,CTT 369.89 PASS AC=1,0;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 0/1:36:99:16,5,13,2 chr2 80097279 . T C 550.68 PASS AC=1;AF=0.5;AN=2;DP=305;FractionInformativeReads=1;MQ=60;set=variant3-variant8-variant10-variant13-variant16-variant18-variant20-variant23-variant26-variant29-variant36-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:9,9:18:99:310,0,354:0,9,1,8 chr2 80101321 . T G 1393.52 PASS AC=1;AF=0.5;AN=2;DP=1349;MQ=60;set=variant3-variant8-variant10-variant13-variant16-variant18-variant20-variant23-variant26-variant29-variant36-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:33,48:81:99:1264,0,780:16,17,24,24 chr2 80101515 . CA C,CAA 97.06 PASS AC=1,0;AF=0.409,0.091;AN=2;DP=443;MQ=60;set=variant2-variant3-variant8-variant16-variant18-variant23-variant24-variant26-variant36-variant39-variant41 GT:DP:GQ:SB 0/1:29:99:5,7,6,11 chr2 80772972 . G A 3566.5 PASS AC=1;AF=0.62;AN=2;DP=3342;set=variant2-variant3-variant4-variant8-variant9-variant13-variant14-variant15-variant17-variant18-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,36:87:99:800,0,1430:29,22,18,18 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 0/1:37,47:84:99:1159,0,918:21,16,28,19 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 0/1:17,12:29:99:328,0,496:6,11,4,8 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 0/1:6,2:8:66:66,0,166:2,4,0,2 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 0/1:13,5:18:73:73,0,254:8,5,5,0 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 0/1:205,185:390:99:4400,0,4914:88,117,83,102 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 0/1:68,53:121:99:1313,0,1768:24,44,16,37 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 1/1:0,177:177:99:5353,530,0:0,0,82,95 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 1/1:0,51:51:99:1421,153,0:0,0,22,29 chr2 84676886 . TAAAAAAA TAAAA,TAAA,TAAAAA,TAAAAAA,TA,TAA,T 235.32 PASS AC=1,1,0,0,0,0,0;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 2/1:16:83:1,0,6,9 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 1/1:54:99:1,0,34,19 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 1/1:0,82:82:99:2511,244,0:0,0,41,41 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 1/1:0,9:9:27:356,27,0:0,0,1,8 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 1/1:0,34:34:99:994,102,0:0,0,19,15 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 1/1:0,32:32:96:940,96,0:0,0,13,19 chr2 84775673 . A T 211.45 PASS AC=2;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 1/1:0,7:7:21:271,21,0:0,0,1,6 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 1/1:0,53:53:99:1610,159,0:0,0,25,28 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 1/1:0,10:10:30:381,30,0:0,0,9,1 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 1/1:0,27:27:81:922,81,0:0,0,21,6 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 1/1:0,5:5:15:222,15,0:0,0,0,5 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 1/1:0,110:110:99:3350,330,0:0,0,69,41 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 1/1:0,70:70:99:2300,210,0:0,0,21,49 chr2 84848596 . G A 1303.27 PASS AC=1;AF=0.5;AN=2;DP=994;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant13-variant16-variant19-variant23-variant28-variant33-variant37 GT:AD:DP:GQ:PL:SB 0/1:62,46:108:99:1100,0,1541:26,36,20,26 chr2 84885618 . T A 333.91 PASS AC=1;AF=0.5;AN=2;DP=46;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.979;QD=7.26;ReadPosRankSum=0.205;SOR=0.562;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:29,17:46:99:362,0,786:11,18,7,10 chr2 84896628 . G A 806.61 PASS AC=2;AF=0.563;AN=2;DP=989;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant8-variant13-variant16-variant19-variant20-variant21-variant23-variant24-variant28-variant33-variant34-variant37-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:1729,168,0:0,0,20,36 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 1/1:0,8:8:24:313,24,0:0,0,8,0 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 1/1:0,64:64:99:1911,192,0:0,0,31,33 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 1/1:0,29:29:87:953,87,0:0,0,19,10 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 1/1:0,33:33:99:1219,99,0:0,0,14,19 chr2 85132767 . G T 1893.99 PASS AC=1;AF=0.563;AN=2;DP=994;MQ=60;set=variant3-variant10-variant12-variant17-variant23-variant25-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:36,61:97:99:1416,0,910:25,11,33,28 chr2 85133698 . AC ACC,A 1117.98 PASS AC=1,0;AF=0.333,0.167;AN=2;DP=539;MQ=60;set=variant23-variant39-variant41 GT:DP:GQ:SB 0/1:156:99:44,53,27,32 chr2 85133861 . C T 203.25 PASS AC=1;AF=0.563;AN=2;DP=169;FractionInformativeReads=1;set=variant3-variant10-variant12-variant17-variant23-variant25-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:9,12:21:99:348,0,335:0,9,2,10 chr2 85273149 . C T 183.35 PASS AC=1;AF=0.556;AN=2;DP=198;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant12-variant15-variant22-variant23-variant28-variant32-variant39 GT:AD:DP:GQ:PL:SB 0/1:10,5:15:71:71,0,367:9,1,4,1 chr2 85276866 . T C 113.43 PASS AC=1;AF=0.6;AN=2;DP=37;FractionInformativeReads=1;MQ=60;set=variant12-variant15-variant23-variant28-variant32 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:75:75,0,79:0,2,0,2 chr2 85360828 . GGGC G 926.79 PASS AC=2;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 1/1:0,48:48:99:2083,144,0:0,0,36,12 chr2 85510777 . A G 651.79 PASS AC=2;AF=0.677;AN=2;DP=3046;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant28-variant29-variant30-variant31-variant33-variant34-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2478,210,0:0,0,31,39 chr2 85510965 . A G 125.14 PASS AC=2;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 1/1:0,20:20:60:703,60,0:0,0,4,16 chr2 85532111 . C T 71.66 PASS AC=1;AF=0.5;AN=2;DP=38;FractionInformativeReads=1;MQ=60;set=variant23-variant29-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:71:100,0,71:2,0,3,2 chr2 85532205 . C G 320.14 PASS AC=1;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 0/1:13,19:32:99:414,0,369:8,5,10,9 chr2 85536128 . CTCTT C 829.18 PASS AC=1;AF=0.5;AN=2;DP=294;MQ=60;set=variant23-variant29-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,24:71:99:866,0,2738:28,19,15,9 chr2 85536726 . C T 1637.74 PASS AC=1;AF=0.5;AN=2;DP=616;FractionInformativeReads=1;MQ=60;set=variant23-variant29-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,65:126:99:1666,0,1513:28,33,37,28 chr2 85537010 . G A 1021.39 PASS AC=1;AF=0.5;AN=2;DP=434;MQ=60;set=variant23-variant29-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,45:95:99:1050,0,1297:22,28,21,24 chr2 85546192 . C T 192.67 PASS AC=1;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 0/1:10,8:18:99:184,0,268:4,6,3,5 chr2 85546615 . C T 199.36 PASS AC=1;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 0/1:12,10:22:99:204,0,269:7,5,6,4 chr2 85546932 . A C 444.94 PASS AC=1;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 0/1:26,28:54:99:677,0,592:12,14,14,14 chr2 85547376 . C G 258.19 PASS AC=1;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 0/1:14,5:19:99:114,0,327:6,8,3,2 chr2 85547429 . G T 325.48 PASS AC=1;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 0/1:8,4:12:85:85,0,244:4,4,2,2 chr2 85547849 . G C 358.8 PASS AC=1;AF=0.5;AN=2;DP=201;FractionInformativeReads=1;MQ=60;set=variant23-variant29-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,17:41:99:387,0,655:14,10,8,9 chr2 85547963 . C T 314.9 PASS AC=1;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 0/1:33,15:48:99:354,0,904:18,15,8,7 chr2 85548068 . TA T 358.05 PASS AC=1;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 0/1:17,11:28:99:292,0,478:8,9,6,5 chr2 85548639 . A G 2749.58 PASS AC=1;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 0/1:52,70:122:99:1925,0,1387:30,22,42,28 chr2 85549595 . T C 399.15 PASS AC=1;AF=0.5;AN=2;DP=177;MQ=60;set=variant23-variant29-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,17:42:99:427,0,666:11,14,8,9 chr2 85549744 . G A 835.41 PASS AC=1;AF=0.5;AN=2;DP=277;FractionInformativeReads=1;MQ=60;set=variant23-variant29-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,37:77:99:864,0,930:20,20,19,18 chr2 85549868 . A G 997.74 PASS AC=1;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 0/1:40,35:75:99:821,0,939:17,23,17,18 chr2 85552186 . C A 831.48 PASS AC=1;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 0/1:17,28:45:99:688,0,492:8,9,13,15 chr2 85553784 . C T 3077.57 PASS AC=1;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 0/1:106,92:198:99:2104,0,2720:50,56,49,43 chr2 85554885 . G A 949.24 PASS AC=1;AF=0.625;AN=2;DP=142;FractionInformativeReads=1;MQ=60;set=variant23-variant29-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,28:48:99:977,0,648:14,6,17,11 chr2 85555210 . A G 1455.45 PASS AC=1;AF=0.625;AN=2;DP=530;MQ=60;set=variant23-variant29-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,59:116:99:1484,0,1348:29,28,28,31 chr2 85555262 . T G 2114.62 PASS AC=1;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 0/1:101,84:185:99:2024,0,2438:58,43,48,36 chr2 85555277 . G A 2464.08 PASS AC=1;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 0/1:117,95:212:99:2235,0,2717:67,50,56,39 chr2 85555478 . C T 1603.56 PASS AC=1;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 0/1:45,59:104:99:1615,0,1295:15,30,24,35 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 0/1:9,8:17:99:309,0,653:8,1,8,0 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 0/1:9,8:17:99:309,0,653:8,1,8,0 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 0/1:9,8:17:99:309,0,653:8,1,8,0 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 0/1:9,8:17:99:309,0,653:8,1,8,0 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 0/1:15,15:30:99:457,0,443:11,4,12,3 chr2 85570442 . C T 358.03 PASS AC=1;AF=0.5;AN=2;DP=224;FractionInformativeReads=1;set=variant23-variant29-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,15:40:99:386,0,599:11,14,5,10 chr2 85571046 . T C 40.55 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=22;FS=6.69;FractionInformativeReads=1;MQ=57.89;MQRankSum=-1.913;QD=1.84;ReadPosRankSum=1.052;SOR=2.807;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:19,3:22:69:69,0,1099:11,8,0,3 chr2 85571047 . G A 40.55 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=22;FS=6.69;FractionInformativeReads=1;MQ=57.89;MQRankSum=-2.392;QD=1.84;ReadPosRankSum=0.191;SOR=2.807;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:19,3:22:69:69,0,1099:11,8,0,3 chr2 85571710 . A G 1275.37 PASS AC=1;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 0/1:44,59:103:99:1664,0,1314:35,9,43,16 chr2 85577310 . C T 1036.8 PASS AC=1;AF=0.5;AN=2;DP=358;MQ=60;set=variant23-variant29-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,44:81:99:1065,0,993:18,19,24,20 chr2 85618569 . C G 791.84 PASS AC=1;AF=0.5;AN=2;DP=125;FractionInformativeReads=1;MQ=60;set=variant23-variant38 GT:AD:DP:GQ:PL:SB 0/1:23,34:57:99:820,0,505:10,13,17,17 chr2 85622059 . T C 2793 PASS AC=2;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 1/1:0,125:125:99:3790,375,0:0,0,57,68 chr2 85622583 . C A 441.02 PASS AC=1;AF=0.5;AN=2;DP=169;FractionInformativeReads=1;MQ=60;set=variant23-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,20:48:99:469,0,731:19,9,11,9 chr2 85622890 . G C 321.08 PASS AC=1;AF=0.5;AN=2;DP=92;FractionInformativeReads=1;MQ=60;set=variant23-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,10:20:99:349,0,346:2,8,1,9 chr2 85625222 . T G 1277.14 PASS AC=1;AF=0.5;AN=2;DP=2016;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant14-variant15-variant21-variant22-variant23-variant26-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,43:81:99:1028,0,881:17,21,19,24 chr2 85625784 . G A 920.28 PASS AC=1;AF=0.5;AN=2;DP=322;MQ=60;set=variant23-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,40:73:99:949,0,870:18,15,22,18 chr2 85626479 . G C 1217.98 PASS AC=1;AF=0.5;AN=2;DP=2642;MQ=60;set=variant-variant2-variant3-variant14-variant15-variant21-variant22-variant23-variant26-variant33-variant34-variant36-variant37-variant38-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,77:149:99:1991,0,1843:24,48,25,52 chr2 85641240 . A G 448.32 PASS AC=1;AF=0.5;AN=2;DP=203;MQ=60;set=variant21-variant23-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:24,30:54:99:709,0,554:11,13,13,17 chr2 85646276 . C G 972.38 PASS AC=1;AF=0.5;AN=2;DP=283;FractionInformativeReads=1;MQ=60;set=variant23-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,41:85:99:1001,0,1114:22,22,18,23 chr2 85646399 . C T 2908.37 PASS AC=1;AF=0.594;AN=2;DP=1071;MQ=60;set=variant-variant2-variant8-variant10-variant12-variant14-variant16-variant17-variant20-variant23-variant24-variant25-variant29-variant31-variant33-variant39 GT:AD:DP:GQ:PL:SB 0/1:28,29:57:99:670,0,761:10,18,12,17 chr2 85646417 . G A 2433.53 PASS AC=1;AF=0.595;AN=2;DP=1132;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant8-variant10-variant12-variant14-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant29-variant31-variant33-variant34-variant36-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:24,17:41:99:452,0,595:10,14,6,11 chr2 85649575 . G A 1632.99 PASS AC=1;AF=0.5;AN=2;DP=531;FractionInformativeReads=1;MQ=60;set=variant23-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:111,80:191:99:1661,0,2472:58,53,43,37 chr2 85649628 . G C 1251.04 PASS AC=1;AF=0.5;AN=2;DP=338;MQ=60;set=variant23-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,52:120:99:1279,0,1851:22,46,22,30 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 0/1:33,26:59:99:605,0,874:18,15,12,14 chr2 85656788 . C A 821.06 PASS AC=1;AF=0.605;AN=2;DP=868;MQ=60;set=variant-variant2-variant8-variant10-variant12-variant14-variant15-variant16-variant17-variant20-variant23-variant24-variant25-variant29-variant31-variant33-variant34-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:24,21:45:99:425,0,619:8,16,8,13 chr2 85658232 . A G 331.77 PASS AC=2;AF=0.6;AN=2;DP=613;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant8-variant10-variant12-variant14-variant15-variant16-variant17-variant20-variant21-variant23-variant24-variant25-variant29-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:675,45,0:0,0,12,3 chr2 85658256 . TC T 632.18 PASS AC=1;AF=0.605;AN=2;DP=566;MQ=60;set=variant-variant2-variant8-variant10-variant12-variant14-variant16-variant17-variant20-variant23-variant24-variant25-variant29-variant31-variant33-variant34-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:14,7:21:99:155,0,371:10,4,3,4 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 0/1:7,14:21:99:325,0,156:3,4,10,4 chr2 85660126 . A G 1589.81 PASS AC=2;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 1/1:0,48:48:99:1439,143,0:0,0,29,19 chr2 85662017 . G A 1897.14 PASS AC=2;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 1/1:0,59:59:99:1632,177,0:0,0,26,33 chr2 85662650 . A G 2562.35 PASS AC=2;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 1/1:0,67:67:99:2317,201,0:0,0,29,38 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 1/1:1,181:182:99:5439,534,0:0,1,85,96 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 0/1:19,30:49:99:867,0,415:12,7,17,13 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 0/1:3,13:16:93:537,0,93:1,2,4,9 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 0/1:33,25:58:99:557,0,838:21,12,16,9 chr2 85776949 . CA C,CAA 88.71 PASS AC=1,0;AF=0.308,0.192;AN=2;DP=898;set=filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant9-filterInvariant18-filterInvariant20-filterInvariant23-filterInvariant24-filterInvariant25-variant27-filterInvariant28-filterInvariant31-filterInvariant41 GT:DP:GQ:SB 0/1:46:99:17,18,3,8 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 0/1:18,6:24:99:173,0,474:11,7,6,0 chr2 85777633 . C G 875.62 PASS AC=1;AF=0.5;AN=2;DP=243;FractionInformativeReads=1;MQ=60;set=variant8-variant12-variant20-variant23-variant36 GT:AD:DP:GQ:PL:SB 0/1:17,30:47:99:738,0,442:13,4,18,12 chr2 85779728 . A G 1218.92 PASS AC=1;AF=0.5;AN=2;DP=208;FractionInformativeReads=1;MQ=60;QD=11.08;set=variant23-variant38 GT:AD:DP:GQ:PL:SB 0/1:52,58:110:99:1247,0,1329:20,32,28,30 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 0/1:47,41:88:99:930,0,1188:20,27,17,24 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 1/1:0,80:80:99:2388,239,0:0,0,40,40 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 0/1:58,51:109:99:1218,0,1302:31,27,25,26 chr2 85788140 . C T 1279.15 PASS AC=1;AF=0.548;AN=2;DP=1328;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant9-variant12-variant17-variant18-variant20-variant23-variant26-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:13,21:34:99:656,0,282:5,8,5,16 chr2 85788175 . T A 1350.44 PASS AC=1;AF=0.621;AN=2;DP=1320;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant33-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,10:27:99:209,0,522:4,13,4,6 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 1/1:1,15:16:21:380,21,0:0,1,11,4 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 1/1:0,26:26:78:823,78,0:0,0,16,10 chr2 85807082 . T A 200.94 PASS AC=1;AF=0.567;AN=2;DP=644;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-filterInvariant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant23-variant25-variant27-variant28-variant29-variant30-variant33-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,11:17:99:291,0,167:1,5,3,8 chr2 85811592 . C T 1153.73 PASS AC=1;AF=0.611;AN=2;DP=581;MQ=60;set=variant3-variant6-variant16-variant18-variant23-variant28-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,29:58:99:720,0,739:15,14,15,14 chr2 85820373 . A G 1426.27 PASS AC=1;AF=0.563;AN=2;DP=750;MQ=60;set=variant6-variant16-variant22-variant23-variant28-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,54:107:99:1260,0,1338:27,26,27,27 chr2 85823167 . TG T 204.54 PASS AC=1;AF=0.58;AN=2;DP=808;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant21-variant22-variant23-variant28-variant29-variant30-variant33-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,15:26:99:428,0,291:2,9,3,12 chr2 85824078 . C T 1790.88 PASS AC=1;AF=0.625;AN=2;DP=985;MQ=60;set=variant6-variant16-variant22-variant23-variant28-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,59:117:99:2227,0,2986:29,29,26,33 chr2 85824084 . G C 1082.27 PASS AC=1;AF=0.62;AN=2;DP=3203;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant21-variant22-variant23-variant28-variant29-variant30-variant33-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,55:113:99:2196,0,3032:31,27,24,31 chr2 85826132 . G A 629.86 PASS AC=1;AF=0.62;AN=2;DP=1504;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant21-variant22-variant23-variant28-variant29-variant30-variant33-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,28:57:99:695,0,753:17,12,18,10 chr2 85826894 . TCTC T 1048.24 PASS AC=1;AF=0.611;AN=2;DP=370;MQ=60;set=variant6-variant16-variant22-variant23-variant28-variant29-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,14:36:99:512,0,1066:9,13,6,8 chr2 85828014 . T G 832.87 PASS AC=1;AF=0.62;AN=2;DP=1738;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant21-variant22-variant23-variant28-variant29-variant30-variant33-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:29,36:65:99:982,0,708:18,11,24,12 chr2 85843348 . C T 1897.52 PASS AC=1;AF=0.611;AN=2;DP=1451;MQ=60;set=variant6-variant16-variant22-variant23-variant28-variant29-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:83,70:153:99:1584,0,2102:45,38,36,34 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 0/1:18,6:24:85:85,0,328:4,14,2,4 chr2 85863158 . CCCTT C 445.84 PASS AC=1;AF=0.5;AN=2;DP=27;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.655;QD=16.51;ReadPosRankSum=0.946;SOR=0.582;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:14,13:27:99:483,0,777:8,6,7,6 chr2 85866577 . CT C,CTT 33.07 PASS AC=0,1;AF=0.393,0.107;AN=2;DP=428;set=variant-variant3-variant4-variant14-filterInvariant15-filterInvariant18-filterInvariant20-variant23-variant29-filterInvariant31-filterInvariant33-variant38-variant43-filterInvariant44 GT:DP:GQ:SB 0/2:18:99:0,11,2,5 chr2 85876224 . CT C 979.56 PASS AC=1;AF=0.62;AN=2;DP=1497;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant21-variant22-variant23-variant28-variant29-variant30-variant33-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,45:73:99:1449,0,822:13,15,18,27 chr2 85886013 . T C 288.25 PASS AC=1;AF=0.688;AN=2;DP=223;FractionInformativeReads=1;MQ=60;set=variant6-variant16-variant22-variant23-variant28-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,19:28:99:427,0,124:4,5,10,9 chr2 85886667 . G C 725.17 PASS AC=1;AF=0.62;AN=2;DP=1739;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant15-variant16-variant19-variant21-variant22-variant23-variant28-variant29-variant30-variant33-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:34,22:56:99:573,0,973:17,17,10,12 chr2 85890753 . A G 1025.21 PASS AC=1;AF=0.688;AN=2;DP=803;MQ=60;set=variant6-variant16-variant22-variant23-variant28-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,44:107:99:1122,0,1627:34,29,21,23 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 1/1:0,110:110:99:3411,329,0:0,0,56,54 chr2 85893616 . CTGTG CTG,CTGTGTG,C 341.26 PASS AC=1,1,0;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 1/2:29:99:1,0,27,1 chr2 85893741 . G A 4955.47 PASS AC=1;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 0/1:91,71:162:99:1704,0,2275:47,44,35,36 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 0/1:34,34:68:99:911,0,751:21,13,18,16 chr2 85981289 . CCT C 296.03 PASS AC=1;AF=0.5;AN=2;DP=967;MQ=60;set=variant10-variant13-filterInvariant15-variant18-filterInvariant23-variant26-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:109,15:124:99:289,0,4561:67,42,0,15 chr2 85981293 . CCT C 68 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=711;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:109,12:121:99:108,0,4709:66,43,0,12 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 0/1:56,34:90:99:795,0,1466:35,21,20,14 chr2 86010678 . T C 80.74 PASS AC=1;AF=0.7;AN=2;DP=241;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant8-variant10-variant11-variant12-variant14-variant15-variant19-variant21-variant23-variant24-variant27-variant28-variant32-variant33-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:31:81,0,31:1,1,2,2 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 0/1:8,6:14:99:158,0,243:7,1,5,1 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 0/1:30,26:56:99:562,0,719:13,17,10,16 chr2 86107840 . G A 84.16 PASS AC=2;AF=0.7;AN=2;DP=244;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant30-variant33-variant34-variant36-variant37-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:304,21,0:0,0,7,0 chr2 86107951 . GA G 665.03 PASS AC=2;AF=0.676;AN=2;DP=1471;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-variant26-variant27-variant29-variant30-variant33-variant34-variant36-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,34:36:53:894,53,0:1,1,18,16 chr2 86107987 . T C 823.41 PASS AC=2;AF=0.676;AN=2;DP=1843;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-variant26-variant27-variant29-variant30-variant33-variant34-variant36-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1279,126,0:0,0,21,21 chr2 86116169 . A G 93.14 PASS AC=1;AF=0.688;AN=2;DP=121;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant8-variant10-variant11-variant14-variant16-variant17-variant21-variant22-variant23-variant24-variant34-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,8:12:99:240,0,105:1,3,3,5 chr2 86247670 . CAAA CAA,CA,CAAAA,CAAAAA,C 174.41 PASS AC=1,0,0,0,0;AF=0.205,0.136,0.114,0.023,0.023;AN=2;DP=1240;set=variant3-variant4-variant10-variant12-variant13-variant14-variant15-filterInvariant16-variant18-variant19-variant22-variant23-variant25-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant42 GT:DP:GQ:SB 0/1:28:99:6,8,13,1 chr2 86248309 . T C 824.71 PASS AC=1;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 0/1:43,38:81:99:943,0,1194:21,22,15,23 chr2 86253581 . T C 2392.18 PASS AC=1;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 0/1:72,101:173:99:2458,0,1590:32,40,43,58 chr2 86254268 . G A 649.64 PASS AC=1;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 0/1:32,29:61:99:830,0,863:9,23,12,17 chr2 86258784 . T G 634.94 PASS AC=1;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 0/1:36,23:59:99:620,0,995:10,26,7,16 chr2 86259443 . C T 710.99 PASS AC=1;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 0/1:57,63:120:99:1473,0,1268:27,30,31,32 chr2 86270052 . A G 360.42 PASS AC=1;AF=0.5;AN=2;DP=28;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant38 GT:AD:DP:GQ:PL:SB 0/1:5,12:17:99:389,0,159:4,1,10,2 chr2 86272191 . G A 103.64 PASS AC=1;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 0/1:3,14:17:86:399,0,86:3,0,10,4 chr2 86275985 . A G 1583.6 PASS AC=1;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 0/1:48,45:93:99:1172,0,1266:33,15,27,18 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 1/1:0,86:86:99:2464,257,0:0,0,41,45 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 1/1:0,34:34:99:1069,102,0:0,0,23,11 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 1/1:0,64:64:99:1995,191,0:0,0,41,23 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 1/1:0,58:58:99:1689,172,0:0,0,34,24 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 1/1:0,33:33:99:1003,99,0:0,0,21,12 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 1/1:1,106:107:99:3199,311,0:0,1,66,40 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 1/1:0,85:85:99:2639,254,0:0,0,57,28 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 1/1:0,54:54:99:1663,162,0:0,0,32,22 chr2 86334312 . C T 815.6 PASS AC=1;AF=0.5;AN=2;DP=79;FS=0.867;FractionInformativeReads=1;MQ=60;MQRankSum=0.438;QD=10.32;ReadPosRankSum=-2.741;SOR=0.518;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:43,36:79:99:844,0,1124:17,26,16,20 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 1/1:0,9:9:27:348,27,0:0,0,7,2 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 1/1:0,12:12:36:493,36,0:0,0,9,3 chr2 86344095 . G T 76.19 PASS AC=1;AF=0.619;AN=2;DP=226;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant6-variant8-variant9-variant10-variant17-variant19-variant21-variant23-variant24-variant26-variant28-variant29-variant31-variant33-variant36-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:192,0,104:3,1,5,2 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 1/1:0,30:30:90:919,90,0:0,0,10,20 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 1/1:0,30:30:90:1070,90,0:0,0,5,25 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 1/1:0,33:33:99:1064,99,0:0,0,22,11 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 1/1:0,50:50:99:1464,149,0:0,0,30,20 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 1/1:0,71:71:99:2035,212,0:0,0,38,33 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 1/1:0,86:86:99:2548,258,0:0,0,53,33 chr2 86359745 . GTTTT GTT,GT,GTTT,G 255.36 PASS AC=0,0,2,0;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 3/3:13:15:0,1,3,9 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 1/1:0,52:52:99:1671,155,0:0,0,15,37 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 1/1:0,127:127:99:3819,381,0:0,0,69,58 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 1/1:0,18:18:54:692,54,0:0,0,4,14 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 1/1:0,96:96:99:3427,289,0:0,0,51,45 chr2 86365607 . T C 1263.95 PASS AC=1;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 0/1:46,48:94:99:1209,0,1243:20,26,24,24 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 1/1:0,79:79:99:2737,236,0:0,0,47,32 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 0/1:68,53:121:99:969,0,1247:34,34,30,23 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 1/1:0,123:123:99:3908,369,0:0,0,60,63 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 0/1:80:99:19,24,25,12 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 1/1:0,326:326:99:10150,977,0:0,0,145,181 chr2 86368804 . G A 2142.22 PASS AC=1;AF=0.56;AN=2;DP=4942;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant13-variant17-variant19-variant21-variant23-variant24-variant26-variant28-variant29-variant31-variant33-variant34-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:100,89:189:99:1950,0,2287:52,48,47,42 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 1/1:0,91:91:99:2891,274,0:0,0,51,40 chr2 86371012 . T C 2389.48 PASS AC=1;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 0/1:86,59:145:99:1606,0,2166:55,31,42,17 chr2 86371883 . T C 967.36 PASS AC=1;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 0/1:50,29:79:99:727,0,1244:19,31,12,17 chr2 86385668 . T C 409.57 PASS AC=1;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 0/1:6,13:19:99:528,0,396:6,0,10,3 chr2 86385682 . TC T 522.46 PASS AC=1;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 0/1:11,15:26:99:584,0,545:8,3,10,5 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 1/1:0,59:59:99:1798,177,0:0,0,28,31 chr2 86398074 . A G 348.94 PASS AC=1;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 0/1:20,19:39:99:444,0,528:6,14,8,11 chr2 86400824 . G A 646.95 PASS AC=1;AF=0.58;AN=2;DP=1283;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant13-variant17-variant19-variant21-variant23-variant24-variant26-variant28-variant29-variant31-variant33-variant34-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:28,25:53:99:586,0,694:16,12,16,9 chr2 86406438 . A G 1428.52 PASS AC=1;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 0/1:27,35:62:99:1135,0,906:24,3,31,4 chr2 86406889 . G A 400.08 PASS AC=1;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 0/1:25,15:40:99:405,0,705:7,18,3,12 chr2 86408385 . A G 905.59 PASS AC=1;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 0/1:31,44:75:99:1093,0,874:19,12,26,18 chr2 86419932 . C G 453.78 PASS AC=1;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 0/1:23,13:36:99:418,0,652:17,6,11,2 chr2 86420255 . G A 168.97 PASS AC=1;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 0/1:6,14:20:99:451,0,210:0,6,2,12 chr2 86422073 . G C 1613.39 PASS AC=1;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 0/1:68,43:111:99:989,0,1551:35,33,24,19 chr2 86422416 . T C 2001.89 PASS AC=1;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 0/1:94,66:160:99:2450,0,4626:50,44,35,31 chr2 86422421 . T G 2182.72 PASS AC=1;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 0/1:92,67:159:99:2490,0,4601:48,44,35,32 chr2 86422660 . C T 1522.71 PASS AC=1;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 0/1:62,71:133:99:1656,0,1567:36,26,37,34 chr2 86422793 . G C 2035.22 PASS AC=1;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 0/1:49,50:99:99:1949,0,3136:20,29,23,27 chr2 86422796 . A AGCT 2068.17 PASS AC=1;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 0/1:49,50:99:99:1949,0,3136:20,29,23,27 chr2 86422816 . T G 976.12 PASS AC=1;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 0/1:46,48:94:99:1216,0,1061:18,28,19,29 chr2 86422906 . C T 422.51 PASS AC=1;AF=0.5;AN=2;DP=28;FS=1.606;FractionInformativeReads=1;MQ=60;MQRankSum=0.302;QD=15.09;ReadPosRankSum=-0.673;SOR=1.127;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:12,16:28:99:451,0,334:4,8,4,12 chr2 86422945 . G A 73.78 PASS AC=1;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 0/1:7,5:12:99:182,0,187:2,5,0,5 chr2 86433240 . C T 631.29 PASS AC=1;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 0/1:18,23:41:99:766,0,657:17,1,20,3 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 1/1:0,25:25:75:901,75,0:0,0,21,4 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 1/1:0,113:113:99:3842,339,0:0,0,75,38 chr2 86438146 . A G 1415.67 PASS AC=1;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 0/1:66,66:132:99:1771,0,1747:24,42,28,38 chr2 86438600 . T C 1482.47 PASS AC=1;AF=0.635;AN=2;DP=2510;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant13-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,47:94:99:1239,0,1294:29,18,26,21 chr2 86440436 . T C 7111.36 PASS AC=1;AF=0.635;AN=2;DP=12443;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant13-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:223,192:415:99:4649,0,5499:108,115,103,89 chr2 86440718 . T C 5034.18 PASS AC=1;AF=0.635;AN=2;DP=9481;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant13-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:181,165:346:99:4385,0,4735:82,99,84,81 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 1/1:0,77:77:99:2750,230,0:0,0,22,55 chr2 86441085 . G T 1184.46 PASS AC=1;AF=0.635;AN=2;DP=1979;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant13-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,31:72:99:914,0,1128:25,16,24,7 chr2 86441303 . A C 2701.3 PASS AC=1;AF=0.635;AN=2;DP=4666;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant13-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,86:148:99:2260,0,1585:21,41,35,51 chr2 86441334 . C CTGTT 2700.52 PASS AC=1;AF=0.635;AN=2;DP=3598;MQ=60;set=variant-variant2-variant5-variant6-variant8-variant9-variant10-variant13-variant17-variant19-variant21-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:46,61:107:99:2382,0,1870:16,30,20,41 chr2 86442112 . CA CAA,C 531.59 PASS AC=1,0;AF=0.468,0.048;AN=2;DP=4704;set=variant-variant2-variant5-variant6-filterInvariant7-variant8-variant9-variant10-variant13-variant14-variant17-filterInvariant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:101:99:20,38,18,25 chr2 86442146 . CTTTT CTTT,CT,C,CTT,CTTTTTTTTTTTTTTTTTT,CTTTTTTT 752.75 PASS AC=0,1,0,0,0,0;AF=0.097,0.226,0.032,0.177,0.016,0.016;AN=2;DP=3419;set=variant-variant3-variant4-variant5-variant8-variant9-variant10-variant12-variant15-variant16-variant18-variant20-filterInvariant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant29-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant43 GT:DP:GQ:SB 0/2:45:99:8,11,3,23 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 0/1:9,10:19:99:341,0,272:8,1,9,1 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 0/1:50,35:85:99:862,0,1283:19,31,11,24 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 0/1:17,11:28:99:295,0,514:13,4,9,2 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 0/1:33,36:69:99:885,0,904:10,23,15,21 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 0/1:44,37:81:99:891,0,1070:25,19,22,15 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 0/1:30,31:61:99:814,0,870:10,20,10,21 chr2 86683642 . A G 280.08 PASS AC=2;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 1/1:0,29:29:87:896,87,0:0,0,15,14 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 0/1:21,37:58:99:847,0,515:16,5,21,16 chr2 86691250 . G A 1304.11 PASS AC=2;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 1/1:0,107:107:99:2910,320,0:0,0,49,58 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 0/1:89,83:172:99:2072,0,2208:45,44,41,42 chr2 86705565 . T C 563.97 PASS AC=1;AF=0.648;AN=2;DP=920;MQ=60;set=variant2-variant4-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant26-variant28-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,13:31:99:445,0,624:11,7,9,4 chr2 86707504 . T C 437.79 PASS AC=2;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 1/1:0,54:54:99:1536,162,0:0,0,24,30 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 0/1:7,5:12:99:167,0,200:4,3,5,0 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 0/1:24,28:52:99:770,0,593:13,11,18,10 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 0/1:9,21:30:99:814,0,306:2,7,5,16 chr2 86732524 . C T 754 PASS AC=1;AF=0.648;AN=2;DP=1796;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant26-variant28-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,23:48:99:616,0,703:13,12,15,8 chr2 86732576 . A G 1058.38 PASS AC=1;AF=0.648;AN=2;DP=2230;MQ=60;set=variant2-variant4-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant26-variant28-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,37:70:99:1037,0,847:19,14,23,14 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 0/1:21,25:46:99:764,0,571:5,16,4,21 chr2 86737649 . G A 1039.24 PASS AC=1;AF=0.653;AN=2;DP=3774;set=variant2-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,37:101:99:916,0,1670:28,36,14,23 chr2 86756209 . C G 658.38 PASS AC=2;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 1/1:0,40:40:99:1416,120,0:0,0,32,8 chr2 86756280 . G A 1300.95 PASS AC=1;AF=0.648;AN=2;DP=3546;MQ=60;set=variant2-variant4-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant23-variant24-variant26-variant28-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,66:132:99:1543,0,1692:39,27,38,28 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 0/1:80,91:171:99:2192,0,1903:39,41,44,47 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 0/1:78,75:153:99:2301,0,2437:34,44,31,44 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 0/1:18,10:28:99:216,0,497:6,12,3,7 chr2 86830514 . T C 1643.38 PASS AC=1;AF=0.654;AN=2;DP=2933;MQ=60;set=variant2-variant4-variant6-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant20-variant21-variant23-variant24-variant26-variant28-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,47:88:99:1369,0,986:26,15,36,11 chr2 86850022 . T C 808.4 PASS AC=2;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 1/1:0,111:111:99:3317,333,0:0,0,49,62 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 1/1:0,135:135:99:4091,402,0:0,0,88,47 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 0/1:26,28:54:99:649,0,682:13,13,14,14 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 0/1:28,39:67:99:1512,0,1115:8,20,15,24 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 0/1:42:99:12,8,16,6 chr2 87000387 . T G 612.75 PASS AC=1;AF=0.5;AN=2;DP=226;FractionInformativeReads=1;MQ=60;set=variant2-variant21-variant23-variant24-variant31-variant38 GT:AD:DP:GQ:PL:SB 0/1:21,18:39:99:522,0,659:14,7,14,4 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 0/1:30,34:64:99:849,0,761:12,18,17,17 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 0/1:12,18:30:99:407,0,351:4,8,7,11 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 0/1:42,29:71:99:727,0,1334:29,13,17,12 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 0/1:185,159:344:99:3769,0,4967:105,80,90,69 chr2 87003846 . C A 743.47 PASS AC=1;AF=0.5;AN=2;DP=295;FractionInformativeReads=1;MQ=60;set=variant2-variant21-variant23-variant24-variant31-variant38 GT:AD:DP:GQ:PL:SB 0/1:16,20:36:99:488,0,479:8,8,10,10 chr2 87003972 . TTATCTC T 1276.51 PASS AC=1;AF=0.5;AN=2;DP=451;MQ=60;set=variant2-variant21-variant23-variant24-variant31-variant38 GT:AD:DP:GQ:PL:SB 0/1:40,27:67:99:997,0,3071:27,13,20,7 chr2 87004434 . T G 1038.53 PASS AC=1;AF=0.5;AN=2;DP=142;FractionInformativeReads=1;MQ=60;set=variant12-variant23 GT:AD:DP:GQ:PL:SB 0/1:35,34:69:99:899,0,1048:12,23,15,19 chr2 87012073 . A G 286.3 PASS AC=1;AF=0.5;AN=2;DP=556;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant21-variant22-variant23-variant24-variant29-variant31-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,24:43:99:637,0,507:8,11,9,15 chr2 87012293 . A G 906.55 PASS AC=1;AF=0.5;AN=2;DP=763;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant21-variant22-variant23-variant24-variant29-variant31-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,32:71:99:891,0,1022:24,15,21,11 chr2 87012399 . T TAA 1713.94 PASS AC=1;AF=0.5;AN=2;DP=1578;MQ=60;set=variant2-variant3-variant21-variant22-variant23-variant24-variant29-variant31-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,46:96:99:1373,0,1519:22,28,23,23 chr2 87015633 . T TGA 1265.36 PASS AC=2;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 1/1:0,39:39:99:1716,120,0:0,0,25,14 chr2 87016506 . A G 1807.26 PASS AC=1;AF=0.5;AN=2;DP=1679;MQ=60;set=variant2-variant3-variant21-variant22-variant23-variant24-variant29-variant31-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,46:101:99:1117,0,1335:28,27,25,21 chr2 87016922 . G GCGCCCC,GCACCCC 2187.83 PASS AC=1,0;AF=0.333,0.194;AN=2;DP=2812;MQ=60;set=variant2-variant3-variant7-variant9-variant16-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant37-variant38-variant39-variant42-variant44 GT:DP:GQ:SB 0/1:122:99:27,39,21,35 chr2 87017034 . C G 349.91 PASS AC=1;AF=0.5;AN=2;DP=343;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant21-variant22-variant23-variant24-variant29-variant31-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,11:27:99:330,0,504:4,12,2,9 chr2 87017069 . C G 160.61 PASS AC=1;AF=0.528;AN=2;DP=358;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant7-variant9-variant16-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,8:19:99:222,0,277:4,7,2,6 chr2 87018452 . A G 1124.19 PASS AC=2;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 1/1:0,62:62:99:1813,186,0:0,0,30,32 chr2 87018547 . A G 836.32 PASS AC=1;AF=0.528;AN=2;DP=1451;MQ=60;set=variant2-variant3-variant7-variant9-variant16-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant31-variant37-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,41:84:99:1093,0,1066:25,18,22,19 chr2 87035139 . T C 615 PASS AC=1;AF=0.536;AN=2;DP=242;MQ=60;set=variant3-variant9-variant16-variant21-variant22-variant23-variant24-variant26-variant28-variant31-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,8:15:99:249,0,203:3,4,4,4 chr2 87035529 . CTG C 250.64 PASS AC=1;AF=0.5;AN=2;DP=29;FS=0;MQ=60;SOR=0.941;set=variant23-variant38 GT:AD:DP:GQ:PL:SB 0/1:2,7:9:74:288,0,74:1,1,4,3 chr2 87048677 . A G 385.3 PASS AC=1;AF=0.533;AN=2;DP=344;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant7-variant9-variant21-variant22-variant23-variant24-variant28-variant29-variant31-variant37-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,18:27:99:414,0,220:7,2,11,7 chr2 87048702 . T G 526.1 PASS AC=2;AF=0.932;AN=2;DP=1550;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1203,111,0:0,0,26,11 chr2 87049281 . G A 412.34 PASS AC=1;AF=0.5;AN=2;DP=177;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant21-variant22-variant23-variant29-variant31-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,15:19:84:404,0,84:3,1,11,4 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 0/1:10,7:17:99:188,0,284:4,6,4,3 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 0/1:17,11:28:99:263,0,375:8,9,6,5 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 0/1:16,8:24:99:177,0,410:11,5,5,3 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 0/1:28,10:38:99:273,0,747:11,17,0,10 chr2 87141072 . C T 846.65 PASS AC=1;AF=0.625;AN=2;DP=377;FractionInformativeReads=1;set=variant4-variant7-variant11-variant21-variant23-variant32-variant33-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,15:18:26:319,0,26:1,2,7,8 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 0/1:23,17:40:99:368,0,637:15,8,12,5 chr2 87169455 . ACGGCCTCGACCTGGCCGGGCGG A 503.39 PASS AC=1;AF=0.658;AN=2;DP=1685;set=variant2-variant4-variant6-variant7-variant11-variant17-variant21-variant22-variant23-variant25-variant27-variant28-variant30-variant32-variant33-variant37-variant39-filterInvariant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,23:44:99:780,0,713:6,15,9,14 chr2 87169471 . C G 627.15 PASS AC=1;AF=0.536;AN=2;DP=987;set=variant-variant10-variant12-variant13-variant14-variant15-variant18-variant19-variant23-variant27-variant29-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,21:60:99:669,0,1431:16,23,6,15 chr2 87169493 . C G 610.37 PASS AC=1;AF=0.5;AN=2;DP=825;set=variant-variant7-variant8-variant10-variant12-variant13-variant14-variant15-variant19-variant23-variant27-variant29-variant38-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,15:55:99:495,0,1528:16,24,4,11 chr2 87169515 . C G 566.27 PASS AC=1;AF=0.5;AN=2;DP=151;FractionInformativeReads=1;set=variant10-variant12-variant19-variant23-variant27-variant40 GT:AD:DP:GQ:PL:SB 0/1:32,6:38:99:195,0,1307:11,21,0,6 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 0/1:17,15:32:99:283,0,349:9,8,7,8 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 0/1:62,52:114:99:1294,0,1518:35,27,33,19 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 0/1:20,7:27:98:98,0,654:5,15,3,4 chr2 87565743 . A C 1120.25 PASS AC=1;AF=0.657;AN=2;DP=1717;set=variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-filterInvariant12-variant13-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,16:47:99:428,0,814:13,18,3,13 chr2 87566063 . C T 546.6 DRAGENHardSNP AC=1;AF=0.655;AN=2;DP=489;FS=0;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:9,5:14:96:96,0,211:9,0,5,0 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 0/1:2,9:11:24:222,0,24:0,2,1,8 chr2 88125212 . C G 419.28 PASS AC=1;AF=0.5;AN=2;DP=210;FractionInformativeReads=1;set=variant13-variant23-variant26 GT:AD:DP:GQ:PL:SB 0/1:52,26:78:99:478,0,1140:26,26,12,14 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 0/1:22,61:83:99:1377,0,332:9,13,35,26 chr2 88272950 . G T 1048.92 PASS AC=1;AF=0.5;AN=2;DP=78;FS=7.93;FractionInformativeReads=1;MQ=30.72;MQRankSum=0.539;QD=13.45;ReadPosRankSum=-1.063;SOR=1.562;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:30,48:78:99:1077,0,503:15,15,16,32 chr2 88289207 . G A 106.77 PASS AC=2;AF=1;AN=2;DP=120;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:156,12,0:0,0,4,0 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 1/1:0,26:26:78:741,78,0:0,0,11,15 chr2 88328163 . CT C,CTT,CTTT,CTTTT,CTTTTT 159.35 PASS AC=0,1,1,0,0;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 2/3:24:99:2,2,4,16 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 1/1:0,9:9:27:405,27,0:0,0,0,9 chr2 88387403 . C A 649.18 PASS AC=2;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 1/1:0,75:75:99:2175,224,0:0,0,42,33 chr2 88408172 . A G 265.56 PASS AC=1;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 0/1:10,9:19:99:264,0,316:2,8,3,6 chr2 88409719 . A AGAGT,AGTGT,AGAGTGTGTGT,AGAGTGTGTGTGT,AGAGTGTGT,AGT,AGTGTGT,AGAGTGTGTGTGTGT 887.92 PASS AC=0,0,0,0,0,1,0,0;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 0/6:24:99:5,3,11,5 chr2 88410102 . C G 560.39 PASS AC=1;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 0/1:34,30:64:99:771,0,901:14,20,9,21 chr2 88410168 . A G 726.61 PASS AC=1;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 0/1:31,17:48:99:484,0,819:13,18,7,10 chr2 88410731 . A G 2004.28 PASS AC=1;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 0/1:57,65:122:99:1712,0,1604:37,20,39,26 chr2 88411305 . C T 630.09 PASS AC=1;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 0/1:21,21:42:99:504,0,533:12,9,11,10 chr2 88411793 . C A 1098.72 PASS AC=1;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 0/1:39,25:64:99:573,0,1186:15,24,11,14 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 1/1:0,41:41:99:1305,122,0:0,0,24,17 chr2 88423510 . A G 1632.47 PASS AC=1;AF=0.571;AN=2;DP=1126;MQ=60;set=variant2-variant3-variant4-variant6-variant8-variant11-variant12-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant31-variant34-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,22:49:99:594,0,670:13,14,9,13 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 1/1:0,52:52:99:1655,156,0:0,0,28,24 chr2 88424066 . T C 4312.85 PASS AC=1;AF=0.571;AN=2;DP=3027;MQ=60;set=variant2-variant3-variant4-variant6-variant8-variant11-variant12-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant31-variant34-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,45:120:99:1010,0,1869:41,34,21,24 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 1/1:0,45:45:99:1267,134,0:0,0,20,25 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 1/1:0,80:80:99:3532,241,0:0,0,27,53 chr2 88469891 . G T 492.82 PASS AC=2;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 1/1:0,69:69:99:3032,208,0:0,0,26,43 chr2 88469933 . TCGCGCCCCGCGCCC T,TCGCGCCCCGCGCCCCGCGCCCCGCGCCCCGCGCCC,TCGCGCCCCGCGCCCCGCGCCC,TCGCGCCC 738.45 PASS AC=0,0,0,2;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 4/4:15:2:0,1,6,8 chr2 88471894 . G T 437.53 PASS AC=2;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 1/1:0,20:20:60:669,60,0:0,0,10,10 chr2 88472141 . G A 399.71 PASS AC=2;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 1/1:0,19:19:57:625,57,0:0,0,11,8 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 1/1:0,50:50:99:1539,149,0:0,0,25,25 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 1/1:0,36:36:99:1164,108,0:0,0,19,17 chr2 88472925 . A G 752.09 PASS AC=2;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 1/1:0,64:64:99:1856,191,0:0,0,29,35 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 1/1:0,97:97:99:3309,291,0:0,0,44,53 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 1/1:1,71:72:99:2509,191,0:1,0,24,47 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 1/1:0,54:54:99:1757,162,0:0,0,30,24 chr2 88748390 . A T 2826.13 PASS AC=1;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 0/1:57,41:98:99:885,0,1413:24,33,16,25 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 1/1:0,36:36:99:1348,108,0:0,0,10,26 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 1/1:0,4:4:12:139,12,0:0,0,3,1 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 1/1:0,11:11:33:291,33,0:0,0,7,4 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 0/1:35:99:5,20,4,6 chr2 88825334 . CAAG C 365.44 PASS AC=1;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 0/1:8,10:18:99:396,0,332:0,8,1,9 chr2 88826184 . AT A 272.17 PASS AC=1;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 0/1:11,10:21:99:223,0,251:5,6,1,9 chr2 88826219 . G A 121.65 PASS AC=1;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 0/1:6,6:12:99:234,0,131:3,3,0,6 chr2 88870632 . A T 649.19 PASS AC=1;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 0/1:8,16:24:99:448,0,159:3,5,4,12 chr2 88874891 . C A 3492.08 PASS AC=1;AF=0.75;AN=2;DP=5412;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:66,46:112:99:1209,0,1779:28,38,19,27 chr2 88882942 . T A 1247.28 PASS AC=1;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 0/1:36,36:72:99:965,0,830:21,15,24,12 chr2 88895123 . T C 3091.6 PASS AC=1;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 0/1:39,34:73:99:729,0,992:20,19,17,17 chr2 88895351 . T C 2065.26 PASS AC=1;AF=0.75;AN=2;DP=2779;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:31,28:59:99:569,0,729:16,15,14,14 chr2 88913273 . G C 571.14 PASS AC=1;AF=0.5;AN=2;DP=1377;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant9-variant11-variant12-variant13-variant16-variant19-variant23-variant24-variant26-variant27-variant30-variant31-variant32-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,28:71:99:671,0,1061:22,21,11,17 chr2 88926729 . CCAG C,CCAGCAG 175.73 PASS AC=1,0;AF=0.667,0.013;AN=2;DP=1692;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:29:99:11,8,7,3 chr2 89050126 . T G 912.3 PASS AC=1;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 0/1:36,31:67:99:861,0,1053:29,7,23,8 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 0/1:83,44:127:99:1385,0,2153:31,52,25,19 chr2 89082495 . T G,A 256.23 PASS AC=1,0;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 0/1:93:99:18,51,14,10 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 0/1:54,40:94:99:1518,0,2949:11,43,21,19 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 0/1:40,29:69:99:1133,0,2649:7,33,13,16 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 0/1:30,17:47:99:701,0,2085:5,25,8,9 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 0/1:22,7:29:99:312,0,1401:4,18,2,5 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 0/1:21,5:26:99:186,0,1410:4,17,0,5 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 0/1:18,5:23:99:147,0,1347:3,15,0,5 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 0/1:17,3:20:75:75,0,1065:3,14,0,3 chr2 89084327 . G C 1472.47 PASS AC=1;AF=0.784;AN=2;DP=1612;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:19,16:35:99:464,0,504:9,10,7,9 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 0/1:76,15:91:99:236,0,2049:46,30,15,0 chr2 89100657 . G A 547.36 PASS AC=1;AF=0.5;AN=2;DP=6848;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:83,36:119:99:797,0,2178:46,37,24,12 chr2 89100697 . C G 1539.39 PASS AC=1;AF=0.5;AN=2;DP=7393;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:75,55:130:99:2165,0,3009:37,38,34,21 chr2 89100701 . A G 1539.39 PASS AC=1;AF=0.5;AN=2;DP=7409;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:76,57:133:99:2165,0,3009:38,38,34,23 chr2 89100725 . G A 1701.57 PASS AC=1;AF=0.5;AN=2;DP=7008;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:60,67:127:99:2421,0,2393:28,32,34,33 chr2 89100759 . A C 1610.33 PASS AC=1;AF=0.5;AN=2;DP=5631;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:43,60:103:99:2318,0,1542:13,30,24,36 chr2 89100764 . A G 1545.53 PASS AC=1;AF=0.5;AN=2;DP=5229;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:40,58:98:99:2281,0,1495:11,29,22,36 chr2 89100805 . A G 735.26 PASS AC=1;AF=0.5;AN=2;DP=2839;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:22,33:55:99:1279,0,815:4,18,10,23 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 0/1:43,10:53:99:228,0,1501:11,32,1,9 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 0/1:21,31:52:99:1235,0,821:4,17,8,23 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 0/1:14,23:37:99:1041,0,636:2,12,5,18 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 0/1:6,8:14:99:259,0,233:0,6,1,7 chr2 89103705 . A G 486.15 PASS AC=1;AF=0.528;AN=2;DP=230;set=variant-variant5-variant7-variant13-variant15-variant19-variant20-variant21-variant23-variant24-variant28-variant30-variant32-variant37-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,7:11:99:160,0,147:4,0,3,4 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 0/1:8,19:27:99:771,0,321:4,4,9,10 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 0/1:9,21:30:99:855,0,315:4,5,10,11 chr2 89103765 . A C 869.7 PASS AC=1;AF=0.5;AN=2;DP=1811;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:9,21:30:99:855,0,315:4,5,10,11 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 0/1:30,11:41:99:250,0,873:13,17,5,6 chr2 89103862 . T C 811.44 PASS AC=1;AF=0.5;AN=2;DP=2599;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:17,23:40:99:605,0,467:8,9,10,13 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 0/1:28,13:41:99:360,0,1120:16,12,5,8 chr2 89103904 . C T 637.52 PASS AC=1;AF=0.557;AN=2;DP=1961;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:26,5:31:99:132,0,1077:16,10,1,4 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 0/1:25,9:34:99:290,0,995:18,7,9,0 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 0/1:23,12:35:99:455,0,922:16,7,12,0 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 0/1:25,18:43:99:627,0,1054:15,10,17,1 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 0/1:39,17:56:99:484,0,1313:25,14,14,3 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 0/1:93,18:111:76:76,0,3391:50,43,12,6 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 0/1:106:99:12,12,47,35 chr2 89104347 . G T 657.97 PASS AC=1;AF=0.5;AN=2;DP=4810;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant9-variant11-variant12-variant13-variant14-filterInvariant15-variant16-variant18-variant19-variant20-filterInvariant21-variant22-filterInvariant23-variant24-variant25-variant26-variant27-filterInvariant28-variant30-variant32-variant33-variant36-filterInvariant37-variant39-variant40-variant41-filterInvariant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:102,17:119:71:71,0,3644:56,46,7,10 chr2 89104364 . A G 2873.31 PASS AC=1;AF=0.5;AN=2;DP=5824;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:20,100:120:99:3143,0,224:8,12,50,50 chr2 89104430 . G C 531.18 PASS AC=1;AF=0.5;AN=2;DP=2030;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-filterInvariant10-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant32-variant33-variant36-variant37-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:40,12:52:99:190,0,1500:8,32,4,8 chr2 89104977 . T TG 663.16 PASS AC=1;AF=0.5;AN=2;DP=1905;set=variant5-variant7-filterInvariant9-filterInvariant10-filterInvariant13-variant16-filterInvariant18-variant19-filterInvariant23-variant25-filterInvariant33-filterInvariant37-filterInvariant38-filterInvariant40-variant41-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:85,11:96:99:120,0,3438:32,53,4,7 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 0/1:96:99:26,42,10,18 chr2 89104990 . C T 172.09 PASS AC=1;AF=0.5;AN=2;DP=3554;set=filterInvariant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant10-filterInvariant11-variant12-variant13-variant14-variant16-variant18-variant19-filterInvariant20-variant22-variant23-filterInvariant24-variant25-variant26-filterInvariant27-variant30-filterInvariant32-filterInvariant33-variant36-variant37-filterInvariant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,23:88:99:598,0,1829:22,43,7,16 chr2 89105008 . T C 895.02 PASS AC=1;AF=0.5;AN=2;DP=4304;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:52,28:80:99:840,0,1408:16,36,9,19 chr2 89105019 . A C 901.79 PASS AC=1;AF=0.5;AN=2;DP=3857;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:44,27:71:99:803,0,1198:14,30,10,17 chr2 89105076 . A T 390.25 PASS AC=1;AF=0.5;AN=2;DP=1165;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant32-variant33-variant36-variant37-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,13:28:99:366,0,490:1,14,2,11 chr2 89157129 . G A 97485.2 PASS AC=2;AF=0.966;AN=2;DP=129362;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:102,3160:3262:99:100482,6584,0:45,57,1788,1372 chr2 89157192 . A ACTTC,AGGTC,AGCTC 1297.16 PASS AC=0,1,0;AF=0.167,0.167,0.167;AN=2;DP=5241;set=filterInvariant21-variant23-variant41 GT:DP:GQ:SB 0/2:1221:99:719,270,24,208 chr2 89157195 . T TCGTTTGATCTCCA,TAGTTTGATCTCCA,TTGATCTCCA,TTGATCTCCACCTTGGTA 1589.87 PASS AC=0,0,0,1;AF=0.1,0.1,0.1,0.2;AN=2;DP=8563;set=filterInvariant11-variant15-filterInvariant21-variant23-variant41 GT:DP:GQ:SB 0/4:1157:99:708,242,0,207 chr2 89157282 . T A 475.75 PASS AC=1;AF=0.5;AN=2;DP=332;MQ=60;set=variant5-variant18-variant19-variant23-variant26-variant33-variant34-variant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,13:32:99:401,0,590:5,14,5,8 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 1/1:0,105:105:99:3313,315,0:0,0,57,48 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 1/1:0,172:172:99:5112,514,0:0,0,97,75 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 1/1:1,51:52:99:1896,123,0:1,0,7,44 chr2 89185449 . G C 84395.1 PASS AC=2;AF=0.92;AN=2;DP=108047;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:145,2278:2423:99:69228,2142,0:81,64,1202,1076 chr2 89185477 . C G 150662 PASS AC=2;AF=0.784;AN=2;DP=137390;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:151,2990:3141:99:126435,1094,0:75,76,1597,1393 chr2 89185492 . C T 160266 PASS AC=2;AF=0.83;AN=2;DP=153774;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:163,3368:3531:99:133014,1867,0:84,79,1784,1584 chr2 89185519 . G C 128388 PASS AC=2;AF=0.966;AN=2;DP=173121;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:148,3875:4023:99:113250,6808,0:80,68,2012,1863 chr2 89185552 . C T 121320 PASS AC=2;AF=0.966;AN=2;DP=173346;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:158,3905:4063:99:111585,5631,0:88,70,1917,1988 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 0/2:753:99:78,82,481,112 chr2 89185669 . TCC T,TTCACTTTCGGCC 8555.42 PASS AC=1,0;AF=0.4,0.1;AN=2;DP=3815;set=variant3-filterInvariant8-variant17-variant18-variant20-variant21-variant23-variant28-filterInvariant34-filterInvariant36 GT:DP:GQ:SB 0/1:250:99:77,83,5,85 chr2 89185774 . G A 1515.16 PASS AC=1;AF=0.553;AN=2;DP=1211;MQ=60;set=variant-variant5-variant6-variant7-variant10-variant13-variant17-variant18-variant22-variant23-variant24-variant25-variant27-variant30-variant33-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,24:49:99:561,0,731:6,19,9,15 chr2 89196757 . G A 2082.85 PASS AC=1;AF=0.568;AN=2;DP=2249;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant22-variant23-variant24-variant25-variant27-variant30-variant33-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,48:96:99:1177,0,1263:27,21,23,25 chr2 89196906 . A C 2039.51 PASS AC=1;AF=0.568;AN=2;DP=2263;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant22-variant23-variant24-variant25-variant27-variant30-variant33-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,36:84:99:921,0,1292:21,27,19,17 chr2 89197190 . C T 2347.9 PASS AC=1;AF=0.568;AN=2;DP=2091;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant22-variant23-variant24-variant25-variant27-variant30-variant33-variant38-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,43:83:99:1086,0,961:18,22,17,26 chr2 89246951 . C T,G 9092.1 PASS AC=1,0;AF=0.444,0.111;AN=2;DP=6394;set=variant-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant22-variant23-variant24-variant25-variant30-variant33-variant41-variant44 GT:DP:GQ:SB 0/1:339:99:89,92,77,81 chr2 89265717 . G C 2346.05 PASS AC=1;AF=0.533;AN=2;DP=1624;set=variant-variant6-variant7-variant10-variant13-variant17-variant18-variant22-variant23-variant24-variant25-variant30-variant33-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,47:87:99:1399,0,947:25,15,35,12 chr2 89265761 . C T 2515.38 PASS AC=1;AF=0.5;AN=2;DP=822;MQ=60;set=variant18-variant23-variant30-variant33-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,76:140:99:2063,0,1634:41,23,50,26 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 0/1:5,5:10:99:100,0,139:5,0,3,2 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 0/1:72,36:108:99:769,0,1687:38,34,19,17 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 0/1:57,52:109:99:1222,0,1390:28,29,26,26 chr2 89292182 . A G 10178.2 PASS AC=1;AF=0.553;AN=2;DP=6480;set=variant-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant22-variant23-variant24-variant25-variant30-variant33-variant34-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:147,150:297:99:3898,0,3715:70,77,70,80 chr2 89292201 . C T 10026.5 PASS AC=1;AF=0.533;AN=2;DP=5141;set=variant-variant6-variant7-variant10-variant13-variant17-variant18-variant22-variant23-variant24-variant25-variant30-variant33-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:138,141:279:99:3664,0,3375:63,75,62,79 chr2 89292401 . T C 2513.36 PASS AC=1;AF=0.556;AN=2;DP=1397;set=variant-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant22-variant23-variant24-variant25-variant30-variant33-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:41,44:85:99:1171,0,1266:10,31,12,32 chr2 89309424 . G A 4003.11 PASS AC=1;AF=0.553;AN=2;DP=2676;set=variant-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant22-variant23-variant24-variant25-variant30-variant33-variant34-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:55,73:128:99:1789,0,1402:37,18,48,25 chr2 89309542 . T G 7823.53 PASS AC=1;AF=0.556;AN=2;DP=5119;set=variant-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant22-variant23-variant24-variant25-variant30-variant33-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:137,121:258:99:3068,0,3416:72,65,63,58 chr2 89309554 . T A 7769.8 PASS AC=1;AF=0.556;AN=2;DP=5219;set=variant-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant22-variant23-variant24-variant25-variant30-variant33-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:146,124:270:99:3212,0,3661:73,73,64,60 chr2 89309735 . A G 9670.53 PASS AC=1;AF=0.556;AN=2;DP=6642;set=variant-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant22-variant23-variant24-variant25-variant30-variant33-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:175,161:336:99:3934,0,4180:88,87,78,83 chr2 89309762 . T G 9717.68 PASS AC=1;AF=0.556;AN=2;DP=6584;set=variant-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant17-variant18-variant22-variant23-variant24-variant25-variant30-variant33-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:167,156:323:99:3911,0,4311:81,86,72,84 chr2 89512775 . T G 150.37 PASS AC=1;AF=0.775;AN=2;DP=1584;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-variant36-variant37-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,23:37:99:726,0,387:11,3,20,3 chr2 89533771 . A G 2850.9 PASS AC=1;AF=0.5;AN=2;DP=473;FractionInformativeReads=1;set=variant4-variant23 GT:AD:DP:GQ:PL:SB 0/1:103,97:200:99:2346,0,2562:54,49,49,48 chr2 89534050 . T C 1238.81 PASS AC=1;AF=0.5;AN=2;DP=281;FractionInformativeReads=1;set=variant18-variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:38,39:77:99:1092,0,1020:10,28,9,30 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 1/1:0,15:15:45:441,45,0:0,0,3,12 chr2 90007670 . G A 1144.47 PASS AC=2;AF=0.77;AN=2;DP=1614;set=variant2-variant3-variant5-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-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:625,63,0:0,0,14,7 chr2 90008208 . T G 2296.05 PASS AC=2;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 1/1:0,17:17:51:576,51,0:0,0,3,14 chr2 90008243 . G C 52.06 PASS AC=2;AF=0.75;AN=2;DP=222;FractionInformativeReads=1;set=filterInvariant2-variant8-variant16-variant17-variant23-variant24-variant34-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:217,18,0:0,0,1,5 chr2 90008287 . A C 319.66 PASS AC=2;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 1/1:0,2:2:6:66,6,0:0,0,0,2 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 1/1:0,39:39:99:1220,117,0:0,0,21,18 chr2 90108778 . G T 1912.82 PASS AC=2;AF=0.854;AN=2;DP=4841;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-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1400,125,0:0,0,29,13 chr2 90121675 . T C 1146.02 PASS AC=2;AF=0.898;AN=2;DP=2780;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:950,78,0:0,0,22,4 chr2 90121732 . A G 336.19 PASS AC=1;AF=0.5;AN=2;DP=166;FractionInformativeReads=1;set=variant-filterInvariant23 GT:AD:DP:GQ:PL:SB 0/1:70,11:81:99:139,0,1818:41,29,11,0 chr2 90121845 . A G 8397 PASS AC=1;AF=0.5;AN=2;DP=7952;set=variant-variant6-variant10-variant12-variant13-variant14-variant17-variant18-variant22-variant23-variant24-variant25-variant30-variant33-variant34-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:145,108:253:99:4230,0,5702:73,72,65,43 chr2 90121849 . A G 8470.57 PASS AC=1;AF=0.5;AN=2;DP=8005;set=variant-variant6-variant10-variant12-variant13-variant14-variant17-variant18-variant22-variant23-variant24-variant25-variant30-variant33-variant34-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:147,112:259:99:4200,0,5791:75,72,68,44 chr2 90121926 . G T 6441.93 PASS AC=1;AF=0.5;AN=2;DP=7934;set=variant-variant6-variant10-variant12-variant13-variant14-variant17-variant18-variant22-variant23-variant24-variant25-variant30-variant33-variant34-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:117,140:257:99:3218,0,3023:58,59,71,69 chr2 90121985 . A G 5548.87 PASS AC=1;AF=0.5;AN=2;DP=7420;set=variant-variant6-variant10-variant12-variant13-variant14-variant17-variant18-variant22-variant23-variant24-variant25-variant30-variant33-variant34-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:124,129:253:99:3182,0,3038:66,58,53,76 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 0/1:1,2:3:37:69,0,37:1,0,2,0 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 0/1:31,22:53:99:442,0,896:22,9,9,13 chr2 90259760 . A T 67.6 PASS AC=1;AF=0.5;AN=2;DP=96;FractionInformativeReads=1;set=variant23-filterInvariant33 GT:AD:DP:GQ:PL:SB 0/1:21,4:25:96:96,0,710:18,3,1,3 chr2 90458538 . T C 1200.33 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=12807;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:119,95:214:99:1999,0,2653:81,38,66,29 chr2 90458594 . T C 4017.35 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=28619;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:253,211:464:99:4166,0,5152:143,110,123,88 chr2 90458745 . T C 1030.78 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=7326;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:71,48:119:99:1083,0,1694:15,56,8,40 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 0/1:143,36:179:99:516,0,3362:95,48,18,18 chr2 91679044 . A G 4264.55 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=30008;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:265,246:511:99:4680,0,5124:117,148,116,130 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 0/1:5,4:9:72:72,0,108:2,3,2,2 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 0/1:92,32:124:99:1027,0,3720:34,58,6,26 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 0/1:91,31:122:99:1027,0,3720:34,57,6,25 chr2 91766729 . C CAG 2478.6 PASS AC=1;AF=0.5;AN=2;DP=4330;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:17,52:69:99:2081,0,569:6,11,18,34 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 0/1:10,6:16:99:181,0,338:9,1,5,1 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 0/1:109,40:149:99:712,0,3074:39,70,16,24 chr2 91809227 . A G 612.8 PASS AC=1;AF=0.5;AN=2;DP=8401;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:77,78:155:99:1752,0,1925:46,31,44,34 chr2 91809324 . C T 1120.08 PASS AC=1;AF=0.5;AN=2;DP=11677;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:149,79:228:99:1584,0,3642:77,72,34,45 chr2 91809385 . C G 827.56 PASS AC=1;AF=0.5;AN=2;DP=9198;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:131,61:192:99:1198,0,3204:59,72,27,34 chr2 91809404 . G C 723.9 PASS AC=1;AF=0.5;AN=2;DP=7729;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:104,53:157:99:1065,0,2624:42,62,22,31 chr2 91809453 . T TAA 65.28 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=346;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:58,7:65:99:109,0,2392:17,41,3,4 chr2 91809454 . GGT G 65.54 DRAGENHardINDEL AC=1;AF=0.5;AN=2;DP=336;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:58,6:64:99:109,0,2392:17,41,2,4 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 0/1:49,13:62:99:210,0,1546:14,35,5,8 chr2 91809468 . C CTAA 190.02 PASS AC=1;AF=0.5;AN=2;DP=3248;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:35,15:50:99:504,0,1425:9,26,6,9 chr2 91809470 . G A 199.23 PASS AC=1;AF=0.5;AN=2;DP=3125;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:35,14:49:99:504,0,1425:9,26,5,9 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 0/1:35,14:49:99:524,0,1424:9,26,5,9 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 0/1:4,4:8:99:105,0,106:4,0,4,0 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 0/1:5,6:11:99:146,0,146:4,1,4,2 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 0/1:4,8:12:99:236,0,105:3,1,6,2 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 0/1:106,19:125:99:385,0,3227:67,39,17,2 chr2 91925022 . C A 1690.56 PASS AC=1;AF=0.5;AN=2;DP=10048;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:101,73:174:99:1791,0,2687:64,37,43,30 chr2 91925139 . C G 737.32 PASS AC=1;AF=0.5;AN=2;DP=10046;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:119,68:187:99:1463,0,3192:44,75,25,43 chr2 91925151 . C T 2717.45 PASS AC=1;AF=0.5;AN=2;DP=9169;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:73,105:178:99:2537,0,1745:26,47,39,66 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 0/1:2,4:6:70:81,0,70:2,0,2,2 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 0/1:35,51:86:99:1157,0,790:21,14,31,20 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 0/1:62,63:125:99:2403,0,2493:40,22,33,30 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 0/1:63,61:124:99:2397,0,2561:40,23,31,30 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 0/1:67,59:126:99:2334,0,2589:41,26,29,30 chr2 91927184 . C T 171.98 PASS AC=1;AF=0.5;AN=2;DP=1792;set=filterInvariant3-filterInvariant8-filterInvariant11-variant21-variant23-variant25-variant27-filterInvariant29-variant36-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:124,28:152:99:424,0,3148:71,53,9,19 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 0/1:104,40:144:99:812,0,2629:60,44,14,26 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 0/1:113,31:144:99:918,0,4631:62,51,11,20 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 0/1:112,30:142:99:918,0,4631:61,51,10,20 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 0/1:137,29:166:99:331,0,3542:51,86,12,17 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 0/1:73,10:83:99:135,0,2226:52,21,9,1 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 0/1:139,25:164:99:399,0,3520:83,56,23,2 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 0/1:177,47:224:99:1121,0,4717:102,75,43,4 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 0/1:227,167:394:99:3923,0,5390:111,116,105,62 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 0/1:217,184:401:99:7108,0,8272:104,113,107,77 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 0/1:217,194:411:99:7326,0,8331:105,112,112,82 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 0/1:24,20:44:99:464,0,659:17,7,12,8 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 0/1:55,48:103:99:1146,0,1314:27,28,25,23 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 0/1:51,43:94:99:968,0,1198:22,29,19,24 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 0/1:18,30:48:99:777,0,407:6,12,10,20 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 0/1:14,21:35:99:638,0,348:4,10,5,16 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 0/1:273,32:305:99:516,0,14598:130,143,27,5 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 0/1:258,38:296:99:711,0,14408:123,135,30,8 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 0/1:157:99:54,75,13,15 chr2 91940568 . T C 491.44 PASS AC=1;AF=0.5;AN=2;DP=1283;set=variant3-variant21-variant23-variant25-variant27-variant29-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:109,25:134:99:392,0,2906:46,63,10,15 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 0/1:85,17:102:99:255,0,2339:47,38,4,13 chr2 91944129 . T C 39.6 PASS AC=1;AF=0.5;AN=2;DP=2055;set=filterInvariant-variant3-filterInvariant7-variant10-variant16-filterInvariant17-variant19-filterInvariant23-filterInvariant25-filterInvariant26-variant28-filterInvariant29-variant30-variant32-filterInvariant34-filterInvariant37-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:104,16:120:99:182,0,2928:40,64,12,4 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 0/1:95,20:115:99:540,0,5055:37,58,13,7 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 0/1:90,22:112:99:611,0,4873:35,55,14,8 chr2 91955209 . G A 1764.97 PASS AC=1;AF=0.5;AN=2;DP=2468;set=variant4-variant7-variant14-variant16-variant23-variant27-variant30 GT:AD:DP:GQ:PL:SB 0/1:230,78:308:99:1522,0,6201:111,119,44,34 chr2 91955237 . G A 997.09 PASS AC=1;AF=0.5;AN=2;DP=341;FS=0.504;FractionInformativeReads=0.997;MQ=59.54;MQRankSum=0.78;QD=2.92;ReadPosRankSum=-0.726;SOR=0.651;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:276,64:340:99:1025,0,7447:141,135,32,32 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 0/1:180,146:326:99:3304,0,4053:85,95,56,90 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 0/1:77,30:107:99:912,0,2047:26,51,3,27 chr2 91960952 . A G 149.4 PASS AC=1;AF=0.5;AN=2;DP=565;FractionInformativeReads=1;set=variant8-filterInvariant9-variant11-variant12-filterInvariant16-variant17-filterInvariant23-variant27-variant28-variant29-filterInvariant30-variant39-filterInvariant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:35,8:43:97:97,0,945:15,20,5,3 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 0/1:39,19:58:99:652,0,1673:20,19,9,10 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 0/1:38,17:55:99:633,0,1654:19,19,8,9 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 0/1:24,12:36:99:239,0,634:11,13,4,8 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 0/1:20,12:32:99:252,0,515:9,11,4,8 chr2 92075615 . A G 551.33 PASS AC=1;AF=0.5;AN=2;DP=3785;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:42,25:67:99:923,0,1645:15,27,13,12 chr2 92075618 . T C 551.33 PASS AC=1;AF=0.5;AN=2;DP=3699;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:39,25:64:99:929,0,1584:14,25,13,12 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 0/1:20,6:26:97:97,0,511:12,8,1,5 chr2 92129749 . T C 2867.22 PASS AC=1;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 0/1:48,50:98:99:1227,0,1205:22,26,23,27 chr2 92150236 . T C 150.13 PASS AC=1;AF=0.5;AN=2;DP=14;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-1.109;QD=10.72;ReadPosRankSum=-0.193;SOR=1.179;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:6,8:14:99:178,0,145:3,3,3,5 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 0/1:70,12:82:99:284,0,2892:39,31,8,4 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 0/1:73,14:87:99:368,0,2886:39,34,9,5 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 0/1:79,13:92:99:309,0,2089:37,42,9,4 chr2 95513854 . G C 88.77 PASS AC=1;AF=0.5;AN=2;DP=688;set=filterInvariant-filterInvariant11-filterInvariant23-filterInvariant24-variant29-filterInvariant33-variant37-filterInvariant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:81,11:92:63:63,0,3317:38,43,8,3 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 0/1:74,16:90:99:491,0,3056:34,40,9,7 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 0/1:74,17:91:99:491,0,3056:34,40,9,8 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 0/1:73,14:87:99:362,0,3107:34,39,7,7 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 0/1:68,16:84:99:458,0,2913:30,38,8,8 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 0/1:22,4:26:68:68,0,781:4,18,0,4 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 0/1:15,4:19:89:89,0,515:2,13,0,4 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 0/1:46,43:89:99:985,0,1109:25,21,25,18 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 0/1:94,112:206:99:2846,0,2243:48,46,61,51 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 0/1:90,70:160:99:1624,0,2348:48,42,39,31 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 0/1:111,87:198:99:2047,0,2696:61,50,48,39 chr2 95537871 . GC GCC,GCCC,G 278.28 PASS AC=1,0,0;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 0/1:26:99:2,14,2,8 chr2 95542340 . A G 444.15 PASS AC=1;AF=0.5;AN=2;DP=12735;FractionInformativeReads=1;set=filterInvariant2-variant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant10-filterInvariant11-filterInvariant13-filterInvariant14-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant25-filterInvariant26-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant37-filterInvariant39-filterInvariant40-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:318,25:343:99:296,0,13326:172,146,21,4 chr2 95542346 . A G 803.98 PASS AC=1;AF=0.5;AN=2;DP=16144;FractionInformativeReads=1;set=filterInvariant2-variant3-variant4-variant5-variant6-filterInvariant7-filterInvariant8-filterInvariant9-variant10-variant11-variant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-variant18-filterInvariant20-filterInvariant21-variant22-filterInvariant23-filterInvariant24-variant25-variant26-filterInvariant27-filterInvariant29-variant30-variant31-filterInvariant32-filterInvariant33-variant34-variant37-variant39-variant40-variant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:330,37:367:99:671,0,13934:178,152,28,9 chr2 95542363 . C G 2409.55 PASS AC=1;AF=0.5;AN=2;DP=19127;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-filterInvariant15-variant16-variant17-variant18-filterInvariant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-filterInvariant36-variant37-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:347,73:420:99:2305,0,15040:183,164,45,28 chr2 95542376 . G T 122.25 PASS AC=1;AF=0.5;AN=2;DP=22357;set=filterInvariant-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-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:372,98:470:99:2990,0,15520:199,173,55,43 chr2 95542377 . C T 125.26 PASS AC=1;AF=0.5;AN=2;DP=22551;set=filterInvariant-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-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:374,100:474:99:2993,0,15478:200,174,56,44 chr2 95542416 . A G 542.23 PASS AC=1;AF=0.5;AN=2;DP=25128;set=variant-variant2-variant3-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-variant36-variant37-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:404,117:521:99:3658,0,16580:204,200,58,59 chr2 95542419 . G A 539.23 PASS AC=1;AF=0.5;AN=2;DP=25245;set=variant-variant2-variant3-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-variant36-variant37-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:406,117:523:99:3655,0,16658:202,204,58,59 chr2 95542421 . C T 4105.51 PASS AC=1;AF=0.5;AN=2;DP=518;FS=0.541;FractionInformativeReads=1;MQ=55;MQRankSum=11.076;QD=7.93;ReadPosRankSum=-2.853;SOR=0.651;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:329,189:518:99:4134,0,10196:160,169,95,94 chr2 95542476 . C T 207.37 PASS AC=1;AF=0.5;AN=2;DP=24395;set=filterInvariant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-filterInvariant12-variant13-filterInvariant14-filterInvariant15-filterInvariant16-variant17-variant18-filterInvariant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-filterInvariant27-variant29-variant30-variant31-variant32-filterInvariant33-filterInvariant34-filterInvariant36-variant37-variant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:426,95:521:99:1584,0,11219:199,227,39,56 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 1/1:0,29:29:87:991,87,0:0,0,7,22 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 0/1:33,33:66:99:838,0,853:22,11,19,14 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 0/1:4,2:6:72:72,0,156:0,4,0,2 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 1/1:2,109:111:99:3273,282,0:1,1,56,53 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 0/1:18,18:36:99:458,0,445:11,7,8,10 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 0/1:18,27:45:99:683,0,557:12,6,13,14 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 0/1:5,13:18:69:296,0,69:4,1,7,6 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 1/1:0,27:27:81:946,81,0:0,0,15,12 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 0/1:37,22:59:99:514,0,1001:22,15,14,8 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 0/1:32,28:60:99:610,0,862:11,21,12,16 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 0/1:87,109:196:99:2936,0,3016:38,49,42,67 chr2 95947099 . G A 2693.65 PASS AC=1;AF=0.667;AN=2;DP=1150;MQ=60;set=variant7-variant16-variant22-variant23-variant29-variant33 GT:AD:DP:GQ:PL:SB 0/1:103,69:172:99:1532,0,4055:39,64,30,39 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 1/1:0,68:68:99:2123,204,0:0,0,32,36 chr2 95955680 . G T 895.29 PASS AC=1;AF=0.71;AN=2;DP=3713;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant28-variant33-variant34-variant36-variant37-variant38-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:61,56:117:99:1385,0,1627:24,37,27,29 chr2 95962959 . G C 181.56 PASS AC=1;AF=0.783;AN=2;DP=400;set=variant2-variant4-variant5-variant8-variant9-variant11-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant26-variant30-variant31-variant33-variant34-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:15,6:21:99:204,0,529:15,0,6,0 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 0/1:35,32:67:99:742,0,709:32,3,22,10 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 0/1:81,95:176:99:2270,0,1910:34,47,42,53 chr2 96040306 . C T 171.32 PASS AC=1;AF=0.5;AN=2;DP=21;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.533;QD=8.16;ReadPosRankSum=0.107;SOR=0.399;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:12,9:21:99:200,0,327:3,9,3,6 chr2 96049917 . TACAC TAC,TACACACAC,TACACAC,TACACACACAC,TACACACACACACAC,TACACACACACAC,T 411.61 PASS AC=0,0,0,2,0,0,0;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 4/4:13:44:0,0,9,4 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 1/1:0,19:19:57:658,57,0:0,0,12,7 chr2 96504594 . C T 3004.92 PASS AC=2;AF=0.679;AN=2;DP=1271;set=variant6-variant7-variant8-variant9-variant20-variant22-variant23-variant29-variant33-variant34-variant36-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:1999,202,0:0,0,34,34 chr2 96517386 . C T 400.33 PASS AC=1;AF=0.5;AN=2;DP=39;FS=0;FractionInformativeReads=1;MQ=60;set=variant8-variant23 GT:AD:DP:GQ:PL:SB 0/1:5,10:15:99:283,0,100:3,2,7,3 chr2 96517471 . A G 223.1 PASS AC=1;AF=0.5;AN=2;DP=2991;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,19:72:99:713,0,2288:29,24,14,5 chr2 96517474 . G A 223.1 PASS AC=1;AF=0.5;AN=2;DP=3101;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:58,24:82:99:917,0,2357:33,25,18,6 chr2 96517484 . T G 369.98 PASS AC=1;AF=0.5;AN=2;DP=3461;FractionInformativeReads=1;set=variant-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,31:94:99:1154,0,2549:35,28,22,9 chr2 96517502 . A C 489.21 PASS AC=1;AF=0.5;AN=2;DP=4201;set=variant-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-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,39:99:99:1457,0,2427:35,25,24,15 chr2 96517518 . A G 531.08 PASS AC=1;AF=0.5;AN=2;DP=4830;set=variant-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-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:68,42:110:99:1524,0,2635:38,30,26,16 chr2 96517640 . T A 586.29 PASS AC=1;AF=0.5;AN=2;DP=1974;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant11-variant12-variant13-variant14-filterInvariant15-variant18-variant19-variant20-variant22-filterInvariant23-filterInvariant24-variant25-variant27-variant30-filterInvariant32-filterInvariant36-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,6:53:99:107,0,2118:15,32,0,6 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 0/1:28,24:52:99:617,0,1205:7,21,7,17 chr2 96517642 . A G 398.93 PASS AC=1;AF=0.5;AN=2;DP=3143;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:23,29:52:99:1149,0,982:5,18,10,19 chr2 96517646 . A G 595.29 PASS AC=1;AF=0.5;AN=2;DP=1807;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant11-variant12-variant13-variant14-filterInvariant15-variant18-variant19-variant20-variant22-filterInvariant23-filterInvariant24-variant25-variant27-variant30-filterInvariant32-filterInvariant36-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,6:50:99:119,0,1970:13,31,0,6 chr2 96517760 . T A 240.14 PASS AC=1;AF=0.5;AN=2;DP=756;set=variant-filterInvariant2-variant3-variant4-variant5-filterInvariant6-variant7-variant10-variant11-variant12-variant13-variant17-variant18-filterInvariant19-variant20-filterInvariant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant36-variant40 GT:AD:DP:GQ:PL:SB 0/1:17,5:22:99:149,0,727:15,2,4,1 chr2 96517783 . CTAA C 518.09 PASS AC=1;AF=0.5;AN=2;DP=1263;set=variant-filterInvariant2-variant3-variant4-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-filterInvariant19-variant20-variant21-variant22-variant23-variant24-variant25-filterInvariant26-variant27-variant28-variant29-variant30-variant32-variant34-variant36-filterInvariant38-variant40-variant42-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:19,8:27:99:279,0,751:14,5,6,2 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 0/1:18,9:27:99:211,0,600:13,5,7,2 chr2 96517824 . C T 1756.23 PASS AC=1;AF=0.5;AN=2;DP=2883;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:22,36:58:99:1049,0,419:12,10,23,13 chr2 96517882 . G A 1029.45 PASS AC=1;AF=0.5;AN=2;DP=5192;set=variant-filterInvariant2-variant3-filterInvariant4-variant5-variant6-variant7-filterInvariant8-filterInvariant10-variant11-variant12-variant13-variant14-filterInvariant15-filterInvariant16-filterInvariant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-filterInvariant31-filterInvariant32-filterInvariant33-variant34-variant36-filterInvariant37-filterInvariant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:102,34:136:99:538,0,2979:50,52,14,20 chr2 96517885 . G A 1893.62 PASS AC=1;AF=0.5;AN=2;DP=5733;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:45,91:136:99:2955,0,847:22,23,42,49 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 0/1:87,48:135:99:940,0,2698:39,48,22,26 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 0/1:86,48:134:99:970,0,2169:37,49,22,26 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 0/1:63,31:94:99:615,0,1935:27,36,12,19 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 0/1:57,38:95:99:769,0,1766:25,32,14,24 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 0/1:100:99:13,13,29,45 chr2 96518022 . G A 259.94 PASS AC=2;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 1/1:0,19:19:60:756,60,0:0,0,4,15 chr2 96519520 . G A 473.51 PASS AC=1;AF=0.5;AN=2;DP=1744;FractionInformativeReads=1;set=variant-filterInvariant2-variant3-filterInvariant4-filterInvariant5-variant6-filterInvariant7-variant10-variant11-variant12-variant13-variant14-filterInvariant18-variant19-filterInvariant20-filterInvariant22-filterInvariant23-variant25-filterInvariant26-filterInvariant27-filterInvariant32-variant33-variant36-variant39 GT:AD:DP:GQ:PL:SB 0/1:54,12:66:99:104,0,1460:29,25,6,6 chr2 96519558 . ATCGT A 745.36 PASS AC=1;AF=0.5;AN=2;DP=2882;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant14-filterInvariant15-filterInvariant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant30-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,14:78:99:395,0,2997:32,32,7,7 chr2 96519587 . T C 759.93 PASS AC=1;AF=0.5;AN=2;DP=2740;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant14-filterInvariant15-filterInvariant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-filterInvariant29-variant30-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,14:74:99:396,0,2642:27,33,7,7 chr2 96519588 . G A 759.93 PASS AC=1;AF=0.5;AN=2;DP=2728;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-filterInvariant9-variant10-variant11-variant12-variant13-variant14-filterInvariant15-filterInvariant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-filterInvariant29-variant30-variant32-variant33-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:60,14:74:99:396,0,2642:27,33,7,7 chr2 96519611 . TGATAA T 380.19 PASS AC=1;AF=0.5;AN=2;DP=2120;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-filterInvariant8-variant10-variant11-variant12-variant13-variant14-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant29-variant30-variant32-variant33-filterInvariant34-variant36-variant37-variant38-variant39-filterInvariant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,11:62:99:308,0,2531:22,29,5,6 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 0/1:90,80:170:99:2069,0,2127:51,39,51,29 chr2 96521220 . G A 971.32 PASS AC=1;AF=0.5;AN=2;DP=19581;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:256,110:366:99:1819,0,7812:130,126,68,42 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 0/1:332,62:394:99:1436,0,13724:176,156,31,31 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 0/1:97,270:367:99:8514,0,1939:48,49,127,143 chr2 96521324 . A G 10694.2 PASS AC=1;AF=0.5;AN=2;DP=17852;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:103,228:331:99:7677,0,3602:55,48,102,126 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 0/1:230,90:320:99:1542,0,8428:118,112,41,49 chr2 96521336 . T C 10288.7 PASS AC=1;AF=0.5;AN=2;DP=17180;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:108,218:326:99:7537,0,4028:56,52,107,111 chr2 96521406 . C T 4495.78 PASS AC=1;AF=0.5;AN=2;DP=14488;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:118,170:288:99:5015,0,2787:63,55,97,73 chr2 96521438 . A G 4788.23 PASS AC=1;AF=0.5;AN=2;DP=14884;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:137,146:283:99:3552,0,3454:69,68,87,59 chr2 96521455 . A G 5263.9 PASS AC=1;AF=0.5;AN=2;DP=16664;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:149,161:310:99:3769,0,3896:81,68,93,68 chr2 96521477 . A AG 3187.63 PASS AC=1;AF=0.5;AN=2;DP=19223;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:240,124:364:99:3125,0,9417:142,98,63,61 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 0/2:355:99:98,71,96,90 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 0/1:409:99:107,73,121,108 chr2 96521486 . G A 3753.22 PASS AC=1;AF=0.5;AN=2;DP=20360;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:210,203:413:99:6457,0,8099:125,85,107,96 chr2 96521512 . A C 8609.47 PASS AC=1;AF=0.5;AN=2;DP=23974;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:197,304:501:99:7901,0,4824:117,80,129,175 chr2 96521548 . G A 10644.3 PASS AC=1;AF=0.5;AN=2;DP=24943;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:255,272:527:99:10456,0,11425:142,113,108,164 chr2 96521552 . C T 134.55 PASS AC=1;AF=0.5;AN=2;DP=6782;set=filterInvariant-filterInvariant3-filterInvariant5-variant8-filterInvariant9-variant10-filterInvariant18-filterInvariant19-filterInvariant23-filterInvariant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:468,65:533:99:305,0,22268:221,247,30,35 chr2 96521556 . T C 10201.5 PASS AC=1;AF=0.5;AN=2;DP=24673;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:273,260:533:99:10163,0,11652:148,125,99,161 chr2 96521563 . G A 5279.32 PASS AC=1;AF=0.5;AN=2;DP=24321;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:340,179:519:99:4813,0,16997:179,161,66,113 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 0/1:335,158:493:99:5624,0,17944:174,161,53,105 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 0/1:336,154:490:99:5602,0,17947:173,163,50,104 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 0/1:336,150:486:99:5573,0,17950:173,163,49,101 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 1/1:0,11:11:33:484,33,0:0,0,9,2 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 1/1:0,11:11:33:484,33,0:0,0,9,2 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 1/1:0,24:24:71:678,71,0:0,0,17,7 chr2 96523096 . T C 97.42 PASS AC=1;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 0/1:20,15:35:99:293,0,433:11,9,8,7 chr2 96525640 . G T 55.03 PASS AC=1;AF=0.5;AN=2;DP=166;FractionInformativeReads=1;set=filterInvariant4-variant8-variant13-variant23-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,4:24:99:108,0,1254:11,9,3,1 chr2 96525652 . T C 163.35 PASS AC=1;AF=0.5;AN=2;DP=507;set=variant4-variant5-variant8-variant11-filterInvariant12-variant13-variant14-variant23-variant24-variant28-filterInvariant31-variant33-variant37-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:24,5:29:99:129,0,1563:14,10,3,2 chr2 96525659 . C T 139.82 PASS AC=1;AF=0.5;AN=2;DP=343;FractionInformativeReads=1;set=variant4-variant5-variant8-filterInvariant11-variant13-variant23-variant33-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:29,5:34:99:123,0,1635:17,12,3,2 chr2 96525717 . A AT 67.78 PASS AC=1;AF=0.5;AN=2;DP=1010;set=filterInvariant-variant4-variant5-filterInvariant6-variant7-variant8-variant9-variant11-variant12-filterInvariant13-variant14-filterInvariant20-variant23-filterInvariant24-variant28-variant33-variant37-filterInvariant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:39,6:45:99:135,0,2306:19,20,3,3 chr2 96525718 . G T 73.82 PASS AC=1;AF=0.5;AN=2;DP=1095;FractionInformativeReads=1;set=filterInvariant-variant4-variant5-filterInvariant6-variant7-variant8-variant9-variant11-variant12-filterInvariant13-variant14-filterInvariant20-variant23-filterInvariant24-variant28-filterInvariant31-variant33-variant37-filterInvariant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:39,6:45:99:135,0,2356:19,20,3,3 chr2 96525723 . C T 73.37 PASS AC=1;AF=0.5;AN=2;DP=1159;FractionInformativeReads=1;set=filterInvariant-variant4-variant5-filterInvariant6-variant7-variant8-variant9-variant11-filterInvariant12-filterInvariant13-variant14-filterInvariant20-variant23-filterInvariant24-filterInvariant26-variant28-variant33-variant37-filterInvariant39-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:40,6:46:99:132,0,2398:19,21,3,3 chr2 96525736 . T C 128.37 PASS AC=1;AF=0.5;AN=2;DP=932;set=variant4-variant5-variant7-filterInvariant8-variant9-variant11-filterInvariant13-filterInvariant14-filterInvariant20-variant23-variant24-filterInvariant26-variant28-filterInvariant29-variant33-variant37-variant42 GT:AD:DP:GQ:PL:SB 0/1:39,6:45:99:135,0,2322:18,21,3,3 chr2 96525750 . T A 121.91 PASS AC=1;AF=0.5;AN=2;DP=528;FractionInformativeReads=1;set=filterInvariant4-variant5-variant7-variant9-variant23-filterInvariant24-filterInvariant26-variant33-variant37 GT:AD:DP:GQ:PL:SB 0/1:38,6:44:99:138,0,2244:18,20,3,3 chr2 96525755 . A T 127.91 PASS AC=1;AF=0.5;AN=2;DP=847;set=variant4-variant5-variant7-filterInvariant8-variant9-variant11-filterInvariant14-filterInvariant20-variant23-filterInvariant24-filterInvariant26-variant28-variant29-variant33-variant37-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:36,6:42:99:138,0,2244:17,19,3,3 chr2 96525768 . G A 43.4 PASS AC=1;AF=0.5;AN=2;DP=857;set=filterInvariant-filterInvariant4-variant5-filterInvariant6-variant7-filterInvariant8-variant9-variant11-variant12-variant14-variant20-variant23-variant24-filterInvariant26-variant28-variant29-variant33-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:31,4:35:99:114,0,1755:14,17,2,2 chr2 96525771 . A C 43.4 PASS AC=1;AF=0.5;AN=2;DP=733;set=filterInvariant-filterInvariant4-variant5-variant7-filterInvariant8-variant9-variant11-variant12-variant14-variant20-filterInvariant23-variant24-filterInvariant26-variant28-variant29-variant33 GT:AD:DP:GQ:PL:SB 0/1:32,4:36:72:72,0,1758:14,18,2,2 chr2 96525782 . T C 58.84 PASS AC=1;AF=0.5;AN=2;DP=650;set=filterInvariant4-variant5-filterInvariant6-variant7-variant9-variant11-variant14-filterInvariant20-filterInvariant23-variant24-filterInvariant25-filterInvariant26-variant28-filterInvariant29-variant33 GT:AD:DP:GQ:PL:SB 0/1:29,4:33:81:81,0,1491:13,16,2,2 chr2 96548068 . C T 856.26 PASS AC=2;AF=0.7;AN=2;DP=540;set=variant6-variant7-variant8-variant9-variant16-variant20-variant22-variant23-variant29-variant33-variant34-variant36-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:590,63,0:0,0,9,12 chr2 96553772 . G C 1866.44 PASS AC=2;AF=0.65;AN=2;DP=1543;set=variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant19-variant20-variant22-variant23-variant29-variant30-variant33-variant34-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1957,183,0:0,0,24,37 chr2 96555522 . C A 1419.39 PASS AC=2;AF=0.7;AN=2;DP=915;FractionInformativeReads=1;set=variant6-variant7-variant8-variant9-variant16-variant20-variant22-variant23-variant29-variant33-variant34-variant36-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1997,162,0:0,0,39,15 chr2 96557739 . G A 124.62 PASS AC=1;AF=0.5;AN=2;DP=57;FractionInformativeReads=1;set=variant16-variant23-variant29 GT:AD:DP:GQ:PL:SB 0/1:11,11:22:99:264,0,336:2,9,4,7 chr2 96557772 . T G 91.64 PASS AC=1;AF=0.5;AN=2;DP=8;FS=3.332;FractionInformativeReads=1;MQ=59.75;MQRankSum=-1.517;QD=11.46;ReadPosRankSum=-0.956;SOR=0.105;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:3,5:8:95:120,0,95:0,3,2,3 chr2 96563206 . A T 775.86 PASS AC=2;AF=0.731;AN=2;DP=388;FractionInformativeReads=1;set=variant6-variant8-variant9-filterInvariant20-variant22-variant23-variant29-variant33-filterInvariant34-variant36-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:222,21,0:0,0,3,4 chr2 96569017 . C T 255.13 PASS AC=2;AF=0.714;AN=2;DP=157;FractionInformativeReads=1;set=variant6-variant7-variant8-variant9-variant16-variant20-variant22-variant23-variant29-variant33-variant34-variant36-variant37-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:211,18,0:0,0,1,5 chr2 96574551 . C T 1217.14 PASS AC=2;AF=0.714;AN=2;DP=427;FractionInformativeReads=1;set=variant6-variant7-variant8-variant9-variant16-variant20-variant23-variant29-variant33-variant34-variant36-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:804,81,0:0,0,10,17 chr2 96578247 . G A 1924.79 PASS AC=2;AF=0.7;AN=2;DP=616;set=variant6-variant7-variant8-variant9-variant16-variant20-variant22-variant23-variant29-variant33-variant34-variant36-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,42:42:99:1390,126,0:0,0,11,31 chr2 96583735 . A C 517.97 PASS AC=2;AF=0.679;AN=2;DP=305;FractionInformativeReads=1;set=variant6-variant7-variant8-variant9-variant16-variant20-variant22-variant23-variant29-variant34-variant36-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:412,36,0:0,0,3,9 chr2 96583823 . G A 163.06 PASS AC=2;AF=0.857;AN=2;DP=75;FractionInformativeReads=1;set=variant6-variant9-variant22-variant23-variant29-variant37-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:247,18,0:0,0,4,2 chr2 96587496 . C T 678.88 PASS AC=2;AF=0.65;AN=2;DP=561;set=variant6-variant7-variant8-variant9-variant10-variant13-variant16-variant19-variant20-variant22-variant23-variant29-variant30-variant33-variant34-variant36-variant37-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1118,111,0:0,0,17,20 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 0/1:74,3:77:71:71,0,3086:42,32,3,0 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 0/1:77,8:85:99:179,0,3329:42,35,4,4 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 0/1:89,15:104:99:344,0,3944:50,39,7,8 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 0/1:95,15:110:99:344,0,3944:52,43,7,8 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 0/1:89,15:104:99:356,0,3767:48,41,7,8 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 0/1:91,15:106:99:356,0,3740:43,48,7,8 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 0/1:92,15:107:99:353,0,3810:42,50,7,8 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 0/1:72,10:82:99:158,0,2837:28,44,3,7 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 0/1:66,7:73:99:136,0,2715:22,44,2,5 chr2 96594697 . G C 154.85 PASS AC=1;AF=0.5;AN=2;DP=1833;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:22,19:41:99:367,0,714:17,5,11,8 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 0/1:34,18:52:99:635,0,2212:24,10,10,8 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 0/1:40,16:56:99:548,0,2470:27,13,9,7 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 0/1:42,16:58:99:545,0,2436:29,13,9,7 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 0/1:49,15:64:99:476,0,2817:31,18,8,7 chr2 96594767 . A C,T 73.35 PASS AC=1,0;AF=0.438,0.063;AN=2;DP=2089;set=filterInvariant-filterInvariant3-variant4-variant5-filterInvariant6-variant7-variant8-variant10-filterInvariant11-variant13-variant15-filterInvariant17-filterInvariant19-filterInvariant20-variant21-filterInvariant23-variant26-variant27-variant28-variant29-variant30-filterInvariant31-filterInvariant32-variant33-filterInvariant34-variant36-filterInvariant37-filterInvariant38-filterInvariant39-variant40-filterInvariant42-variant43 GT:DP:GQ:SB 0/1:67:94:33,23,6,5 chr2 96594777 . C T 70.37 PASS AC=1;AF=0.5;AN=2;DP=2659;FractionInformativeReads=1;set=filterInvariant-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant13-variant14-variant15-filterInvariant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant28-variant29-variant30-filterInvariant31-variant32-variant33-variant34-variant36-variant39-variant40-variant41-filterInvariant42-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:61,12:73:99:359,0,3172:33,28,5,7 chr2 96594791 . A G 345.6 PASS AC=1;AF=0.5;AN=2;DP=2148;FractionInformativeReads=1;set=variant3-filterInvariant4-variant5-variant6-filterInvariant7-filterInvariant8-filterInvariant10-filterInvariant11-variant13-filterInvariant14-filterInvariant15-variant18-filterInvariant19-variant22-filterInvariant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-filterInvariant28-variant29-filterInvariant31-variant32-filterInvariant33-variant39-variant40-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:66,9:75:99:173,0,3370:35,31,1,8 chr2 96594802 . A T 73.55 PASS AC=1;AF=0.5;AN=2;DP=1433;FractionInformativeReads=1;set=filterInvariant3-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant11-variant13-filterInvariant15-filterInvariant19-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant27-filterInvariant29-filterInvariant32-variant40-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:80,7:87:89:89,0,3731:40,40,1,6 chr2 96594874 . C A 166.21 PASS AC=1;AF=0.5;AN=2;DP=2133;FractionInformativeReads=1;set=variant-filterInvariant2-filterInvariant3-variant5-filterInvariant6-variant8-variant11-variant12-filterInvariant13-filterInvariant15-filterInvariant20-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-variant26-filterInvariant28-filterInvariant29-variant31-variant32-variant33-filterInvariant34-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:85,8:93:77:77,0,3587:35,50,3,5 chr2 96594878 . G C 166.21 PASS AC=1;AF=0.5;AN=2;DP=2187;FractionInformativeReads=1;set=variant-filterInvariant2-filterInvariant3-variant5-variant6-variant8-variant11-variant12-filterInvariant13-filterInvariant15-filterInvariant20-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-variant26-filterInvariant28-filterInvariant29-variant31-variant32-variant33-filterInvariant34-filterInvariant37-filterInvariant40 GT:AD:DP:GQ:PL:SB 0/1:84,8:92:83:83,0,3503:34,50,3,5 chr2 96594881 . G A 192.95 PASS AC=1;AF=0.5;AN=2;DP=2242;FractionInformativeReads=1;set=variant-filterInvariant2-filterInvariant3-variant5-variant6-variant8-variant11-variant12-filterInvariant13-filterInvariant15-filterInvariant20-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-variant26-filterInvariant28-filterInvariant29-variant31-variant32-variant33-filterInvariant34-filterInvariant37-filterInvariant40-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:82,8:90:90:90,0,3501:34,48,3,5 chr2 96594883 . C T 198.97 PASS AC=1;AF=0.5;AN=2;DP=2226;FractionInformativeReads=1;set=variant-filterInvariant2-filterInvariant3-variant5-variant6-variant8-variant11-variant12-filterInvariant13-variant15-filterInvariant20-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-variant26-filterInvariant28-filterInvariant29-variant31-variant32-variant33-filterInvariant34-filterInvariant37-filterInvariant40-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:79,9:88:96:96,0,3417:33,46,4,5 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 0/1:68,8:76:99:131,0,2757:26,42,4,4 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 0/1:66,8:74:99:134,0,2736:25,41,4,4 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 0/1:58,8:66:99:155,0,2495:24,34,4,4 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 0/1:31,11:42:99:244,0,832:12,19,6,5 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 0/1:19,10:29:99:241,0,411:7,12,4,6 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 0/1:24,4:28:96:96,0,979:9,15,1,3 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 0/1:28,24:52:99:571,0,595:18,10,16,8 chr2 96601296 . A ATGATTAAT 2297.79 PASS AC=1;AF=0.5;AN=2;DP=4730;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:55,49:104:99:1248,0,2103:29,26,27,22 chr2 96601312 . G A 893.4 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=5297;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:90,31:121:99:414,0,1914:45,45,16,15 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 0/1:91:99:25,27,18,21 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 0/1:48,44:92:99:940,0,1033:23,25,18,26 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 0/1:4,2:6:72:72,0,238:0,4,0,2 chr2 96601550 . AAGGACCAAAT A 67.63 PASS AC=1;AF=0.5;AN=2;DP=113;FractionInformativeReads=1;set=variant6-variant11-variant12-variant21-variant23-variant24-variant26-variant31-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,2:6:72:72,0,238:0,4,0,2 chr2 96604452 . C A 42.9 PASS AC=1;AF=0.5;AN=2;DP=311;FractionInformativeReads=1;set=filterInvariant18-variant23-variant26-filterInvariant28-filterInvariant29 GT:AD:DP:GQ:PL:SB 0/1:39,9:48:99:200,0,1432:38,1,8,1 chr2 96604473 . T A 719.46 PASS AC=1;AF=0.5;AN=2;DP=2784;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant6-filterInvariant7-variant8-variant10-variant11-variant13-variant14-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-filterInvariant26-filterInvariant27-filterInvariant30-variant32-variant33-variant34-variant38-variant39-filterInvariant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:69,13:82:99:270,0,2533:62,7,12,1 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 0/1:176:99:23,14,104,35 chr2 96604591 . A G 7666.28 PASS AC=1;AF=0.5;AN=2;DP=19381;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:73,333:406:99:8916,0,855:39,34,157,176 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 0/1:324,54:378:99:340,0,10440:145,179,30,24 chr2 96604632 . A T 6850.98 PASS AC=1;AF=0.5;AN=2;DP=16994;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:72,282:354:99:8294,0,994:33,39,112,170 chr2 96604679 . C T 3878.31 PASS AC=1;AF=0.5;AN=2;DP=9345;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:45,135:180:99:3986,0,1777:16,29,34,101 chr2 96604730 . T C 714.98 PASS AC=1;AF=0.5;AN=2;DP=2410;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:17,20:37:99:578,0,673:4,13,0,20 chr2 96604767 . C A 112.64 PASS AC=1;AF=0.5;AN=2;DP=739;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-variant27-variant28-variant29-variant31-variant32-variant33-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,8:12:99:324,0,169:0,4,0,8 chr2 96606944 . C T 82.55 PASS AC=1;AF=0.5;AN=2;DP=708;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant33-variant34-variant36-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,8:23:99:146,0,358:8,7,4,4 chr2 96606985 . T C 226.57 PASS AC=1;AF=0.5;AN=2;DP=673;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant33-variant36-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,7:23:99:225,0,926:8,8,3,4 chr2 96606998 . C T 226.57 PASS AC=1;AF=0.5;AN=2;DP=592;FractionInformativeReads=1;set=variant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant15-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant33-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,6:22:99:204,0,932:8,8,2,4 chr2 96607003 . G A 226.56 PASS AC=1;AF=0.5;AN=2;DP=557;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant10-variant13-variant14-variant15-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant33-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,5:21:99:162,0,935:8,8,1,4 chr2 96607028 . T C 145.59 PASS AC=1;AF=0.5;AN=2;DP=381;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant7-variant10-variant13-variant15-variant21-variant22-variant23-variant25-variant26-variant28-variant29-variant31-variant33-variant36-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,4:19:99:123,0,882:7,8,0,4 chr2 96607048 . G A 151.61 PASS AC=1;AF=0.5;AN=2;DP=248;FractionInformativeReads=1;set=variant-variant2-variant3-variant5-variant7-variant10-variant13-variant15-variant21-variant22-variant23-variant28-variant29-variant31-variant33-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,4:17:99:129,0,749:6,7,0,4 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 0/1:49,22:71:99:370,0,1362:34,15,13,9 chr2 96610395 . C CA 873.71 PASS AC=1;AF=0.5;AN=2;DP=5264;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:78,39:117:99:1397,0,3168:42,36,20,19 chr2 96610399 . C A 879.76 PASS AC=1;AF=0.5;AN=2;DP=5267;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:81,39:120:99:1391,0,3212:42,39,20,19 chr2 96610410 . T A 885.77 PASS AC=1;AF=0.5;AN=2;DP=5253;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:79,39:118:99:1400,0,3160:40,39,20,19 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 0/1:78,39:117:99:1397,0,3202:39,39,20,19 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 0/1:79,39:118:99:1397,0,3175:38,41,20,19 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 0/1:84,15:99:95:95,0,2382:37,47,6,9 chr2 96610479 . A G 45.44 PASS AC=1;AF=0.5;AN=2;DP=1302;set=filterInvariant-variant5-filterInvariant6-filterInvariant7-variant8-filterInvariant9-filterInvariant12-filterInvariant15-variant18-variant23-filterInvariant26-variant27-variant30-variant31-filterInvariant36-filterInvariant37 GT:AD:DP:GQ:PL:SB 0/1:57,13:70:99:185,0,1716:23,34,4,9 chr2 96610668 . C T 34.68 PASS AC=1;AF=0.5;AN=2;DP=9;FS=0;FractionInformativeReads=1;MQ=53.87;MQRankSum=-1.666;QD=3.85;ReadPosRankSum=1.666;SOR=2.225;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:7,2:9:63:63,0,480:2,5,2,0 chr2 96610759 . T A 150.28 PASS AC=1;AF=0.5;AN=2;DP=683;FractionInformativeReads=1;set=variant-variant2-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant36-variant37-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,6:10:99:237,0,192:4,0,6,0 chr2 96610768 . T G 273.65 PASS AC=1;AF=0.5;AN=2;DP=933;set=variant-variant2-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant36-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,6:17:99:219,0,389:10,1,6,0 chr2 96610787 . C CA 1405.28 PASS AC=1;AF=0.5;AN=2;DP=2312;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:19,21:40:99:951,0,726:14,5,21,0 chr2 96610805 . AAGAAAG A 133.79 PASS AC=1;AF=0.5;AN=2;DP=4591;set=filterInvariant-variant2-variant3-variant5-variant7-filterInvariant8-variant9-filterInvariant10-filterInvariant11-variant12-variant14-filterInvariant15-filterInvariant16-filterInvariant17-variant19-filterInvariant20-filterInvariant21-variant22-filterInvariant23-filterInvariant24-variant25-variant26-variant27-filterInvariant29-variant30-variant31-filterInvariant32-variant33-variant36-variant37-filterInvariant38-filterInvariant39-variant40-filterInvariant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,16:90:99:140,0,2787:57,17,14,2 chr2 96610809 . AAG A 433.93 PASS AC=1;AF=0.5;AN=2;DP=3178;set=variant-filterInvariant3-filterInvariant4-variant6-variant8-filterInvariant10-variant11-variant12-variant13-variant14-variant15-variant16-filterInvariant17-variant18-variant19-filterInvariant21-variant23-variant24-variant25-filterInvariant26-filterInvariant27-variant30-variant32-filterInvariant33-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:64,26:90:99:516,0,2549:49,15,22,4 chr2 96610836 . T C 6020.84 PASS AC=1;AF=0.5;AN=2;DP=10747;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:40,154:194:99:5179,0,995:21,19,109,45 chr2 96610899 . T C 13827.2 PASS AC=1;AF=0.5;AN=2;DP=20014;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:67,298:365:99:12065,0,1921:38,29,183,115 chr2 96610921 . T G 14826.9 PASS AC=1;AF=0.5;AN=2;DP=21280;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:59,316:375:99:12701,0,1685:30,29,179,137 chr2 96610923 . C G 1722.39 PASS AC=1;AF=0.5;AN=2;DP=13955;set=variant-filterInvariant3-variant4-variant6-variant8-filterInvariant9-variant10-variant11-filterInvariant12-variant13-filterInvariant14-variant16-filterInvariant17-variant18-variant19-variant20-filterInvariant22-filterInvariant23-variant24-variant25-filterInvariant26-filterInvariant27-filterInvariant30-variant32-variant33-variant34-variant38-filterInvariant39-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:313,45:358:99:116,0,9183:174,139,24,21 chr2 96610952 . T C 9921.75 PASS AC=1;AF=0.5;AN=2;DP=19242;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:57,284:341:99:7850,0,583:27,30,137,147 chr2 96610958 . G T 1091.75 PASS AC=1;AF=0.5;AN=2;DP=9958;set=variant-filterInvariant2-variant3-variant5-variant7-filterInvariant8-filterInvariant10-filterInvariant15-variant21-variant22-filterInvariant23-filterInvariant25-filterInvariant26-filterInvariant29-filterInvariant30-variant31-filterInvariant32-variant33-variant36-variant37-variant40-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:283,49:332:99:390,0,8823:132,151,25,24 chr2 96611013 . A T 1001.98 PASS AC=1;AF=0.5;AN=2;DP=4990;set=variant2-variant4-variant5-filterInvariant6-filterInvariant7-variant8-variant9-filterInvariant11-filterInvariant13-filterInvariant16-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant28-variant29-variant31-filterInvariant32-variant33-filterInvariant37-filterInvariant38-variant39-filterInvariant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:147,24:171:99:273,0,5657:47,100,6,18 chr2 96611018 . G A 5017.04 PASS AC=1;AF=0.5;AN=2;DP=8528;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:30,123:153:99:4149,0,453:12,18,34,89 chr2 96611038 . T A 83.23 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=211;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:95,12:107:99:111,0,3919:16,79,2,10 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 0/1:54,9:63:99:173,0,2094:3,51,1,8 chr2 96611078 . T G 2043.99 PASS AC=1;AF=0.5;AN=2;DP=2927;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:9,47:56:99:1918,0,340:1,8,3,44 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 0/1:9,43:52:99:1800,0,349:1,8,3,40 chr2 96614212 . A G 46.96 PASS AC=2;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 1/1:0,2:2:6:82,6,0:0,0,2,0 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 0/1:50,10:60:99:269,0,2758:23,27,5,5 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 0/1:46,10:56:99:272,0,2737:21,25,5,5 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 0/1:15,25:40:99:1005,0,906:9,6,23,2 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 0/1:29,11:40:99:325,0,1623:22,7,10,1 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 0/1:26,14:40:99:468,0,1352:19,7,13,1 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 0/1:29,11:40:99:325,0,1623:22,7,10,1 chr2 96616361 . A C 166.19 PASS AC=1;AF=0.5;AN=2;DP=1567;FractionInformativeReads=1;set=variant2-filterInvariant3-variant5-filterInvariant7-variant9-filterInvariant11-variant12-filterInvariant15-variant16-filterInvariant17-filterInvariant19-variant22-filterInvariant23-filterInvariant26-variant27-filterInvariant29-variant30-filterInvariant34-filterInvariant36-filterInvariant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,6:49:99:122,0,2256:31,12,6,0 chr2 96616362 . A T 166.17 PASS AC=1;AF=0.5;AN=2;DP=1595;set=variant2-filterInvariant3-variant5-filterInvariant7-variant9-filterInvariant11-variant12-filterInvariant15-variant16-filterInvariant17-filterInvariant19-variant22-filterInvariant23-filterInvariant26-variant27-filterInvariant29-variant30-filterInvariant34-filterInvariant36-filterInvariant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,6:49:99:119,0,2298:31,12,6,0 chr2 96616378 . C T 1420.08 PASS AC=1;AF=0.5;AN=2;DP=3987;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:23,41:64:99:1372,0,1114:15,8,32,9 chr2 96616442 . C A 2224.37 PASS AC=1;AF=0.5;AN=2;DP=6541;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:26,78:104:99:3219,0,817:11,15,42,36 chr2 96616448 . G T 2224.37 PASS AC=1;AF=0.5;AN=2;DP=6535;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:27,78:105:99:3174,0,842:11,16,41,37 chr2 96616485 . C G 1892.5 PASS AC=1;AF=0.5;AN=2;DP=6060;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:24,73:97:99:2654,0,748:11,13,32,41 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 0/1:25,58:83:99:2405,0,866:11,14,19,39 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 0/1:25,56:81:99:2276,0,881:11,14,17,39 chr2 96616532 . T G 1021.08 PASS AC=1;AF=0.5;AN=2;DP=3677;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:19,40:59:99:1647,0,662:7,12,8,32 chr2 96616571 . C A 208.25 PASS AC=1;AF=0.5;AN=2;DP=1713;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:13,14:27:99:536,0,495:5,8,1,13 chr2 96616576 . T C 178.4 PASS AC=1;AF=0.5;AN=2;DP=1554;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:12,13:25:99:540,0,462:5,7,1,12 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 0/1:12,10:22:99:468,0,468:5,7,1,9 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 0/1:10,9:19:99:342,0,477:5,5,3,6 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 0/1:11,9:20:99:387,0,432:5,6,3,6 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 0/1:8,8:16:99:312,0,312:3,5,4,4 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 0/1:6,6:12:99:234,0,234:2,4,4,2 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 0/1:3,6:9:99:243,0,108:1,2,3,3 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 0/1:3,6:9:99:243,0,108:1,2,3,3 chr2 96616947 . G A 269.1 PASS AC=1;AF=0.5;AN=2;DP=304;FractionInformativeReads=1;set=variant2-variant5-variant6-variant7-variant10-variant11-variant12-variant13-variant14-variant15-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant29-variant32-variant34-variant36-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,2:9:63:63,0,288:6,1,2,0 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 0/1:7,2:9:63:63,0,288:6,1,2,0 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 0/1:9,4:13:99:167,0,405:8,1,3,1 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 0/1:10,5:15:99:167,0,405:9,1,3,2 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 0/1:14,10:24:99:308,0,516:13,1,6,4 chr2 96617023 . C A 772.3 PASS AC=1;AF=0.5;AN=2;DP=1905;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:26,22:48:99:834,0,1138:20,6,15,7 chr2 96617025 . C A 769.29 PASS AC=1;AF=0.5;AN=2;DP=2072;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:30,22:52:99:834,0,1138:21,9,15,7 chr2 96617029 . GA G 101.31 PASS AC=1;AF=0.5;AN=2;DP=1377;set=variant2-variant3-filterInvariant4-variant5-variant7-variant8-variant9-variant11-variant12-variant14-variant19-variant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant26-variant27-variant32-variant34-variant36-variant38-filterInvariant39-variant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:45,10:55:99:101,0,1104:30,15,7,3 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 0/1:34,32:66:99:881,0,1202:22,12,20,12 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 0/1:51,52:103:99:2217,0,2009:32,19,35,17 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 0/1:66,64:130:99:2531,0,2576:41,25,44,20 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 0/1:71,77:148:99:3019,0,2749:42,29,46,31 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 0/1:71,78:149:99:3058,0,2788:41,30,46,32 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 0/1:71,78:149:99:3097,0,2827:41,30,46,32 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 0/1:77,81:158:99:3163,0,3073:44,33,45,36 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 0/1:77,79:156:99:3079,0,3079:43,34,43,36 chr2 96617155 . A G 2383.85 PASS AC=1;AF=0.5;AN=2;DP=7215;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:79,76:155:99:2920,0,2903:39,40,37,39 chr2 96617182 . A C 58.9 PASS AC=1;AF=0.5;AN=2;DP=3205;set=filterInvariant-variant6-variant8-variant10-variant13-filterInvariant14-variant16-variant17-filterInvariant18-filterInvariant19-variant20-filterInvariant23-filterInvariant24-variant25-filterInvariant26-variant28-variant32-filterInvariant34-filterInvariant38-filterInvariant39-filterInvariant41 GT:AD:DP:GQ:PL:SB 0/1:121,24:145:99:282,0,5238:56,65,10,14 chr2 96617194 . A G 1819.3 PASS AC=1;AF=0.5;AN=2;DP=6574;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:88,56:144:99:1930,0,4725:44,44,23,33 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 0/1:80,45:125:99:1716,0,4955:37,43,14,31 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 0/1:91,17:108:99:251,0,5863:33,58,2,15 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 0/1:72,32:104:99:1160,0,4918:29,43,3,29 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 0/1:62,20:82:99:683,0,4603:25,37,0,20 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 0/1:57,18:75:99:623,0,4273:22,35,0,18 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 0/1:37,7:44:99:130,0,2533:14,23,0,7 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 0/1:8,3:11:59:59,0,360:7,1,3,0 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 0/1:9,3:12:59:59,0,360:8,1,3,0 chr2 96619688 . T G 1326.56 PASS AC=1;AF=0.5;AN=2;DP=4300;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:39,20:59:99:512,0,935:27,12,17,3 chr2 96619734 . C T 2545.12 PASS AC=1;AF=0.5;AN=2;DP=9351;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:79,88:167:99:2325,0,1797:50,29,59,29 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 0/1:193,27:220:99:109,0,6618:113,80,17,10 chr2 96619774 . G A 3994.44 PASS AC=1;AF=0.5;AN=2;DP=13083;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:97,124:221:99:3907,0,2137:57,40,73,51 chr2 96619799 . A C 4041.73 PASS AC=1;AF=0.5;AN=2;DP=14181;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:119,133:252:99:3545,0,2791:70,49,73,60 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 0/1:153,101:254:99:3058,0,5787:74,79,46,55 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 0/1:225:99:62,63,43,57 chr2 96619837 . C G 4169.79 PASS AC=1;AF=0.5;AN=2;DP=12243;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:123,118:241:99:4667,0,4978:61,62,50,68 chr2 96619838 . A C 4088.82 PASS AC=1;AF=0.5;AN=2;DP=12153;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:123,116:239:99:4625,0,4981:61,62,50,66 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 0/1:174,34:208:99:763,0,5088:78,96,12,22 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 0/1:140,27:167:99:649,0,4413:55,85,9,18 chr2 96626292 . C T 452.58 PASS AC=2;AF=0.955;AN=2;DP=1013;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:724,69,0:0,0,6,17 chr2 96681081 . C T 38 PASS AC=2;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 1/1:0,10:10:30:315,30,0:0,0,8,2 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 1/1:2,39:41:88:1178,88,0:1,1,20,19 chr2 96685021 . A G 607.56 PASS AC=2;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 1/1:0,18:18:54:624,54,0:0,0,6,12 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 1/1:0,21:21:63:935,63,0:0,0,6,15 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 1/1:0,21:21:63:935,63,0:0,0,6,15 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 0/1:50,55:105:99:1254,0,1227:22,28,23,32 chr2 96789787 . T C 6227.09 PASS AC=2;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 1/1:0,172:172:99:5186,515,0:0,0,81,91 chr2 96795608 . T G 2682.82 PASS AC=2;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 1/1:2,92:94:99:2654,232,0:1,1,45,47 chr2 96795714 . G A 2665.32 PASS AC=2;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 1/1:1,105:106:99:3297,276,0:0,1,59,46 chr2 96795857 . T C 2568.51 PASS AC=2;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 1/1:0,104:104:99:3099,312,0:0,0,46,58 chr2 96795944 . A G 1226.38 PASS AC=2;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 1/1:0,58:58:99:1719,173,0:0,0,21,37 chr2 96798510 . G A 2126.32 PASS AC=2;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 1/1:0,75:75:99:2156,224,0:0,0,32,43 chr2 96809331 . T C 1006.59 PASS AC=2;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 1/1:0,87:87:99:2760,261,0:0,0,32,55 chr2 96851119 . C A 1811.1 PASS AC=2;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 1/1:0,204:204:99:6079,611,0:0,0,108,96 chr2 96874096 . T C 921.2 PASS AC=1;AF=0.5;AN=2;DP=81;FS=0.862;FractionInformativeReads=1;MQ=60;MQRankSum=-0.663;QD=11.37;ReadPosRankSum=-0.176;SOR=0.801;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:46,35:81:99:949,0,1256:17,29,12,23 chr2 96874307 . C G 2167.13 PASS AC=1;AF=0.5;AN=2;DP=828;MQ=60;set=variant6-variant8-variant12-variant23-variant34-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,83:149:99:1811,0,1594:36,30,46,37 chr2 96917588 . T G 685.24 PASS AC=2;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 1/1:0,88:88:99:2778,263,0:0,0,34,54 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 0/1:51,68:119:99:1573,0,1271:23,28,31,37 chr2 96944553 . G A 3509.84 PASS AC=2;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 1/1:0,251:251:99:7351,748,0:0,0,130,121 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 1/1:0,79:79:99:2415,236,0:0,0,34,45 chr2 96961468 . T C 375.12 PASS AC=1;AF=0.5;AN=2;DP=46;FS=4.885;FractionInformativeReads=0.978;MQ=60;MQRankSum=-0.597;QD=8.15;ReadPosRankSum=0.246;SOR=0.241;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:28,17:45:99:403,0,794:6,22,6,11 chr2 96963684 . A G 559.01 PASS AC=2;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 1/1:0,13:13:39:457,39,0:0,0,3,10 chr2 96964499 . G A 1204.76 PASS AC=1;AF=0.5;AN=2;DP=110;FS=1.502;FractionInformativeReads=1;MQ=60;MQRankSum=-0.688;QD=10.95;ReadPosRankSum=-1.041;SOR=0.779;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:57,53:110:99:1233,0,1410:28,29,28,25 chr2 96991492 . A G 583.6 PASS AC=2;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 1/1:0,128:128:99:3941,383,0:0,0,71,57 chr2 97025861 . C T 1126.75 PASS AC=1;AF=0.5;AN=2;DP=87;FS=0.806;FractionInformativeReads=1;MQ=60;MQRankSum=0.786;QD=12.95;ReadPosRankSum=0.353;SOR=0.563;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:42,45:87:99:1155,0,965:23,19,23,22 chr2 97164943 . C T 1779.62 PASS AC=1;AF=0.5;AN=2;DP=359;MQ=60;set=variant23-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:62,73:135:99:1808,0,1509:34,28,39,34 chr2 97166204 . A G 2401.78 PASS AC=2;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 1/1:0,195:195:99:5950,585,0:0,0,85,110 chr2 97166296 . A G 1380.07 PASS AC=1;AF=0.5;AN=2;DP=425;FractionInformativeReads=1;MQ=60;set=variant23-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:79,62:141:99:1408,0,2003:37,42,28,34 chr2 97166743 . T C 84.19 PASS AC=1;AF=0.5;AN=2;DP=27;FractionInformativeReads=1;MQ=60;set=variant23-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:112,0,156:2,3,1,3 chr2 97202490 . T C 31.99 PASS AC=1;AF=0.5;AN=2;DP=57;FS=0;FractionInformativeReads=1;MQ=60;set=variant8-variant23-variant34 GT:AD:DP:GQ:PL:SB 0/1:13,8:21:99:140,0,378:6,7,4,4 chr2 97203137 . A C 1308.78 PASS AC=2;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 1/1:0,79:79:99:2381,237,0:0,0,43,36 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 1/1:0,68:68:99:1988,204,0:0,0,31,37 chr2 97271090 . G A 761.41 PASS AC=1;AF=0.5;AN=2;DP=52;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.551;QD=14.64;ReadPosRankSum=0.513;SOR=0.818;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:19,33:52:99:790,0,367:11,8,20,13 chr2 97285062 . C T 1169.23 PASS AC=1;AF=0.5;AN=2;DP=321;FractionInformativeReads=1;MQ=60;set=variant23-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:52,50:102:99:1197,0,1360:27,25,25,25 chr2 97293759 . G T 752.04 PASS AC=1;AF=0.5;AN=2;DP=72;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-2.546;QD=10.45;ReadPosRankSum=0.676;SOR=0.707;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:37,35:72:99:780,0,928:21,16,20,15 chr2 97329411 . C G 386.08 PASS AC=1;AF=0.5;AN=2;DP=44;FS=2.923;FractionInformativeReads=1;MQ=60;MQRankSum=-1.086;QD=8.77;ReadPosRankSum=0.622;SOR=1.387;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:28,16:44:99:414,0,729:11,17,4,12 chr2 97336089 . G C 289.35 PASS AC=1;AF=0.5;AN=2;DP=73;MQ=60;set=variant23-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,12:27:99:318,0,443:3,12,3,9 chr2 97339052 . G A 1155.46 PASS AC=1;AF=0.5;AN=2;DP=92;FS=4.17;FractionInformativeReads=1;MQ=60;MQRankSum=-0.012;QD=12.56;ReadPosRankSum=-0.895;SOR=0.358;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:44,48:92:99:1184,0,1233:13,31,19,29 chr2 97351840 . A G 2933.29 PASS AC=1;AF=0.607;AN=2;DP=4895;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant12-variant13-variant16-variant17-variant20-variant21-variant23-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:89,80:169:99:2060,0,2048:40,49,36,44 chr2 97353725 . G A 2270.78 PASS AC=1;AF=0.556;AN=2;DP=1795;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant12-variant13-variant16-variant17-variant20-variant21-variant23-variant29-variant33-variant36-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,50:94:99:1294,0,1204:14,30,15,35 chr2 97360079 . C T 1039.25 PASS AC=1;AF=0.556;AN=2;DP=1109;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant12-variant13-variant16-variant17-variant21-variant23-variant29-variant32-variant33-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:30,30:60:99:653,0,695:17,13,16,14 chr2 97365213 . C T 851.29 PASS AC=1;AF=0.5;AN=2;DP=166;FractionInformativeReads=1;MQ=60;set=variant8-variant11-variant23-variant28 GT:AD:DP:GQ:PL:SB 0/1:20,16:36:99:396,0,505:13,7,10,6 chr2 97371581 . C T 52.7 PASS AC=1;AF=0.5;AN=2;DP=6;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.72;QD=8.78;ReadPosRankSum=-0.72;SOR=0.693;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:31:81,0,31:1,1,2,2 chr2 97400324 . A G 2475.21 PASS AC=1;AF=0.596;AN=2;DP=2483;set=variant-variant3-variant6-variant7-variant8-variant9-variant12-variant13-variant16-variant17-variant21-variant23-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,35:83:99:808,0,1356:17,31,14,21 chr2 97403110 . G A 243.05 PASS AC=1;AF=0.559;AN=2;DP=176;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant7-variant8-variant9-variant12-variant13-variant16-variant17-variant21-variant23-variant29-variant32-variant33-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,2:8:63:63,0,237:0,6,0,2 chr2 97463095 . T C 303.12 PASS AC=1;AF=0.596;AN=2;DP=503;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant6-variant7-variant8-variant9-variant12-variant13-variant16-variant17-variant21-variant23-variant29-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:221,0,188:2,4,3,3 chr2 97482487 . C T 198.18 PASS AC=1;AF=0.5;AN=2;DP=12;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.289;QD=16.52;ReadPosRankSum=-1.239;SOR=1.179;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:4,8:12:63:226,0,63:2,2,5,3 chr2 97503684 . C CTGAT 400.41 PASS AC=1;AF=0.5;AN=2;DP=20;FS=1.871;FractionInformativeReads=0.95;MQ=60;MQRankSum=1.362;QD=20.02;ReadPosRankSum=-0.619;SOR=0.591;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:8,11:19:99:438,0,432:3,5,6,5 chr2 97508139 . C T 98.75 PASS AC=1;AF=0.5;AN=2;DP=21;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.634;QD=4.7;ReadPosRankSum=-1.082;SOR=0.446;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:14,7:21:99:127,0,441:5,9,3,4 chr2 97529360 . T A 726.91 PASS AC=1;AF=0.548;AN=2;DP=1691;MQ=60;set=variant2-variant3-variant5-variant7-variant9-variant15-variant18-variant20-variant21-variant23-variant24-variant25-variant30-variant31-variant32-variant34-variant36-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,37:74:99:1013,0,915:22,15,25,12 chr2 97543936 . T C 185.85 PASS AC=1;AF=0.545;AN=2;DP=440;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant7-variant9-variant13-variant15-variant18-variant21-variant23-variant24-variant25-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:152,0,141:1,3,2,2 chr2 97544016 . G A 382.02 PASS AC=1;AF=0.5;AN=2;DP=173;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant9-variant13-variant23-variant30-variant34-variant37 GT:AD:DP:GQ:PL:SB 0/1:8,10:18:99:355,0,222:6,2,8,2 chr2 97544089 . G C 773.96 PASS AC=1;AF=0.525;AN=2;DP=1503;MQ=60;set=variant2-variant3-variant7-variant9-variant13-variant15-variant18-variant21-variant23-variant24-variant25-variant30-variant31-variant32-variant34-variant36-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,27:49:99:697,0,538:15,7,14,13 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 0/1:27,20:47:99:556,0,754:16,11,10,10 chr2 97568453 . A G 817.22 PASS AC=1;AF=0.563;AN=2;DP=1051;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant5-variant9-variant10-variant13-variant16-variant17-variant23-variant30-variant31-variant34-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,34:60:99:791,0,653:10,16,14,20 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 1/1:0,49:49:99:1577,146,0:0,0,18,31 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 1/1:0,36:36:99:1099,108,0:0,0,15,21 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 1/1:0,36:36:99:1168,108,0:0,0,20,16 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 1/1:0,21:21:63:672,63,0:0,0,7,14 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 1/1:0,229:229:99:6534,684,0:0,0,126,103 chr2 97617227 . A G 5472.07 PASS AC=2;AF=0.864;AN=2;DP=8303;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,165:165:99:5228,494,0:0,0,75,90 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 1/1:0,36:36:99:1123,107,0:0,0,22,14 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 1/1:0,202:202:99:5943,603,0:0,0,103,99 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 1/1:0,59:59:99:2268,177,0:0,0,18,41 chr2 97643576 . T C 3354.48 PASS AC=1;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 0/1:103,70:173:99:1595,0,2447:54,49,30,40 chr2 97643684 . G A 449.59 PASS AC=1;AF=0.5;AN=2;DP=90;MQ=60;set=variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:9,18:27:99:478,0,189:4,5,10,8 chr2 97693966 . A G 1990.46 PASS AC=1;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 0/1:40,31:71:99:653,0,941:17,23,13,18 chr2 97747894 . T C 340.68 PASS AC=2;AF=0.932;AN=2;DP=1841;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,37:37:99:1273,111,0:0,0,13,24 chr2 97747978 . C T 472.79 PASS AC=1;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 0/1:6,9:15:99:328,0,142:2,4,2,7 chr2 97751782 . T C 61.77 PASS AC=1;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 0/1:15,7:22:99:249,0,590:5,10,3,4 chr2 97751783 . G A 61.77 PASS AC=1;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 0/1:13,7:20:99:249,0,590:5,8,3,4 chr2 97751786 . G A 61.77 PASS AC=1;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 0/1:12,6:18:99:258,0,483:4,8,3,3 chr2 97751832 . C A 95.37 PASS AC=1;AF=0.5;AN=2;DP=101;FractionInformativeReads=1;set=variant5-variant10-variant15-variant17-variant18-variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:9,8:17:99:263,0,354:5,4,4,4 chr2 97751849 . C A 221.84 PASS AC=1;AF=0.5;AN=2;DP=33;FS=0;FractionInformativeReads=1;set=variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:250,0,412:6,5,3,4 chr2 97757067 . C T 65.04 PASS AC=2;AF=0.972;AN=2;DP=74;FS=0;FractionInformativeReads=1;MQRankSum=-1.881;ReadPosRankSum=1.159;set=filterInvariant6-filterInvariant8-variant10-filterInvariant11-filterInvariant12-filterInvariant14-filterInvariant15-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant28-filterInvariant31-filterInvariant33-variant36-variant41-variant42-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:100,9,0:0,0,3,0 chr2 97757509 . C T 2851.35 PASS AC=1;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 0/1:64,71:135:99:1614,0,1568:24,40,30,41 chr2 97784295 . C A 1010.22 PASS AC=1;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 0/1:8,12:20:99:334,0,225:0,8,0,12 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 0/1:49,10:59:93:93,0,1355:30,19,4,6 chr2 97810180 . G C 40.66 PASS AC=1;AF=0.5;AN=2;DP=447;FractionInformativeReads=1;set=variant2-variant5-variant6-variant7-variant8-filterInvariant10-variant13-variant20-variant21-variant23-variant25-variant27-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,6:23:79:79,0,480:12,5,3,3 chr2 97810195 . A G 82.98 PASS AC=1;AF=0.5;AN=2;DP=481;set=variant5-variant6-variant7-variant8-variant10-variant20-variant21-filterInvariant23-filterInvariant25-variant27-variant28-variant29-variant30-variant31-filterInvariant33-variant34-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,6:28:64:64,0,570:14,8,3,3 chr2 97814956 . G A 4544.24 PASS AC=1;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 0/1:68,57:125:99:1235,0,1564:33,35,31,26 chr2 97817393 . A T 682.83 PASS AC=1;AF=0.5;AN=2;DP=1592;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:9,22:31:99:899,0,299:9,0,20,2 chr2 97817394 . T G 682.83 PASS AC=1;AF=0.5;AN=2;DP=1645;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:9,23:32:99:899,0,299:9,0,21,2 chr2 97817420 . G A 2314.15 PASS AC=1;AF=0.5;AN=2;DP=3471;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:21,53:74:99:2369,0,749:17,4,37,16 chr2 97817429 . A C 2560.07 PASS AC=1;AF=0.5;AN=2;DP=3917;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:23,62:85:99:2660,0,770:17,6,41,21 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 0/1:31,81:112:99:3330,0,1055:21,10,45,36 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 0/1:31,81:112:99:3330,0,1055:21,10,45,36 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 0/1:37,80:117:99:3167,0,1212:23,14,40,40 chr2 97817511 . T C 1701.54 PASS AC=1;AF=0.5;AN=2;DP=5447;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:40,82:122:99:1830,0,807:22,18,36,46 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 0/1:73,35:108:99:643,0,2251:34,39,10,25 chr2 97817563 . C CA 1122.57 PASS AC=1;AF=0.5;AN=2;DP=3477;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:31,34:65:99:1284,0,1153:16,15,5,29 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 2/1:61:99:0,0,19,42 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 0/1:38,23:61:99:852,0,1322:18,20,1,22 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 0/1:4,9:13:99:408,0,138:3,1,5,4 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 0/1:7,12:19:99:483,0,258:5,2,6,6 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 0/1:7,14:21:99:567,0,252:5,2,7,7 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 0/1:9,16:25:99:687,0,414:4,5,7,9 chr2 97818192 . A G 322.43 PASS AC=1;AF=0.5;AN=2;DP=1865;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:10,17:27:99:684,0,481:5,5,7,10 chr2 97818197 . G T 319.43 PASS AC=1;AF=0.5;AN=2;DP=1950;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:10,17:27:99:684,0,481:5,5,7,10 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 0/1:16,17:33:99:653,0,734:10,6,7,10 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 0/1:21,16:37:99:609,0,959:13,8,7,9 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 0/1:21,16:37:99:606,0,980:13,8,7,9 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 0/1:21,12:33:99:441,0,950:12,9,5,7 chr2 97823971 . T C 684.08 PASS AC=1;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 0/1:8,17:25:99:458,0,193:2,6,5,12 chr2 97824043 . C T 85.7 PASS AC=1;AF=0.5;AN=2;DP=18;FractionInformativeReads=1;set=variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:99:114,0,159:1,3,2,1 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 0/1:9,7:16:99:202,0,358:4,5,5,2 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 0/1:11,12:23:99:313,0,407:5,6,7,5 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 0/1:9,17:26:99:687,0,327:4,5,10,7 chr2 97827790 . T C 101.33 PASS AC=1;AF=0.5;AN=2;DP=240;set=variant4-variant9-variant10-variant13-variant23-variant25-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,6:26:90:90,0,781:12,8,2,4 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 0/1:8,17:25:99:690,0,285:3,5,10,7 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 0/1:13,9:22:99:172,0,455:8,5,5,4 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 0/1:14,10:24:99:160,0,549:8,6,6,4 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 0/1:7,16:23:99:535,0,125:4,3,9,7 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 0/1:1,12:13:0:378,0,0:1,0,10,2 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 0/1:10,16:26:99:367,0,251:8,2,8,8 chr2 97829003 . CAAAAATAA C 809.79 PASS AC=1;AF=0.5;AN=2;DP=1461;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:16,15:31:99:571,0,626:9,7,7,8 chr2 97829029 . G A 722.49 PASS AC=1;AF=0.5;AN=2;DP=1596;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:23,15:38:99:561,0,910:12,11,6,9 chr2 97829030 . T G 722.49 PASS AC=1;AF=0.5;AN=2;DP=1604;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:23,15:38:99:561,0,910:12,11,6,9 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 0/1:29,4:33:81:81,0,1206:13,16,0,4 chr2 97829125 . ACTT A 151.43 PASS AC=1;AF=0.5;AN=2;DP=583;set=variant-variant2-filterInvariant5-filterInvariant6-variant8-variant12-variant13-filterInvariant14-variant16-variant20-variant22-filterInvariant23-variant25-filterInvariant31-variant37-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:28,3:31:81:81,0,1206:12,16,0,3 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 0/1:20,12:32:99:201,0,536:13,7,6,6 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 0/1:48,12:60:99:117,0,1261:29,19,6,6 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 0/1:8,12:20:99:420,0,200:7,1,12,0 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 0/1:14,26:40:99:743,0,277:10,4,20,6 chr2 97833199 . A T 132.11 PASS AC=1;AF=0.5;AN=2;DP=1137;set=filterInvariant2-variant3-filterInvariant5-filterInvariant7-variant9-filterInvariant11-variant12-filterInvariant14-filterInvariant16-filterInvariant19-variant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant30-filterInvariant31-filterInvariant32-filterInvariant36-variant41-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:37,7:44:64:64,0,1217:27,10,5,2 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 0/1:21,43:64:99:1726,0,783:13,8,25,18 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 0/1:21,43:64:99:1726,0,783:13,8,25,18 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 0/1:49,35:84:99:803,0,1166:23,26,11,24 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 0/1:62:99:23,23,4,12 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 0/1:24,7:31:99:204,0,584:9,15,7,0 chr2 97833553 . C T 218.8 PASS AC=1;AF=0.511;AN=2;DP=722;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:3,16:19:67:446,0,67:1,2,6,10 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 0/1:6,12:18:99:323,0,284:2,4,3,9 chr2 97833569 . C T 214.68 PASS AC=1;AF=0.523;AN=2;DP=694;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:4,14:18:98:525,0,98:1,3,4,10 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 0/1:4,12:16:99:387,0,121:1,3,2,10 chr2 97847606 . A G 653.01 PASS AC=1;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 0/1:15,9:24:99:251,0,475:5,10,5,4 chr2 97849219 . T C 816.64 PASS AC=1;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 0/1:16,9:25:99:153,0,463:7,9,5,4 chr2 97851069 . A G 2389.73 PASS AC=1;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 0/1:42,38:80:99:788,0,1076:26,16,21,17 chr2 97851324 . G GGGC 156.9 PASS AC=1;AF=0.5;AN=2;DP=214;set=variant12-variant23-filterInvariant24-filterInvariant26-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:15,4:19:99:123,0,683:4,11,2,2 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 0/1:123,50:173:99:905,0,3020:72,51,27,23 chr2 97860529 . G A 1220.66 PASS AC=1;AF=0.5;AN=2;DP=3090;set=variant4-variant5-variant9-variant10-variant13-variant16-variant17-variant18-variant23-variant25-variant30-variant31-variant34-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:180,46:226:99:628,0,4301:96,84,22,24 chr2 97862260 . T A 3299.91 PASS AC=2;AF=0.932;AN=2;DP=3896;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,116:116:99:3516,347,0:0,0,70,46 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 0/1:122,49:171:99:952,0,3277:56,66,23,26 chr2 97864185 . C T 121.22 PASS AC=1;AF=0.5;AN=2;DP=156;FractionInformativeReads=1;MQ=60;set=filterInvariant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:92,15:107:99:149,0,2322:53,39,8,7 chr2 97864288 . T C 2756.12 PASS AC=1;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 0/1:31,60:91:99:1438,0,717:16,15,27,33 chr2 97864333 . C A 2716.77 PASS AC=1;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 0/1:24,31:55:99:1219,0,1005:9,15,9,22 chr2 97864334 . C T 2716.77 PASS AC=1;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 0/1:24,31:55:99:1219,0,1005:9,15,9,22 chr2 97864374 . G T 1382.59 PASS AC=1;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 0/1:19,13:32:99:381,0,509:6,13,2,11 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 0/1:34,11:45:99:313,0,1136:6,28,3,8 chr2 97867870 . G C 2367.85 PASS AC=1;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 0/1:25,59:84:99:1681,0,500:16,9,40,19 chr2 97869890 . C CT 417.22 PASS AC=1;AF=0.5;AN=2;DP=140;set=variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:52,20:72:99:454,0,1572:27,25,8,12 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 0/1:14,8:22:99:151,0,406:4,10,3,5 chr2 97873515 . C T 843.92 PASS AC=1;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 0/1:22,14:36:99:332,0,520:9,13,8,6 chr2 97873630 . A T 851.47 PASS AC=1;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 0/1:22,22:44:99:459,0,514:10,12,11,11 chr2 97877292 . C A 2242.22 PASS AC=2;AF=0.932;AN=2;DP=2890;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2157,189,0:0,0,40,23 chr2 97877399 . T C 5181.84 PASS AC=2;AF=0.932;AN=2;DP=6451;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,165:165:99:4763,492,0:0,0,90,75 chr2 97877440 . T C 1817.69 PASS AC=1;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 0/1:137,50:187:99:808,0,3525:65,72,25,25 chr2 97877478 . G A 2345.21 PASS AC=1;AF=0.5;AN=2;DP=5176;set=variant-variant3-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant36-variant38-filterInvariant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:82,86:168:99:1926,0,1811:38,44,36,50 chr2 97877528 . A T 474.29 PASS AC=1;AF=0.5;AN=2;DP=155;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:71,26:97:99:503,0,2003:25,46,9,17 chr2 97877591 . C A 139.63 PASS AC=1;AF=0.5;AN=2;DP=41;FractionInformativeReads=1;MQ=60;set=variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:21,6:27:99:168,0,758:6,15,0,6 chr2 97881267 . G A 585.25 PASS AC=1;AF=0.529;AN=2;DP=1354;FractionInformativeReads=1;set=variant4-variant5-variant9-variant10-variant13-variant16-variant17-variant18-variant23-variant25-variant30-variant31-variant34-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:74,25:99:99:382,0,1995:38,36,13,12 chr2 97882648 . G A 151.42 PASS AC=1;AF=0.548;AN=2;DP=414;FractionInformativeReads=1;set=variant2-variant4-variant5-variant9-variant10-variant13-variant16-variant17-variant18-variant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,6:24:99:165,0,608:14,4,6,0 chr2 97884715 . A G 49.68 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=40;FS=0;FractionInformativeReads=1;MQ=55.48;MQRankSum=2.418;QD=1.24;ReadPosRankSum=0.287;SOR=0.484;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:32,8:40:78:78,0,748:18,14,4,4 chr2 97884763 . T C 251.02 PASS AC=1;AF=0.595;AN=2;DP=767;set=variant2-variant4-variant5-variant9-variant10-variant13-variant16-variant17-variant18-filterInvariant23-variant24-variant25-variant27-variant30-variant31-variant32-variant34-variant37-variant38-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:33,8:41:75:75,0,783:15,18,4,4 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 0/1:28,9:37:99:377,0,1167:14,14,6,3 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 0/1:28,10:38:99:377,0,1167:14,14,6,4 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 0/1:27,11:38:99:380,0,1148:12,15,7,4 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 0/1:27,11:38:99:380,0,1148:12,15,7,4 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 0/1:9,14:23:99:561,0,352:2,7,8,6 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 0/1:9,14:23:99:561,0,410:2,7,8,6 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 0/1:9,14:23:99:561,0,410:2,7,8,6 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 0/1:9,14:23:99:561,0,410:2,7,8,6 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 0/1:9,14:23:99:312,0,171:2,7,8,6 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 0/1:7,9:16:99:358,0,336:1,6,3,6 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 0/1:7,8:15:99:345,0,341:1,6,3,5 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 0/1:7,6:13:99:231,0,350:1,6,2,4 chr2 97916008 . A C 321.89 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=52;FS=0;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:5,2:7:66:66,0,290:4,1,1,1 chr2 97916014 . A G 41.67 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=48;FS=0;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:6,2:8:66:66,0,290:4,2,1,1 chr2 98128093 . G A 106.77 DRAGENHardSNP AC=2;AF=0.9;AN=2;DP=172;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,1:1:15:225,15,0:0,0,1,0 chr2 98128098 . G A 218.32 DRAGENHardSNP AC=2;AF=0.853;AN=2;DP=367;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:352,24,0:0,0,8,0 chr2 98128099 . A C 218.32 DRAGENHardSNP AC=2;AF=0.853;AN=2;DP=387;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:352,24,0:0,0,8,0 chr2 98128128 . G A 445.95 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1596;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:53,10:63:95:95,0,1464:45,8,8,2 chr2 98128135 . G A 2671.77 DRAGENHardSNP AC=2;AF=0.807;AN=2;DP=5507;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:3825,256,0:0,0,63,17 chr2 98128139 . C T 221.81 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2808;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:75,14:89:99:130,0,1934:56,19,11,3 chr2 98128143 . T C 3200.56 DRAGENHardSNP AC=2;AF=0.807;AN=2;DP=6729;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,101:101:99:4710,325,0:0,0,72,29 chr2 98128150 . G A 1734.46 DRAGENHardSNP AC=1;AF=0.568;AN=2;DP=8022;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:24,112:136:99:2626,0,232:15,9,70,42 chr2 98128172 . C A 6271.77 DRAGENHardSNP AC=2;AF=0.807;AN=2;DP=11877;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,194:194:99:9090,608,0:0,0,103,91 chr2 98128183 . C G 459.48 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=6440;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:194,30:224:71:71,0,4187:97,97,15,15 chr2 98128194 . G C 6766.77 DRAGENHardSNP AC=2;AF=0.807;AN=2;DP=13568;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,224:224:99:10080,674,0:0,0,112,112 chr2 98128195 . G A 6766.77 DRAGENHardSNP AC=2;AF=0.807;AN=2;DP=13560;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,224:224:99:10080,674,0:0,0,112,112 chr2 98128196 . T C 6766.77 DRAGENHardSNP AC=2;AF=0.807;AN=2;DP=13552;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,224:224:99:10080,674,0:0,0,112,112 chr2 98128228 . G A 518.69 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=6082;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:185,39:224:99:293,0,3916:91,94,20,19 chr2 98128256 . C T 5956.77 DRAGENHardSNP AC=2;AF=0.807;AN=2;DP=11393;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,196:196:99:8715,596,0:0,0,85,111 chr2 98128258 . G C 5911.77 DRAGENHardSNP AC=2;AF=0.807;AN=2;DP=11097;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,189:189:99:8666,590,0:0,0,78,111 chr2 98128300 . A G 834.32 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=4463;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:50,26:76:99:521,0,1188:10,40,3,23 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 0/1:5,27:32:49:723,0,49:1,4,2,25 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 0/1:9,4:13:99:141,0,398:5,4,2,2 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 0/1:9,4:13:99:141,0,398:5,4,2,2 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 0/1:9,4:13:80:80,0,189:5,4,2,2 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 0/1:9,4:13:60:60,0,184:5,4,2,2 chr2 98129670 . C T 226.2 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=587;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:11,6:17:99:108,0,252:5,6,4,2 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 0/1:8,13:21:99:522,0,321:4,4,8,5 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 0/1:8,13:21:99:522,0,321:4,4,8,5 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 0/1:8,13:21:99:519,0,363:4,4,8,5 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 0/1:8,13:21:99:519,0,363:4,4,8,5 chr2 98129707 . G T 334.63 DRAGENHardSNP AC=1;AF=0.511;AN=2;DP=1607;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:11,17:28:99:681,0,415:6,5,9,8 chr2 98129716 . A G 370.59 DRAGENHardSNP AC=1;AF=0.511;AN=2;DP=1647;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:10,17:27:99:681,0,415:5,5,9,8 chr2 98129717 . C T 370.59 DRAGENHardSNP AC=1;AF=0.511;AN=2;DP=1649;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:10,17:27:99:684,0,393:5,5,9,8 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 0/1:10,17:27:99:684,0,393:5,5,9,8 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 0/1:10,17:27:99:684,0,393:5,5,9,8 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 0/1:10,17:27:99:684,0,393:5,5,9,8 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 0/1:10,18:28:99:705,0,390:5,5,9,9 chr2 98129817 . T C 31.68 DRAGENHardSNP AC=1;AF=0.514;AN=2;DP=810;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:8,10:18:99:204,0,154:3,5,4,6 chr2 98154623 . C T 35.29 DRAGENHardSNP AC=2;AF=1;AN=2;DP=2;FS=0;FractionInformativeReads=1;MQ=27.02;QD=17.65;SOR=2.303;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:64,6,0:0,0,2,0 chr2 98164020 . C T 771.01 PASS AC=2;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 1/1:0,19:19:57:828,57,0:0,0,10,9 chr2 98164021 . T C 771.01 PASS AC=2;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 1/1:0,19:19:57:828,57,0:0,0,10,9 chr2 98164084 . T A 395.14 PASS AC=2;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 1/1:0,27:27:81:799,81,0:0,0,13,14 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 0/1:29,27:56:99:659,0,636:14,15,15,12 chr2 98165920 . A G 434.99 PASS AC=1;AF=0.5;AN=2;DP=92;set=variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,19:44:99:463,0,659:14,11,12,7 chr2 98169583 . G T 239.21 PASS AC=2;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 1/1:0,11:11:33:352,33,0:0,0,8,3 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 0/1:8,19:27:99:391,0,230:3,5,10,9 chr2 98173368 . C T 1740.66 PASS AC=2;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 1/1:2,35:37:19:1468,19,0:1,1,19,16 chr2 98173369 . A G 1740.66 PASS AC=2;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 1/1:2,35:37:19:1468,19,0:1,1,19,16 chr2 98175198 . C T 301.56 PASS AC=1;AF=0.5;AN=2;DP=95;FractionInformativeReads=1;set=variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:21,14:35:99:330,0,567:13,8,8,6 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 0/1:31,28:59:99:669,0,729:16,15,13,15 chr2 98177305 . C G 232.58 PASS AC=2;AF=0.833;AN=2;DP=263;FractionInformativeReads=1;set=variant-variant3-filterInvariant4-variant6-variant7-variant8-variant11-variant12-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant33-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:119,9,0:0,0,0,3 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 0/1:11,9:20:99:373,0,758:9,2,6,3 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 0/1:13,13:26:99:481,0,824:11,2,10,3 chr2 98201508 . C A 1297.8 PASS AC=1;AF=0.5;AN=2;DP=377;FractionInformativeReads=1;set=variant23-variant42 GT:AD:DP:GQ:PL:SB 0/1:125,71:196:99:1326,0,3277:79,46,42,29 chr2 98205924 . C G 737.08 PASS AC=2;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 1/1:0,19:19:57:823,57,0:0,0,19,0 chr2 98206188 . C G 3652.09 PASS AC=2;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 1/1:0,116:116:99:3620,346,0:0,0,39,77 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 0/1:21,26:47:99:603,0,526:8,13,11,15 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 0/1:53,26:79:99:630,0,1505:32,21,11,15 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 0/1:57,58:115:99:1318,0,1528:29,28,31,27 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 0/1:10,3:13:85:85,0,329:3,7,3,0 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 0/1:72,90:162:99:2389,0,1780:36,36,50,40 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 0/1:20,12:32:99:451,0,3730:3,17,0,12 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 0/1:52,31:83:99:728,0,1255:23,29,14,17 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 0/1:22,16:38:99:419,0,546:7,15,4,12 chr2 98330052 . C A 1057.38 PASS AC=1;AF=0.632;AN=2;DP=888;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant8-variant11-variant14-variant16-variant17-variant21-variant23-variant27-variant28-variant29-variant31-variant33-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,9:32:99:146,0,578:13,10,3,6 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 1/1:0,29:29:87:1009,87,0:0,0,22,7 chr2 98351654 . TG T 1620.36 PASS AC=1;AF=0.579;AN=2;DP=1330;MQ=60;set=variant-variant6-variant7-variant8-variant11-variant12-variant14-variant16-variant17-variant21-variant23-variant28-variant31-variant33-variant36-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,32:54:99:926,0,560:17,5,30,2 chr2 98353847 . C T 559.11 PASS AC=1;AF=0.579;AN=2;DP=601;MQ=60;set=variant-variant6-variant7-variant8-variant11-variant12-variant14-variant16-variant17-variant21-variant23-variant24-variant28-variant31-variant33-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,16:30:99:395,0,389:11,3,9,7 chr2 98354139 . G T 6245.72 PASS AC=1;AF=0.579;AN=2;DP=5940;MQ=60;set=variant-variant6-variant7-variant8-variant11-variant12-variant14-variant16-variant17-variant21-variant23-variant24-variant28-variant31-variant33-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:147,147:294:99:3551,0,3621:82,65,78,69 chr2 98354511 . G A 1806.5 PASS AC=1;AF=0.583;AN=2;DP=1609;MQ=60;set=variant-variant6-variant7-variant8-variant11-variant12-variant14-variant16-variant17-variant21-variant23-variant28-variant31-variant33-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,32:67:99:693,0,952:18,17,15,17 chr2 98355990 . G A 1586.29 PASS AC=1;AF=0.583;AN=2;DP=1486;set=variant-variant6-variant7-variant8-variant11-variant12-variant14-variant16-variant17-variant21-variant23-variant28-variant31-variant33-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,23:48:99:586,0,755:8,17,9,14 chr2 98372980 . A G 3977.38 PASS AC=1;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 0/1:190,143:333:99:3320,0,4685:92,98,68,75 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 1/1:0,332:332:99:9846,993,0:0,0,150,182 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 1/1:0,12:12:36:392,36,0:0,0,9,3 chr2 98377512 . A T 868.5 PASS AC=1;AF=0.605;AN=2;DP=605;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant8-variant11-variant12-variant14-variant16-variant21-variant23-variant28-variant29-variant31-variant33-variant34-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,9:27:99:266,0,566:4,14,1,8 chr2 98382886 . G A 1264.56 PASS AC=1;AF=0.605;AN=2;DP=869;MQ=60;set=variant-variant6-variant7-variant8-variant11-variant12-variant14-variant16-variant20-variant21-variant23-variant28-variant29-variant31-variant33-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,17:41:99:509,0,724:17,7,14,3 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 0/1:23,35:58:99:933,0,676:19,4,22,13 chr2 98409046 . G A 7107.49 PASS AC=1;AF=0.611;AN=2;DP=3448;MQ=60;set=variant-variant6-variant7-variant8-variant11-variant12-variant14-variant16-variant21-variant23-variant28-variant29-variant31-variant33-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:99,72:171:99:1779,0,2647:50,49,35,37 chr2 98409565 . T C 672 PASS AC=1;AF=0.605;AN=2;DP=519;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant8-variant11-variant12-variant14-variant16-variant21-variant23-variant28-variant29-variant31-variant33-variant34-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,12:26:99:292,0,282:7,7,4,8 chr2 98413781 . C T 409.1 PASS AC=2;AF=0.656;AN=2;DP=107;FractionInformativeReads=1;MQ=60;set=variant-variant6-variant7-variant8-variant11-variant14-variant21-variant23-variant29-variant31-variant33-variant34-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:87,6,0:0,0,2,0 chr2 98418812 . CA C 330.69 PASS AC=1;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 0/1:7,6:13:99:173,0,210:6,1,5,1 chr2 98443694 . C T 2056.24 PASS AC=1;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 0/1:81,93:174:99:2171,0,1954:53,28,58,35 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 1/1:0,19:19:57:612,57,0:0,0,13,6 chr2 98451036 . TA T 78.79 PASS AC=1;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 0/1:4,4:8:65:81,0,65:4,0,3,1 chr2 98460441 . TAG T 217.55 PASS AC=1;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 0/1:5,3:8:99:109,0,198:5,0,3,0 chr2 98460742 . G A 193.94 PASS AC=1;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 0/1:6,2:8:66:66,0,208:1,5,0,2 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 1/1:0,55:55:99:1561,165,0:0,0,25,30 chr2 98544058 . T C 134.92 PASS AC=1;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 0/1:7,3:10:92:92,0,206:2,5,0,3 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 1/1:0,15:15:45:550,45,0:0,0,12,3 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 1/1:1,80:81:99:2266,231,0:0,1,41,39 chr2 98612260 . T C 3420.92 PASS AC=1;AF=0.605;AN=2;DP=2217;MQ=60;set=variant-variant6-variant7-variant8-variant11-variant12-variant14-variant16-variant21-variant23-variant28-variant29-variant31-variant33-variant34-variant36-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,53:100:99:1233,0,978:27,20,25,28 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 1/1:0,101:101:99:3765,306,0:0,0,52,49 chr2 98703659 . G T 76.34 PASS AC=1;AF=0.574;AN=2;DP=1372;FractionInformativeReads=1;MQ=60;set=filterInvariant-variant2-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant15-variant16-variant18-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant39-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:32,31:63:99:813,0,772:14,18,20,11 chr2 98795873 . T TG 6131.85 PASS AC=1;AF=0.854;AN=2;DP=5943;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-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:54,65:119:99:1954,0,1569:23,31,28,37 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 0/1:14,11:25:99:309,0,409:4,10,1,10 chr2 98804314 . G A 855.91 PASS AC=2;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 1/1:0,28:28:84:994,84,0:0,0,23,5 chr2 98810904 . A G 922.44 PASS AC=1;AF=0.5;AN=2;DP=110;FractionInformativeReads=1;MQ=60;set=variant16-variant23 GT:AD:DP:GQ:PL:SB 0/1:24,23:47:99:610,0,646:15,9,12,11 chr2 98811075 . A G 1340.37 PASS AC=2;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 1/1:0,35:35:99:1145,105,0:0,0,11,24 chr2 98833446 . C CCA 271.31 PASS AC=1;AF=0.5;AN=2;DP=198;MQ=60;set=variant-variant6-variant8-variant9-variant11-variant12-variant14-variant23-variant29-variant32 GT:AD:DP:GQ:PL:SB 0/1:13,7:20:99:221,0,498:1,12,0,7 chr2 98833449 . G C,A 331.63 PASS AC=2,0;AF=0.786,0.095;AN=2;DP=396;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant-variant20-variant21-variant29-variant23-variant42-variant24-variant43 GT:DP:GQ:SB 1/1:22:66:0,0,2,20 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 0/1:5,7:12:99:258,0,121:4,1,7,0 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 0/1:62,56:118:99:1369,0,1452:39,23,35,21 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 0/1:38,43:81:99:1061,0,1049:16,22,17,26 chr2 98862097 . A G 852.69 PASS AC=2;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 1/1:0,39:39:99:1399,117,0:0,0,10,29 chr2 98872662 . C CT,CTT 545.65 PASS AC=2,0;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 1/1:25:18:0,2,6,17 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 0/1:33,29:62:99:796,0,812:22,11,21,8 chr2 98928494 . G A 2477.28 PASS AC=2;AF=0.966;AN=2;DP=3758;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2875,279,0:0,0,52,41 chr2 98993635 . A G 46.75 PASS AC=2;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 1/1:0,11:11:33:330,33,0:0,0,7,4 chr2 98994414 . T C 1043.23 PASS AC=2;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 1/1:0,73:73:99:2405,219,0:0,0,48,25 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 1/1:0,2:2:6:64,6,0:0,0,2,0 chr2 99219111 . CA C 118.49 PASS AC=1;AF=0.5;AN=2;DP=547;set=variant2-variant5-variant6-filterInvariant8-variant10-variant14-variant16-variant17-variant19-variant21-filterInvariant23-variant25-variant26-variant29-filterInvariant31-filterInvariant32-variant34-variant36-filterInvariant38-variant39-filterInvariant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:20,7:27:76:76,0,374:11,9,4,3 chr2 99232873 . T C 1876.39 PASS AC=1;AF=0.5;AN=2;DP=1719;MQ=60;set=variant-variant2-variant6-variant9-variant10-variant18-variant21-variant22-variant23-variant25-variant31-variant34-variant36-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:51,45:96:99:1079,0,1443:26,25,20,25 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 0/1:30,16:46:99:211,0,603:24,6,12,4 chr2 99271712 . T C 121.45 PASS AC=1;AF=0.658;AN=2;DP=221;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant10-variant19-variant21-variant22-variant23-variant29-variant30-variant31-variant32-variant36-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:1,4:5:31:162,0,31:1,0,4,0 chr2 99272057 . T C 195.66 PASS AC=1;AF=0.685;AN=2;DP=387;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant10-variant12-variant16-variant18-variant19-variant21-variant22-variant23-variant25-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:222,0,214:0,6,1,6 chr2 99274653 . T C 770.39 PASS AC=1;AF=0.685;AN=2;DP=1846;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant9-variant10-variant12-variant16-variant18-variant19-variant21-variant22-variant23-variant25-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,29:54:99:642,0,558:14,11,17,12 chr2 99295003 . C A 49.52 PASS AC=1;AF=0.5;AN=2;DP=367;MQ=60;set=filterInvariant2-variant3-variant6-variant9-variant10-variant18-variant21-variant23-variant31-variant36-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:8,10:18:99:371,0,186:3,5,0,10 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 0/1:137,111:248:99:2630,0,3401:54,83,44,67 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 0/1:194,177:371:99:4187,0,4836:95,99,86,91 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 0/1:30,44:74:99:1144,0,724:20,10,29,15 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 0/1:9,8:17:99:268,0,343:9,0,7,1 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 0/1:21,19:40:99:527,0,649:5,16,6,13 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 1/1:0,100:100:99:3104,298,0:0,0,32,68 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 0/1:33,24:57:99:499,0,930:24,9,15,9 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 0/1:104,110:214:99:2534,0,2213:59,45,63,47 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 0/1:56,56:112:99:2298,0,7537:32,24,29,27 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 0/1:75,56:131:99:2128,0,3592:39,36,29,27 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 0/1:71,57:128:99:2134,0,3548:36,35,28,29 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 0/1:92,78:170:99:1834,0,2555:31,61,30,48 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 0/1:45,41:86:99:1094,0,1294:12,33,11,30 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 0/1:17,12:29:99:441,0,501:10,7,4,8 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 0/1:43,42:85:99:951,0,1093:19,24,21,21 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 0/1:53,47:100:99:1071,0,1301:29,24,24,23 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 0/1:159,79:238:99:1189,0,3505:70,89,40,39 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 0/1:4,10:14:99:327,0,137:0,4,2,8 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 1/1:0,61:61:99:1919,183,0:0,0,34,27 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 0/1:24,21:45:99:628,0,715:18,6,15,6 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 0/1:99,96:195:99:2073,0,2320:40,59,45,51 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 0/1:10,7:17:99:252,0,291:4,6,6,1 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 0/1:30,43:73:99:1010,0,741:15,15,18,25 chr2 99859954 . CAGATAGATAGATAGAT CAGATAGATAGAT,CAGATAGATAGATAGATAGATAGAT,CAGATAGATAGATAGATAGAT,CAGATAGAT,C 212.98 PASS AC=1,1,0,0,0;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 1/2:12:99:0,0,2,10 chr2 99870872 . AAGATAGTATTCTCACAGGCTC A 148.19 PASS AC=1;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 0/1:6,5:11:99:192,0,1100:0,6,1,4 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 1/1:0,3:3:9:119,9,0:0,0,2,1 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 1/1:0,5:5:15:150,15,0:0,0,5,0 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 1/1:0,22:22:66:753,66,0:0,0,16,6 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 1/1:0,17:17:51:593,51,0:0,0,12,5 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 1/1:1,64:65:99:1786,184,0:0,1,35,29 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 0/1:31,26:57:99:701,0,832:20,11,18,8 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 1/1:0,78:78:99:2323,234,0:0,0,45,33 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 0/1:12,20:32:99:647,0,309:6,6,11,9 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 1/1:0,13:13:39:447,39,0:0,0,1,12 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 1/1:0,14:14:42:475,42,0:0,0,11,3 chr2 99995458 . AT A,ATT 50.99 PASS AC=1,0;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 0/1:16:2:1,1,9,5 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 0/1:24,11:35:99:296,0,613:13,11,6,5 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 1/1:1,165:166:99:4782,451,0:1,0,77,88 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 1/1:0,20:20:60:691,60,0:0,0,14,6 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 1/1:0,50:50:99:1779,150,0:0,0,39,11 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 0/1:76:99:19,24,14,19 chr2 100006904 . T TA,TTA 346.72 PASS AC=1,0;AF=0.375,0.125;AN=2;DP=325;set=variant10-variant8-variant23-variant27 GT:DP:GQ:SB 0/1:66:99:19,24,10,13 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 0/1:22,21:43:99:540,0,564:15,7,15,6 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 1/1:0,28:28:84:836,84,0:0,0,12,16 chr2 100017454 . T C 910.55 PASS AC=1;AF=0.5;AN=2;DP=72;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-2.546;QD=12.65;ReadPosRankSum=2.298;SOR=0.702;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:37,35:72:99:939,0,781:20,17,19,16 chr2 100017906 . CAA C,CA,CAAA,CAAAA 30.23 PASS AC=0,0,2,0;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 3/3:13:1:0,2,4,7 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 1/1:0,47:47:99:1416,140,0:0,0,20,27 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 1/1:0,17:17:51:637,51,0:0,0,5,12 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 1/1:0,86:86:99:2771,258,0:0,0,31,55 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 1/1:0,4:4:12:139,12,0:0,0,3,1 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 1/1:0,72:72:99:2266,216,0:0,0,49,23 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 1/1:0,44:44:99:1339,132,0:0,0,23,21 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 0/1:54,27:81:99:605,0,1234:25,29,13,14 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 1/1:0,16:16:48:530,48,0:0,0,4,12 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 0/1:16,21:37:99:493,0,385:11,5,13,8 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 1/1:0,41:41:99:1549,123,0:0,0,27,14 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 1/1:0,4:4:12:180,12,0:0,0,0,4 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 1/1:7:21:0,0,3,4 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 100171382 . G A 492.04 PASS AC=1;AF=0.591;AN=2;DP=272;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant8-variant9-variant11-variant19-variant22-variant23-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:221,0,325:2,9,2,5 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 0/1:30,38:68:99:984,0,839:20,10,22,16 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 1/1:0,86:86:99:2650,258,0:0,0,45,41 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 1/1:0,56:56:99:2217,168,0:0,0,27,29 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 0/1:4,4:8:99:136,0,112:2,2,1,3 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 1/1:0,40:40:99:1204,119,0:0,0,16,24 chr2 100892018 . G A 1053.24 PASS AC=2;AF=0.667;AN=2;DP=1376;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1407,135,0:0,0,22,23 chr2 100892516 . C T 1930.17 PASS AC=2;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 1/1:0,67:67:99:2237,201,0:0,0,20,47 chr2 100893113 . C A 4496.03 PASS AC=2;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 1/1:3,148:151:99:3777,367,0:1,2,56,92 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 0/1:34,14:48:99:486,0,1645:18,16,8,6 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 0/1:34,14:48:99:486,0,1645:18,16,8,6 chr2 100894491 . C A 1983.98 PASS AC=2;AF=0.667;AN=2;DP=1828;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1191,120,0:0,0,19,21 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 0/1:49,44:93:99:1048,0,1134:22,27,17,27 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 0/1:30,29:59:99:830,0,720:12,18,10,19 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 0/1:31,20:51:99:469,0,813:18,13,11,9 chr2 100895784 . ACC AC,A 1255.44 PASS AC=1,0;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 0/1:72:99:20,18,20,14 chr2 100895872 . G A 2318.19 PASS AC=1;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 0/1:52,46:98:99:1211,0,1560:26,26,21,25 chr2 100896110 . T C 3216.09 PASS AC=1;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 0/1:29,19:48:99:658,0,1727:14,15,6,13 chr2 100896112 . C T 3216.09 PASS AC=1;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 0/1:28,16:44:99:658,0,1727:13,15,4,12 chr2 100896242 . A G 1612.02 PASS AC=1;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 0/1:40,23:63:99:523,0,1039:23,17,13,10 chr2 100896311 . G T 1891.03 PASS AC=1;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 0/1:45,28:73:99:664,0,1252:19,26,13,15 chr2 100896376 . G C 1550.22 PASS AC=1;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 0/1:38,16:54:99:426,0,1092:17,21,8,8 chr2 100896415 . C T 1837.96 PASS AC=1;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 0/1:41,13:54:99:332,0,1261:19,22,6,7 chr2 100896512 . G A 1501.15 PASS AC=1;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 0/1:37,16:53:99:355,0,907:18,19,6,10 chr2 100896964 . A G 331.77 PASS AC=1;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 0/1:8,8:16:99:312,0,381:3,5,1,7 chr2 100896966 . G A 331.77 PASS AC=1;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 0/1:8,8:16:99:312,0,381:3,5,1,7 chr2 100897008 . C T 112.51 PASS AC=1;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 0/1:4,3:7:99:101,0,125:1,3,1,2 chr2 100897214 . G A 2117.35 PASS AC=1;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 0/1:23,33:56:99:936,0,657:18,5,25,8 chr2 100897351 . T A 8594.84 PASS AC=1;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 0/1:141,140:281:99:3412,0,3385:83,58,75,65 chr2 100897573 . G A 8689 PASS AC=1;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 0/1:149,171:320:99:4259,0,3657:66,83,76,95 chr2 100897674 . T A 5188.8 PASS AC=1;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 0/1:72,78:150:99:2071,0,1840:28,44,30,48 chr2 100897739 . GTTTT G 5160.92 PASS AC=1;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 0/1:55,53:108:99:1935,0,2562:26,29,26,27 chr2 100898634 . G T 1281.89 PASS AC=1;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 0/1:18,21:39:99:552,0,456:10,8,10,11 chr2 100899258 . GAAAACTAAAAGAAAAATTAATAATATTATAA G 447.44 PASS AC=1;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 0/1:42,7:49:99:190,0,3845:12,30,2,5 chr2 100899292 . TCTTTATCTACTGAAACTAC T 453.26 PASS AC=1;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 0/1:37,7:44:99:207,0,3653:10,27,2,5 chr2 100899328 . T TA 393.96 PASS AC=1;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 0/1:23,7:30:99:237,0,1910:6,17,2,5 chr2 100899665 . G A 7126.25 PASS AC=1;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 0/1:118,87:205:99:2213,0,3152:70,48,59,28 chr2 100899676 . T C 8273.52 PASS AC=1;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 0/1:143,102:245:99:2346,0,3575:81,62,63,39 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 0/1:97:99:24,45,8,20 chr2 100900304 . T C 1813.59 PASS AC=1;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 0/1:35,24:59:99:530,0,865:18,17,12,12 chr2 100900406 . G A 1564.56 PASS AC=1;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 0/1:46,26:72:99:611,0,1080:22,24,13,13 chr2 100915629 . T C 1913.99 PASS AC=1;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 0/1:24,40:64:99:1095,0,708:16,8,25,15 chr2 100915772 . A G 2008.14 PASS AC=1;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 0/1:35,38:73:99:989,0,944:15,20,14,24 chr2 100916051 . T C 160.45 PASS AC=1;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 0/1:5,3:8:98:98,0,121:3,2,3,0 chr2 100916306 . A G 1103.52 PASS AC=1;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 0/1:24,25:49:99:927,0,1166:11,13,11,14 chr2 100916315 . A G 1065.74 PASS AC=1;AF=0.645;AN=2;DP=1231;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,23:45:99:866,0,1133:10,12,8,15 chr2 100917109 . C T 4540.88 PASS AC=1;AF=0.683;AN=2;DP=3923;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:79,74:153:99:1648,0,1939:37,42,38,36 chr2 100925803 . A G 156.17 PASS AC=1;AF=0.759;AN=2;DP=161;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:115,0,117:1,3,2,2 chr2 100925934 . C A 169.59 PASS AC=1;AF=0.717;AN=2;DP=689;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-filterInvariant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:59:148,0,59:2,0,4,2 chr2 100938226 . G C 336.35 PASS AC=1;AF=0.731;AN=2;DP=366;MQ=60;set=variant-variant5-variant6-variant7-variant8-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant41-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:8,11:19:99:284,0,141:4,4,4,7 chr2 100938328 . T C 377.99 PASS AC=1;AF=0.74;AN=2;DP=275;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant8-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,7:13:99:187,0,142:3,3,5,2 chr2 100938481 . C G 880.07 PASS AC=1;AF=0.7;AN=2;DP=1419;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,50:75:99:1301,0,571:17,8,31,19 chr2 100938917 . G C 4295.11 PASS AC=1;AF=0.683;AN=2;DP=5991;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:115,88:203:99:1956,0,2760:55,60,47,41 chr2 100938952 . T C 4531.6 PASS AC=1;AF=0.7;AN=2;DP=5951;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:115,89:204:99:1900,0,2709:53,62,45,44 chr2 100939117 . A G 2831.26 PASS AC=1;AF=0.719;AN=2;DP=3479;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,50:100:99:1302,0,1165:24,26,23,27 chr2 100986964 . A C 1780.38 PASS AC=1;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 0/1:21,26:47:99:726,0,639:5,16,9,17 chr2 101009326 . T C 1246.71 PASS AC=1;AF=0.727;AN=2;DP=1761;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,26:49:99:595,0,641:9,14,15,11 chr2 101009600 . G A 1830.36 PASS AC=1;AF=0.717;AN=2;DP=2134;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,27:65:99:737,0,1047:24,14,12,15 chr2 101010082 . G C 6128.22 PASS AC=1;AF=0.727;AN=2;DP=6206;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:96,102:198:99:2512,0,2211:41,55,49,53 chr2 101011724 . C T 740.29 PASS AC=1;AF=0.721;AN=2;DP=837;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:13,19:32:99:471,0,315:9,4,13,6 chr2 101011877 . T C 3378.2 PASS AC=1;AF=0.717;AN=2;DP=2822;set=variant-variant2-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,35:59:99:1054,0,707:14,10,19,16 chr2 101014247 . C A 503.73 PASS AC=1;AF=0.734;AN=2;DP=711;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant9-variant11-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,8:22:99:210,0,463:12,2,6,2 chr2 101014363 . C T 2856.79 PASS AC=1;AF=0.707;AN=2;DP=2909;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:53,31:84:99:795,0,1473:33,20,18,13 chr2 101022886 . C T 946.53 PASS AC=1;AF=0.717;AN=2;DP=660;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:376,0,308:7,4,9,3 chr2 101031561 . G T 1301.64 PASS AC=1;AF=0.707;AN=2;DP=1366;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:541,0,423:5,11,7,10 chr2 101033697 . G A 328.13 PASS AC=1;AF=0.714;AN=2;DP=448;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant28-variant29-variant30-variant31-variant33-variant34-variant36-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,13:19:99:321,0,192:3,3,5,8 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 1/1:0,15:15:45:432,45,0:0,0,8,7 chr2 101126124 . T A 7735.36 PASS AC=2;AF=0.898;AN=2;DP=11299;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,224:224:99:6939,670,0:0,0,101,123 chr2 101179045 . C T 159.14 PASS AC=1;AF=0.5;AN=2;DP=164;MQ=60;set=variant3-variant4-variant17-variant23-variant24-variant26-variant28-variant31-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:13,4:17:88:88,0,363:7,6,2,2 chr2 101436708 . C CGCGGCG,CGCG,CGCGGCGGCGGCGGCG 97.73 PASS AC=1,0,0;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 0/1:5:99:1,1,1,2 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 1/1:0,7:7:24:290,24,0:0,0,7,0 chr2 101521173 . ATTT AT,ATT,A,ATTTT 665.56 PASS AC=1,1,0,0;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 1/2:27:84:0,0,13,14 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 1/1:1,72:73:99:2258,208,0:0,1,23,49 chr2 101541872 . C T 403.2 PASS AC=1;AF=0.5;AN=2;DP=561;MQ=60;set=variant-variant2-variant3-variant5-variant9-variant12-variant13-variant15-variant16-variant17-variant19-variant23-variant24-variant26-variant27-variant30-variant31-variant33 GT:AD:DP:GQ:PL:SB 0/1:15,3:18:81:81,0,438:4,11,0,3 chr2 101554036 . C T 408.11 PASS AC=1;AF=0.5;AN=2;DP=335;FractionInformativeReads=1;MQ=60;set=variant5-variant6-variant9-variant12-variant14-variant16-variant19-variant20-variant23-variant24-variant32-variant33-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,21:27:99:643,0,175:3,3,15,6 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 1/1:86:99:0,0,52,34 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 1/1:0,34:34:99:1186,102,0:0,0,10,24 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 1/1:0,64:64:99:1893,191,0:0,0,37,27 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 1/1:0,23:23:69:659,69,0:0,0,16,7 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 1/1:0,47:47:99:1536,141,0:0,0,35,12 chr2 101587455 . C T 1083.89 PASS AC=1;AF=0.542;AN=2;DP=1023;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant8-variant13-variant17-variant23-variant28-variant31-variant32-variant34-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:41,36:77:99:897,0,1030:20,21,20,16 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 1/1:0,105:105:99:3184,315,0:0,0,53,52 chr2 101591443 . A C 477.79 PASS AC=1;AF=0.528;AN=2;DP=819;FractionInformativeReads=1;MQ=60;set=variant4-variant6-variant7-variant8-variant13-variant17-variant19-variant21-variant23-variant28-variant29-variant30-variant31-variant32-variant34-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:25,28:53:99:626,0,589:10,15,10,18 chr2 101594454 . T C 50.66 PASS AC=1;AF=0.542;AN=2;DP=344;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant8-variant13-variant17-variant23-variant28-variant31-variant32-variant34-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:13,12:25:99:410,0,323:4,9,3,9 chr2 101598677 . C T 1924.07 PASS AC=1;AF=0.553;AN=2;DP=2861;MQ=60;set=variant6-variant7-variant8-variant10-variant13-variant15-variant16-variant17-variant21-variant23-variant24-variant26-variant27-variant28-variant31-variant32-variant34-variant36-variant41 GT:AD:DP:GQ:PL:SB 0/1:57,64:121:99:1528,0,1242:31,26,34,30 chr2 101607387 . G A 383.1 PASS AC=1;AF=0.5;AN=2;DP=23;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.535;QD=16.66;ReadPosRankSum=0.598;SOR=0.948;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:9,14:23:99:411,0,280:3,6,4,10 chr2 101609827 . C T 1588.85 PASS AC=2;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 1/1:0,176:176:99:5091,525,0:0,0,93,83 chr2 101611707 . A C 53.91 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=33;FS=11.458;FractionInformativeReads=1;MQ=60;MQRankSum=2.079;QD=1.63;ReadPosRankSum=-0.693;SOR=3.671;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:25,8:33:82:82,0,524:15,10,8,0 chr2 101612568 . C T 1872.74 PASS AC=2;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 1/1:0,95:95:99:2826,284,0:0,0,51,44 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 1/1:0,83:83:99:2186,248,0:0,0,44,39 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 1/1:0,96:96:99:2868,288,0:0,0,50,46 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 1/1:0,4:4:12:171,12,0:0,0,0,4 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 1/1:0,178:178:99:5240,532,0:0,0,94,84 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 1/1:0,189:189:99:5447,565,0:0,0,94,95 chr2 101622728 . C T 3913.11 PASS AC=2;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 1/1:0,293:293:99:8761,877,0:0,0,143,150 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 0/1:61,45:106:99:1127,0,1343:31,30,18,27 chr2 101623745 . T A 911.42 PASS AC=2;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 1/1:0,60:60:99:1943,180,0:0,0,19,41 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 1/1:0,170:170:99:5312,510,0:0,0,95,75 chr2 101634793 . GTTCA G 1279.27 PASS AC=2;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 1/1:0,49:49:99:2147,148,0:0,0,17,32 chr2 101635538 . C T 707.23 PASS AC=2;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 1/1:0,69:69:99:2104,207,0:0,0,35,34 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 1/1:0,107:107:99:3336,319,0:0,0,54,53 chr2 101644855 . G A 1456.57 PASS AC=2;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 1/1:0,165:165:99:4469,490,0:0,0,94,71 chr2 101646359 . G C 38.97 PASS AC=2;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 1/1:0,11:11:33:323,33,0:0,0,3,8 chr2 101652732 . C T 710.33 PASS AC=2;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 1/1:0,41:41:99:1309,122,0:0,0,13,28 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 1/1:0,118:118:99:3308,352,0:0,0,54,64 chr2 101675808 . A G 625.78 PASS AC=2;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 1/1:0,29:29:87:1008,87,0:0,0,19,10 chr2 101870073 . T C 395.69 PASS AC=1;AF=0.533;AN=2;DP=479;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant11-variant12-variant15-variant23-variant24-variant25-variant26-variant27-variant28-variant34-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,22:41:99:656,0,499:5,14,6,16 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 0/1:3,4:7:99:159,0,254:3,0,4,0 chr2 101883046 . A G 347.03 PASS AC=1;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 0/1:5,7:12:99:255,0,311:5,0,6,1 chr2 101898412 . G C 2408.65 PASS AC=1;AF=0.864;AN=2;DP=3273;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:29,33:62:99:867,0,619:14,15,20,13 chr2 101925026 . T C 4044.61 PASS AC=2;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 1/1:0,275:275:99:8848,825,0:0,0,115,160 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 0/1:8,18:26:99:494,0,237:6,2,13,5 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 0/1:25,31:56:99:1006,0,1100:17,8,22,9 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 0/1:26,38:64:99:1244,0,1079:18,8,26,12 chr2 101965367 . G A 9391 PASS AC=1;AF=0.909;AN=2;DP=9558;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:99,79:178:99:1995,0,2703:40,59,33,46 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 0/1:87,73:160:99:1811,0,2352:38,49,35,38 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 0/1:49,55:104:99:1510,0,1436:30,19,34,21 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 0/1:169,148:317:99:3265,0,3898:81,88,69,79 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 0/1:149,116:265:99:2111,0,4501:76,73,53,63 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 0/1:44,51:95:99:1423,0,1210:26,18,28,23 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 0/1:14,26:40:99:761,0,313:5,9,7,19 chr2 102003633 . G T 655.93 PASS AC=1;AF=0.5;AN=2;DP=385;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant17-variant21-variant23-variant25-variant28 GT:AD:DP:GQ:PL:SB 0/1:22,21:43:99:564,0,573:13,9,11,10 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 0/1:27,14:41:99:404,0,821:10,17,3,11 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 0/1:72,73:145:99:1643,0,1831:38,34,33,40 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 0/1:13,18:31:99:491,0,284:5,8,7,11 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 1/1:0,22:22:65:805,65,0:0,0,19,3 chr2 102031489 . C G 2040.65 PASS AC=1;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 0/1:19,14:33:99:391,0,574:6,13,4,10 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 1/1:0,5:5:15:225,15,0:0,0,5,0 chr2 102035192 . C T 1761.03 PASS AC=1;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 0/1:30,32:62:99:629,0,758:16,14,16,16 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 1/1:0,129:129:99:3770,386,0:0,0,56,73 chr2 102045607 . C T 357.98 PASS AC=1;AF=0.6;AN=2;DP=226;FractionInformativeReads=1;MQ=60;set=variant23-variant28-variant32-variant34-variant41 GT:AD:DP:GQ:PL:SB 0/1:16,16:32:99:386,0,418:5,11,5,11 chr2 102066878 . A T 141.1 PASS AC=1;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 0/1:2,4:6:65:121,0,65:2,0,3,1 chr2 102067083 . T C 1790.74 PASS AC=1;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 0/1:39,42:81:99:901,0,908:22,17,22,20 chr2 102068872 . T A 591.86 PASS AC=1;AF=0.63;AN=2;DP=1061;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant33-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,37:55:99:759,0,332:10,8,18,19 chr2 102069002 . T C 239.81 PASS AC=1;AF=0.636;AN=2;DP=236;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant28-variant30-variant33-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:110,0,216:0,6,2,3 chr2 102083393 . T C 840.25 PASS AC=2;AF=0.575;AN=2;DP=1570;MQ=60;set=variant6-variant7-variant9-variant10-variant13-variant16-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant32-variant33-variant34-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,66:66:99:2228,198,0:0,0,29,37 chr2 102091220 . C T 268.24 PASS AC=2;AF=0.575;AN=2;DP=489;MQ=60;set=variant6-variant7-variant9-variant10-variant13-variant16-variant17-variant19-variant20-variant23-variant24-variant25-variant26-variant28-variant32-variant33-variant34-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:797,63,0:0,0,3,18 chr2 102314437 . T C 1986.88 PASS AC=1;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 0/1:53,86:139:99:2109,0,1143:31,22,52,34 chr2 102440723 . G A 211.36 PASS AC=1;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 0/1:4,5:9:72:82,0,72:2,2,2,3 chr2 102448164 . CT C 992.15 PASS AC=1;AF=0.5;AN=2;DP=163;FractionInformativeReads=1;MQ=60;set=variant8-variant23 GT:AD:DP:GQ:PL:SB 0/1:51,26:77:99:618,0,1416:38,13,17,9 chr2 102504563 . T A 131.43 PASS AC=1;AF=0.5;AN=2;DP=11;FS=0;FractionInformativeReads=1;MQ=60;set=variant8-variant23 GT:AD:DP:GQ:PL:SB 0/1:2,2:4:75:75,0,79:0,2,0,2 chr2 102505434 . A G 782.19 PASS AC=1;AF=0.5;AN=2;DP=142;FractionInformativeReads=1;MQ=60;set=variant8-variant23 GT:AD:DP:GQ:PL:SB 0/1:30,44:74:99:1026,0,665:10,20,18,26 chr2 102508146 . G A 1369.39 PASS AC=1;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 0/1:42,47:89:99:1067,0,1104:25,17,21,26 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 0/1:10,10:20:99:349,0,293:2,8,2,8 chr2 102641201 . A G 718.68 PASS AC=1;AF=0.5;AN=2;DP=1218;MQ=60;set=variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant33-variant34-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,26:57:99:626,0,848:12,19,9,17 chr2 102642558 . G GT 393.76 PASS AC=1;AF=0.5;AN=2;DP=496;MQ=60;set=variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:23,17:40:99:385,0,581:20,3,14,3 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 0/1:29,21:50:99:502,0,643:13,16,12,9 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 0/1:5,6:11:97:121,0,97:2,3,2,4 chr2 102759293 . A C 44.34 PASS AC=1;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 0/1:10,8:18:99:215,0,269:5,5,6,2 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 0/1:26,34:60:99:717,0,589:15,11,19,15 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 0/1:4,10:14:99:324,0,137:4,0,8,2 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 1/1:0,80:80:99:2368,239,0:0,0,30,50 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 0/1:54,44:98:99:1037,0,1485:25,29,24,20 chr2 102804538 . A AACC 631.17 PASS AC=1;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 0/1:22,20:42:99:773,0,942:3,19,1,19 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 0/1:13,20:33:99:672,0,362:10,3,18,2 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 0/1:4,3:7:90:90,0,128:4,0,3,0 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 0/1:4,3:7:99:111,0,106:1,3,0,3 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 0/1:18:70:10,3,4,1 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 0/1:37,19:56:99:567,0,1143:29,8,17,2 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 0/1:103,94:197:99:2108,0,2524:60,43,57,37 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 0/1:142,153:295:99:3607,0,3188:71,71,80,73 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 0/1:73,72:145:99:2808,0,2884:28,45,26,46 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 0/1:75,73:148:99:2808,0,2884:28,47,27,46 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 0/1:46,41:87:99:1170,0,1245:18,28,16,25 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 0/1:27,27:54:99:1039,0,1142:11,16,12,15 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 0/1:28,28:56:99:1077,0,1128:12,16,13,15 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 0/1:36,22:58:99:819,0,2631:19,17,12,10 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 0/1:36,24:60:99:864,0,2365:17,19,12,12 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 0/1:50,40:90:99:841,0,1185:27,23,18,22 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 0/1:4,7:11:99:282,0,100:0,4,0,7 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 0/1:8,9:17:99:273,0,214:2,6,2,7 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 0/1:33,25:58:99:644,0,911:19,14,17,8 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 0/1:35,19:54:99:317,0,851:20,15,11,8 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 0/1:56,39:95:99:902,0,1454:27,29,18,21 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 0/1:15,19:34:99:602,0,377:6,9,8,11 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 0/1:9,6:15:99:181,0,315:8,1,5,1 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 0/1:38,37:75:99:947,0,1001:24,14,25,12 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 0/1:15,34:49:99:917,0,370:4,11,11,23 chr2 103036335 . A G 91.72 PASS AC=1;AF=0.75;AN=2;DP=197;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant19-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant31-variant34-variant36-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:2,4:6:61:121,0,61:0,2,1,3 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 0/1:22,24:46:99:699,0,582:16,6,18,6 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 0/1:13,17:30:99:666,0,951:12,1,13,4 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 0/1:15,17:32:99:666,0,951:14,1,13,4 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 0/1:17,13:30:99:370,0,491:14,3,10,3 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 0/1:29,17:46:99:422,0,808:20,9,10,7 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 1/1:0,71:71:99:2235,213,0:0,0,38,33 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 0/1:12,17:29:99:482,0,332:9,3,11,6 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 0/1:54,34:88:99:804,0,1413:33,21,21,13 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 0/1:67,50:117:99:1170,0,1755:38,29,26,24 chr2 103089678 . C T 33.51 PASS AC=1;AF=0.536;AN=2;DP=104;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant5-variant17-variant18-variant20-variant22-variant23-variant24-variant32-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:4,3:7:73:73,0,162:2,2,2,1 chr2 103090127 . C T 495.65 PASS AC=1;AF=0.548;AN=2;DP=945;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant17-variant18-variant20-variant22-variant23-variant24-variant30-variant31-variant32-variant37-variant38-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,18:43:99:553,0,661:12,13,7,11 chr2 103095404 . G A 883.53 PASS AC=1;AF=0.603;AN=2;DP=4959;MQ=60;set=variant-variant2-variant3-variant4-variant7-variant9-variant10-variant12-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,67:126:99:1627,0,1379:29,30,37,30 chr2 103120232 . G A 2821.58 PASS AC=2;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 1/1:0,63:63:99:2122,189,0:0,0,20,43 chr2 103120311 . G A 1160.03 PASS AC=2;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 1/1:0,17:17:51:612,51,0:0,0,3,14 chr2 103120356 . C T 412.43 PASS AC=2;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 1/1:0,7:7:21:285,21,0:0,0,0,7 chr2 103121536 . G A 154.82 PASS AC=2;AF=0.742;AN=2;DP=422;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:48:570,48,0:0,0,13,3 chr2 103125182 . C T 148.54 PASS AC=2;AF=0.855;AN=2;DP=168;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant30-variant31-variant32-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:334,24,0:0,0,8,0 chr2 103125457 . A G 2991.22 PASS AC=2;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 1/1:0,43:43:99:1874,129,0:0,0,19,24 chr2 103125466 . T C 2921.46 PASS AC=2;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 1/1:0,41:41:99:1874,129,0:0,0,18,23 chr2 103128866 . T C 1254.92 PASS AC=2;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 1/1:0,45:45:99:1416,134,0:0,0,14,31 chr2 103136309 . T C 2787 PASS AC=2;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 1/1:0,111:111:99:3245,333,0:0,0,53,58 chr2 103136446 . T G 1408.49 PASS AC=2;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 1/1:0,41:41:99:1339,123,0:0,0,12,29 chr2 103141447 . A G 662.4 PASS AC=2;AF=0.716;AN=2;DP=3008;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2587,275,0:0,0,52,40 chr2 103141651 . G C 658.03 PASS AC=2;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 1/1:0,21:21:63:705,63,0:0,0,7,14 chr2 103149100 . G A 780.66 PASS AC=2;AF=0.716;AN=2;DP=2973;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2541,239,0:0,0,36,44 chr2 103149162 . A G 1092.38 PASS AC=2;AF=0.716;AN=2;DP=2732;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2354,216,0:0,0,35,37 chr2 103149182 . A G 1130.59 PASS AC=2;AF=0.716;AN=2;DP=2700;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2299,201,0:0,0,33,34 chr2 103149698 . A C 272.24 PASS AC=2;AF=0.703;AN=2;DP=1498;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:902,78,0:0,0,8,18 chr2 103281417 . A C 763.77 PASS AC=1;AF=0.673;AN=2;DP=880;MQ=60;set=variant-variant3-variant4-variant5-variant8-variant10-variant11-variant12-variant13-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant28-variant29-variant31-variant32-variant34-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,16:29:99:465,0,319:9,4,11,5 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 1/1:0,8:8:24:351,24,0:0,0,0,8 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 0/1:13,13:26:99:414,0,456:12,1,11,2 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 0/1:38,43:81:99:1036,0,810:22,16,25,18 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 0/1:19,26:45:99:646,0,552:6,13,10,16 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 0/1:10,16:26:99:410,0,255:8,2,8,8 chr2 103300506 . A G 1152.38 PASS AC=2;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 1/1:0,77:77:99:2489,231,0:0,0,46,31 chr2 103317676 . A G 697.62 PASS AC=1;AF=0.5;AN=2;DP=97;FractionInformativeReads=1;MQ=60;set=variant12-variant23 GT:AD:DP:GQ:PL:SB 0/1:27,17:44:99:367,0,597:10,17,7,10 chr2 103324575 . T C 599.69 PASS AC=1;AF=0.591;AN=2;DP=764;MQ=60;set=variant4-variant6-variant7-variant10-variant12-variant13-variant15-variant20-variant21-variant22-variant23-variant25-variant26-variant31-variant32-variant33-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,23:32:99:556,0,232:6,3,14,9 chr2 103326908 . TAA T 2779.47 PASS AC=1;AF=0.591;AN=2;DP=2694;MQ=60;set=variant4-variant6-variant7-variant10-variant12-variant13-variant15-variant20-variant21-variant22-variant23-variant25-variant26-variant31-variant32-variant33-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,63:129:99:2427,0,2639:36,30,33,30 chr2 103327241 . G C 1660.18 PASS AC=1;AF=0.568;AN=2;DP=2988;MQ=60;set=variant4-variant6-variant7-variant10-variant12-variant13-variant15-variant20-variant21-variant22-variant23-variant25-variant26-variant31-variant32-variant33-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:67,48:115:99:1237,0,1956:40,27,25,23 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 0/1:150,167:317:99:4121,0,3826:78,72,91,76 chr2 103333230 . A G 2402.65 PASS AC=1;AF=0.568;AN=2;DP=3848;MQ=60;set=variant4-variant6-variant7-variant10-variant12-variant13-variant15-variant20-variant21-variant22-variant23-variant25-variant26-variant31-variant32-variant33-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:71,84:155:99:1957,0,1469:34,37,38,46 chr2 103333544 . A T 89.18 PASS AC=2;AF=0.676;AN=2;DP=106;FractionInformativeReads=1;MQ=60;set=variant6-variant7-variant10-variant12-variant13-variant15-variant21-variant23-variant25-variant26-variant31-variant32-variant33-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:90,6,0:0,0,0,2 chr2 103343234 . G C 194.35 PASS AC=1;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 0/1:6,4:10:99:147,0,201:5,1,3,1 chr2 103343275 . GAA GA,GAAA,G 202.4 PASS AC=1,0,0;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 0/1:21:76:9,4,6,2 chr2 103343603 . TCA T 852.06 PASS AC=1;AF=0.5;AN=2;DP=75;FS=2.205;FractionInformativeReads=0.907;MQ=60;MQRankSum=-1.458;QD=11.36;ReadPosRankSum=0.814;SOR=0.419;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:42,26:68:99:889,0,1534:13,29,10,16 chr2 103375056 . T G 1464.67 PASS AC=1;AF=0.63;AN=2;DP=3306;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant34-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:72,54:126:99:1339,0,1800:32,40,27,27 chr2 103378581 . CT C 305.07 PASS AC=1;AF=0.606;AN=2;DP=1369;set=variant-variant2-variant3-variant4-variant5-filterInvariant6-variant7-variant8-variant9-variant10-variant11-filterInvariant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant31-variant34-filterInvariant37-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:12,21:33:99:420,0,194:9,3,12,9 chr2 103378857 . C G 1165.62 PASS AC=1;AF=0.63;AN=2;DP=2500;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant34-variant38-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:29,40:69:99:1224,0,770:8,21,9,31 chr2 103380998 . C G 430.38 PASS AC=1;AF=0.595;AN=2;DP=793;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant27-variant28-variant30-variant34-variant39 GT:AD:DP:GQ:PL:SB 0/1:15,9:24:99:292,0,479:3,12,2,7 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 1/1:0,231:231:99:6759,690,0:0,0,114,117 chr2 103432318 . T C 6234.7 PASS AC=1;AF=0.641;AN=2;DP=5084;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant30-variant34-variant36-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:80,72:152:99:1949,0,2107:51,29,48,24 chr2 103432337 . A G 8486.27 PASS AC=1;AF=0.615;AN=2;DP=5751;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant27-variant28-variant30-variant34-variant36-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:103,104:207:99:2726,0,2608:63,40,66,38 chr2 103433624 . T A 8351.41 PASS AC=1;AF=0.611;AN=2;DP=7718;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant10-variant11-variant13-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant27-variant28-variant30-variant34-variant36-variant37-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:119,119:238:99:3110,0,3028:49,70,51,68 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 1/1:0,14:14:42:380,42,0:0,0,6,8 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 1/1:0,39:39:99:1027,116,0:0,0,19,20 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 1/1:0,166:166:99:5001,497,0:0,0,77,89 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 1/1:0,127:127:99:3799,380,0:0,0,54,73 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 1/1:0,88:88:99:2630,264,0:0,0,54,34 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 1/1:0,92:92:99:2654,274,0:0,0,45,47 chr2 105654446 . A G 891.84 PASS AC=2;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 1/1:0,75:75:99:2311,225,0:0,0,39,36 chr2 105654716 . C T 935.02 PASS AC=2;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 1/1:0,123:123:99:3723,369,0:0,0,49,74 chr2 105654830 . G T 220.9 PASS AC=2;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 1/1:0,30:30:90:1134,90,0:0,0,5,25 chr2 105696591 . C T 230.44 PASS AC=2;AF=0.625;AN=2;DP=167;FractionInformativeReads=1;MQ=60;set=variant2-variant11-variant15-variant17-variant21-variant23-variant37-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:620,45,0:0,0,1,14 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 1/1:0,64:64:99:1944,192,0:0,0,22,42 chr2 105881486 . A G 4500.79 PASS AC=1;AF=0.5;AN=2;DP=1265;MQ=60;set=variant10-variant23-variant31-variant34 GT:AD:DP:GQ:PL:SB 0/1:143,145:288:99:3558,0,3566:76,67,74,71 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 0/1:91,98:189:99:2601,0,2251:51,40,58,40 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 0/1:25,22:47:99:488,0,738:9,16,10,12 chr2 105883624 . TTTCCATGTACATTCATAGAGCCTGGTCA T 2297.15 PASS AC=1;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 0/1:64,21:85:99:634,0,4196:36,28,11,10 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 0/1:40,46:86:99:1167,0,1082:22,18,22,24 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 0/1:51,76:127:99:1958,0,1180:26,25,32,44 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 1/1:0,32:32:93:867,93,0:0,0,11,21 chr2 105924017 . C T 398.32 PASS AC=2;AF=0.605;AN=2;DP=688;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant12-variant16-variant18-variant20-variant21-variant23-variant25-variant31-variant32-variant34-variant37-variant38 GT:AD:DP:GQ:PL:SB 1/1:0,27:27:81:787,81,0:0,0,16,11 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 1/1:0,123:123:99:5058,382,0:0,0,72,51 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 1/1:0,123:123:99:5419,375,0:0,0,40,83 chr2 105974162 . CT C 960.69 PASS AC=1;AF=0.556;AN=2;DP=1098;MQ=60;set=variant-variant5-variant6-filterInvariant7-variant9-variant12-variant15-variant16-variant18-variant23-variant24-variant25-variant28-variant31-variant34-variant37-variant38-filterInvariant43 GT:AD:DP:GQ:PL:SB 0/1:24,33:57:99:686,0,453:19,5,23,10 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 0/1:55,39:94:99:916,0,1518:24,31,22,17 chr2 105975463 . G A 542.23 PASS AC=1;AF=0.563;AN=2;DP=1022;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant9-variant12-variant15-variant16-variant18-variant19-variant23-variant25-variant28-variant31-variant34-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:33,17:50:99:381,0,946:16,17,8,9 chr2 105975550 . G A 938.45 PASS AC=1;AF=0.563;AN=2;DP=1422;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant9-variant12-variant15-variant16-variant18-variant19-variant23-variant25-variant28-variant31-variant34-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:29,28:57:99:770,0,826:15,14,18,10 chr2 105975656 . CT C 3214.26 PASS AC=1;AF=0.563;AN=2;DP=3168;MQ=60;set=variant-variant5-variant6-variant9-variant12-variant15-variant16-variant18-variant19-variant23-variant25-variant28-variant31-variant34-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:92,73:165:99:2411,0,3158:50,42,39,34 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 1/1:0,32:32:96:976,96,0:0,0,13,19 chr2 105977761 . G A 1317.13 PASS AC=1;AF=0.563;AN=2;DP=2071;MQ=60;set=variant-variant5-variant6-variant9-variant12-variant15-variant16-variant18-variant19-variant23-variant25-variant28-variant31-variant34-variant37-variant38 GT:AD:DP:GQ:PL:SB 0/1:45,58:103:99:1472,0,1161:21,24,28,30 chr2 105979599 . C CAGAT 316.48 PASS AC=1;AF=0.5;AN=2;DP=140;MQ=60;set=variant3-variant4-variant8-variant17-variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:13,6:19:99:255,0,720:11,2,5,1 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 0/1:92,93:185:99:2188,0,2134:54,38,53,40 chr2 105979752 . G A 2502.26 PASS AC=1;AF=0.5;AN=2;DP=214;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.8;QD=11.69;ReadPosRankSum=1.368;SOR=0.676;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:103,111:214:99:2530,0,2259:58,45,62,49 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 0/1:5,5:10:99:132,0,113:4,1,4,1 chr2 105994498 . C A 1477.47 PASS AC=1;AF=0.5;AN=2;DP=666;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant23-variant25-variant30-variant42 GT:AD:DP:GQ:PL:SB 0/1:53,62:115:99:1590,0,1265:32,21,34,28 chr2 106006876 . C T 118.41 PASS AC=1;AF=0.688;AN=2;DP=150;MQ=60;set=variant2-variant3-variant4-variant7-variant12-variant14-variant17-variant21-variant22-variant23-variant24-variant25-variant27-variant28-variant30-variant40 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:72:154,0,72:2,2,1,4 chr2 106013216 . T C 4622.78 PASS AC=2;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 1/1:0,291:291:99:9153,871,0:0,0,151,140 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 0/1:150,173:323:99:4210,0,3565:75,75,86,87 chr2 106013467 . GTTT G,GTT,GTTTTTTT,GTTTTTT,GTTTT,GTTTTT 66.54 PASS AC=0,0,0,1,0,0;AF=0.017,0.267,0.033,0.083,0.1,0.117;AN=2;DP=672;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant34-variant37-variant40-variant41-variant43 GT:DP:GQ:SB 0/4:11:88:0,3,1,7 chr2 106015412 . G C 3111.41 PASS AC=1;AF=0.5;AN=2;DP=963;MQ=60;set=variant4-variant7-variant23-variant25-variant30-variant33 GT:AD:DP:GQ:PL:SB 0/1:69,90:159:99:2690,0,1946:43,26,59,31 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 1/1:0,17:17:51:519,51,0:0,0,11,6 chr2 106468480 . T A 108.25 PASS AC=1;AF=0.5;AN=2;DP=19;FS=0;FractionInformativeReads=1;MQ=60;set=variant12-variant23 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:154,0,115:2,3,1,4 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 1/1:0,30:30:90:1175,90,0:0,0,25,5 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 1/1:0,82:82:99:2394,246,0:0,0,49,33 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 1/1:24:50:0,2,5,17 chr2 106509907 . C T 772.61 PASS AC=1;AF=0.571;AN=2;DP=1554;MQ=60;set=variant-variant5-variant6-variant8-variant12-variant13-variant14-variant15-variant20-variant22-variant23-variant24-variant26-variant29-variant30-variant32-variant38-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,23:63:99:656,0,1054:17,23,6,17 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 1/1:0,84:84:99:4015,273,0:0,0,55,29 chr2 106510455 . G GCA,GCACA 516.29 PASS AC=1,1;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 1/2:18:99:0,1,4,13 chr2 106679686 . C T 291.16 PASS AC=1;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 0/1:11,6:17:99:138,0,284:7,4,3,3 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 0/1:25,33:58:99:739,0,552:9,16,14,19 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 1/1:0,29:29:86:1072,86,0:0,0,4,25 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 0/1:6,10:16:99:225,0,143:2,4,4,6 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 1/1:0,8:8:24:222,24,0:0,0,5,3 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 1/1:0,180:180:99:5596,540,0:0,0,111,69 chr2 106710665 . C T 461.4 PASS AC=1;AF=0.5;AN=2;DP=87;FractionInformativeReads=1;MQ=60;set=variant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:22,25:47:99:747,0,624:6,16,6,19 chr2 106710668 . C CGCAGGAAGGAAGTGCCACCTT 1119.91 PASS AC=2;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 1/1:0,17:17:43:664,43,0:0,0,5,12 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 1/1:35:99:0,0,11,24 chr2 106717171 . T C 218.84 PASS AC=2;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 1/1:0,4:4:12:180,12,0:0,0,4,0 chr2 106717274 . A G 965.78 PASS AC=2;AF=0.818;AN=2;DP=1642;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:864,84,0:0,0,19,9 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 0/1:2,8:10:31:201,0,31:1,1,1,7 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 1/1:0,83:83:99:2432,249,0:0,0,42,41 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 1/1:0,67:67:99:1946,200,0:0,0,31,36 chr2 106754734 . A G 2276.93 PASS AC=1;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 0/1:57,41:98:99:1025,0,1583:32,25,22,19 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 1/1:0,16:16:48:513,48,0:0,0,10,6 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 1/1:0,28:28:90:1309,90,0:0,0,15,13 chr2 106781332 . C T 1485.65 PASS AC=1;AF=0.5;AN=2;DP=376;FractionInformativeReads=1;MQ=60;set=variant-variant17-variant23-variant32 GT:AD:DP:GQ:PL:SB 0/1:38,40:78:99:979,0,849:19,19,22,18 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 1/1:0,19:19:57:629,57,0:0,0,12,7 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 1/1:0,352:352:99:9771,1052,0:0,0,146,206 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 1/1:0,27:27:81:959,81,0:0,0,20,7 chr2 107007576 . A T 811.98 PASS AC=1;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 0/1:18,18:36:99:545,0,614:2,16,3,15 chr2 107007994 . TA T,TAA 341.34 PASS AC=1,0;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 0/1:24:99:7,7,3,7 chr2 107008058 . A G 785.8 PASS AC=1;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 0/1:9,3:12:59:59,0,203:5,4,2,1 chr2 107008153 . C A 51.92 PASS AC=1;AF=0.8;AN=2;DP=24;FractionInformativeReads=1;set=variant19-variant22-variant23-variant28-variant37 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:82:82,0,141:1,5,2,1 chr2 107032279 . T C 3636.03 PASS AC=1;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 0/1:82,51:133:99:1047,0,2112:49,33,29,22 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 0/1:49,30:79:99:680,0,1331:16,33,10,20 chr2 107039817 . G A 243.32 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=521;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:40,8:48:70:70,0,890:11,29,2,6 chr2 107049714 . C G 204.26 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2185;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:36,29:65:99:554,0,825:7,29,12,17 chr2 107050624 . G A 206.23 PASS AC=1;AF=0.5;AN=2;DP=58;FractionInformativeReads=1;set=filterInvariant11-filterInvariant22-variant23 GT:AD:DP:GQ:PL:SB 0/1:12,6:18:99:114,0,295:9,3,3,3 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 0/1:43,30:73:99:622,0,900:22,21,17,13 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 0/1:43,33:76:99:612,0,899:21,22,15,18 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 0/1:67,53:120:99:1362,0,1628:31,36,21,32 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 0/1:21,12:33:99:389,0,676:5,16,2,10 chr2 107107511 . C T 1431.04 PASS AC=1;AF=0.5;AN=2;DP=1694;set=variant-variant8-variant11-variant21-variant22-variant23-variant26-variant32-variant36 GT:AD:DP:GQ:PL:SB 0/1:93,86:179:99:2122,0,2341:51,42,45,41 chr2 107107567 . G C 2856.18 PASS AC=1;AF=0.682;AN=2;DP=6698;set=variant-variant2-variant3-variant5-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant36-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:105,79:184:99:1860,0,2653:48,57,35,44 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 1/1:0,29:29:87:1162,87,0:0,0,1,28 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 1/1:0,26:26:78:886,78,0:0,0,19,7 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 1/1:0,29:29:87:911,87,0:0,0,9,20 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 1/1:1,28:29:61:799,61,0:0,1,14,14 chr2 107123363 . A T 167.55 PASS AC=1;AF=0.591;AN=2;DP=691;FractionInformativeReads=1;set=variant2-variant3-variant4-filterInvariant7-filterInvariant9-variant10-filterInvariant12-variant13-filterInvariant14-variant15-variant16-variant17-filterInvariant18-variant21-variant23-variant28-variant29-variant30-variant34-variant38-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:22,13:35:99:258,0,530:10,12,8,5 chr2 107418036 . T C 399.49 PASS AC=1;AF=0.708;AN=2;DP=396;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,5:7:70:160,0,70:1,1,4,1 chr2 107418902 . C CT 1947.88 PASS AC=1;AF=0.591;AN=2;DP=2036;MQ=60;set=variant5-variant8-variant10-variant11-variant23-variant24-variant31-variant36-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:81,70:151:99:1522,0,1861:53,28,45,25 chr2 107420068 . TAACAACAAC TAAC,TAACAAC,T 59.04 PASS AC=0,1,0;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 0/2:12:99:0,5,2,5 chr2 107420143 . C T 409.26 PASS AC=1;AF=0.711;AN=2;DP=750;FractionInformativeReads=1;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-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,14:23:99:451,0,319:4,5,8,6 chr2 107420409 . T C 4996.99 PASS AC=1;AF=0.744;AN=2;DP=14314;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-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:162,133:295:99:3065,0,4120:92,70,78,55 chr2 107421297 . CAA CAAA,CAAAA,CAAAAA,C 1002.71 PASS AC=0,1,0,0;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 0/2:18:19:3,0,13,2 chr2 107423188 . G A 2630.99 PASS AC=1;AF=0.697;AN=2;DP=7127;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-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:94,73:167:99:1824,0,2473:39,55,33,40 chr2 107423395 . T G 847.73 PASS AC=1;AF=0.75;AN=2;DP=3447;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-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,44:83:99:1162,0,939:19,20,20,24 chr2 107429570 . GT GTT,G 74.02 PASS AC=0,1;AF=0.419,0.081;AN=2;DP=5575;set=filterInvariant-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-variant7-filterInvariant8-filterInvariant9-filterInvariant10-filterInvariant11-variant14-filterInvariant16-variant20-filterInvariant22-filterInvariant23-filterInvariant24-filterInvariant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant33-filterInvariant34-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-variant40-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/2:107:99:31,54,4,18 chr2 107429801 . C T 315.57 PASS AC=2;AF=0.805;AN=2;DP=1090;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-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:504,39,0:0,0,1,12 chr2 107446396 . T C 504.4 PASS AC=2;AF=0.837;AN=2;DP=797;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:865,72,0:0,0,18,6 chr2 107446430 . T C 863.3 PASS AC=2;AF=0.852;AN=2;DP=1367;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1211,117,0:0,0,23,16 chr2 107449321 . A T 326.37 PASS AC=2;AF=0.924;AN=2;DP=303;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant27-variant28-variant29-variant30-variant31-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:107,12,0:0,0,2,2 chr2 107460474 . T G 943.97 PASS AC=1;AF=0.681;AN=2;DP=4161;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:42,55:97:99:1322,0,920:15,27,21,34 chr2 107503324 . C T 587.2 PASS AC=2;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 1/1:0,6:6:18:228,18,0:0,0,6,0 chr2 108443325 . T C 950.21 PASS AC=2;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 1/1:0,20:20:63:931,63,0:0,0,16,4 chr2 108443328 . A T 950.21 PASS AC=2;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 1/1:0,21:21:63:931,63,0:0,0,17,4 chr2 108443511 . C G 2043.16 PASS AC=2;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 1/1:0,133:133:99:3928,398,0:0,0,67,66 chr2 108443567 . G A 2302.57 PASS AC=2;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 1/1:0,105:105:99:4366,315,0:0,0,49,56 chr2 108443591 . A C 2109.33 PASS AC=2;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 1/1:0,85:85:99:3820,259,0:0,0,40,45 chr2 108443598 . G C 1875.42 PASS AC=2;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 1/1:0,84:84:99:3750,253,0:0,0,39,45 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 1/1:2,32:34:53:1044,53,0:1,1,10,22 chr2 108475928 . C T 136.19 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=2492;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:192,38:230:99:280,0,4538:99,93,19,19 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 0/1:36,175:211:99:4105,0,290:18,18,80,95 chr2 108479432 . G A 1634.17 DRAGENHardSNP AC=2;AF=0.738;AN=2;DP=3449;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,81:81:99:2148,242,0:0,0,31,50 chr2 108479487 . A T 835.5 PASS AC=2;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 1/1:0,41:41:99:1148,123,0:0,0,15,26 chr2 108487097 . G A 494.99 DRAGENHardSNP AC=2;AF=0.792;AN=2;DP=593;FS=0;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:632,69,0:0,0,23,0 chr2 108487330 . A G 3988.11 PASS AC=2;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 1/1:0,105:105:99:3093,315,0:0,0,38,67 chr2 108487826 . C T 468.16 DRAGENHardSNP AC=1;AF=0.886;AN=2;DP=451;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:2,19:21:36:679,0,36:1,1,2,17 chr2 108487829 . G C 435.64 PASS AC=1;AF=0.886;AN=2;DP=300;FractionInformativeReads=1;set=filterInvariant-filterInvariant3-variant4-filterInvariant5-filterInvariant6-filterInvariant9-filterInvariant11-filterInvariant12-filterInvariant15-filterInvariant16-filterInvariant19-filterInvariant21-filterInvariant22-variant23-filterInvariant24-filterInvariant25-filterInvariant27-filterInvariant32-filterInvariant37-filterInvariant38-filterInvariant41-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:2,13:15:42:635,0,42:1,1,0,13 chr2 108488742 . G T 1521.36 DRAGENHardSNP AC=2;AF=0.617;AN=2;DP=6994;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,209:209:99:5232,625,0:0,0,67,142 chr2 108496435 . T A 1775.19 PASS AC=2;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 1/1:0,39:39:99:1266,116,0:0,0,29,10 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 1/1:0,8:8:24:211,24,0:0,0,4,4 chr2 108507268 . T C 1338.11 PASS AC=2;AF=0.625;AN=2;DP=3205;set=variant-variant2-variant4-variant5-variant6-variant8-variant9-variant11-variant12-variant15-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant27-variant28-variant30-variant31-variant32-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,105:106:99:2725,270,0:0,1,53,52 chr2 108520467 . A G 52.1 PASS AC=1;AF=0.5;AN=2;DP=70;FractionInformativeReads=1;set=variant3-variant21-variant23-variant25-variant41 GT:AD:DP:GQ:PL:SB 0/1:7,2:9:60:60,0,339:4,3,2,0 chr2 108618128 . CA CAA,CAAAA,C,CAAA 96.4 PASS AC=0,0,1,0;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 0/3:13:91:6,1,5,1 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 1/1:0,42:42:99:1817,127,0:0,0,8,34 chr2 108627917 . G A 8271.95 PASS AC=2;AF=0.875;AN=2;DP=27575;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,468:469:99:14483,1392,0:0,1,232,236 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 0/1:53,50:103:99:1935,0,2737:26,27,28,22 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 0/1:54,51:105:99:1935,0,2737:27,27,29,22 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 1/1:0,143:143:99:4526,428,0:0,0,88,55 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 0/1:172,197:369:99:4772,0,3920:92,80,100,97 chr2 108863650 . A C 898.95 PASS AC=2;AF=0.667;AN=2;DP=1296;FractionInformativeReads=1;MQ=60;set=variant2-variant8-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant34-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2341,228,0:0,0,48,28 chr2 108863767 . A C 1599.65 PASS AC=2;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 1/1:0,127:127:99:3669,381,0:0,0,59,68 chr2 108868736 . G A 135.18 PASS AC=2;AF=0.667;AN=2;DP=249;MQ=60;set=variant2-variant8-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant23-variant26-variant28-variant34-variant36-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,21:21:63:783,63,0:0,0,17,4 chr2 108875464 . AAAACTTGGTCAGGTGATGTTAT A 2767.1 PASS AC=2;AF=0.65;AN=2;DP=3127;set=variant2-variant8-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant26-variant28-variant34-variant36-variant37-variant38-variant39-variant40 GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:4480,305,0:0,0,45,55 chr2 108876948 . C T 70.21 PASS AC=2;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 1/1:0,7:7:21:219,21,0:0,0,6,1 chr2 108877062 . T A 680.67 PASS AC=2;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 1/1:0,72:72:99:2219,216,0:0,0,45,27 chr2 108915136 . T C 408.15 PASS AC=2;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 1/1:0,38:38:99:1058,114,0:0,0,18,20 chr2 108915263 . C T 306.94 PASS AC=2;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 1/1:0,19:19:57:580,57,0:0,0,7,12 chr2 108925572 . G A 687.84 PASS AC=2;AF=0.593;AN=2;DP=1456;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant34-variant36-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1541,159,0:0,0,24,29 chr2 108925780 . T C 1255.78 PASS AC=2;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 1/1:0,32:32:96:1427,96,0:0,0,13,19 chr2 108925786 . CT C 642.84 PASS AC=2;AF=0.593;AN=2;DP=1050;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant8-variant12-variant13-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant28-variant29-variant30-variant32-variant34-variant36-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,30:30:93:1392,93,0:0,0,13,17 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 0/1:19:99:8,3,5,3 chr2 109065123 . C T 1774.33 PASS AC=2;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 1/1:1,176:177:99:5059,517,0:0,1,81,95 chr2 109065481 . C CA 1690.71 PASS AC=2;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 1/1:0,131:131:99:4925,397,0:0,0,75,56 chr2 109065858 . T C 1330.13 PASS AC=2;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 1/1:0,74:74:99:2529,222,0:0,0,26,48 chr2 109065919 . T C 1054.47 PASS AC=2;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 1/1:0,69:69:99:2262,207,0:0,0,36,33 chr2 109067337 . C T 148.64 PASS AC=2;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 1/1:0,11:11:33:436,33,0:0,0,10,1 chr2 109067359 . G A 293.44 PASS AC=2;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 1/1:0,23:23:75:1095,75,0:0,0,18,5 chr2 109067360 . T A 293.44 PASS AC=2;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 1/1:0,25:25:75:1095,75,0:0,0,19,6 chr2 109069008 . T C 535.67 PASS AC=2;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 1/1:0,21:21:63:677,63,0:0,0,7,14 chr2 109085373 . A G 1707.71 PASS AC=2;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 1/1:0,123:123:99:3532,369,0:0,0,65,58 chr2 109089404 . C G 560.22 PASS AC=2;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 1/1:0,26:26:78:927,78,0:0,0,7,19 chr2 109092121 . G A 765.17 PASS AC=2;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 1/1:1,48:49:99:1435,101,0:1,0,24,24 chr2 109098994 . T C 205.39 PASS AC=2;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 1/1:0,9:9:27:353,27,0:0,0,1,8 chr2 109099477 . A G 671.97 PASS AC=2;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 1/1:0,57:57:99:1637,170,0:0,0,30,27 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 1/1:0,42:42:99:1204,126,0:0,0,18,24 chr2 109103108 . C T 883.77 PASS AC=2;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 1/1:0,70:70:99:2270,210,0:0,0,22,48 chr2 109104356 . ATT AT,A 164.51 PASS AC=1,0;AF=0.35,0.15;AN=2;DP=1227;set=variant3-variant4-filterInvariant5-variant7-variant11-variant13-variant15-variant19-filterInvariant21-filterInvariant22-variant23-filterInvariant28-filterInvariant29-filterInvariant30-variant32-variant33-variant36-filterInvariant40-filterInvariant42-filterInvariant43 GT:DP:GQ:SB 0/1:18:76:2,5,1,10 chr2 109106381 . A G 1139.85 PASS AC=2;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 1/1:0,53:53:99:1585,159,0:0,0,32,21 chr2 109116613 . CAT C 551.74 PASS AC=2;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 1/1:0,18:18:54:769,54,0:0,0,9,9 chr2 109123950 . T A 167.47 PASS AC=2;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 1/1:0,10:10:30:317,30,0:0,0,6,4 chr2 109123988 . C CT,CTT 180.8 PASS AC=2,0;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 1/1:16:20:1,0,9,6 chr2 109204726 . GA G 32.38 PASS AC=2;AF=0.917;AN=2;DP=95;FS=0;MQ=60;set=variant2-variant3-variant4-variant7-variant11-variant14-variant20-variant21-variant22-variant23-variant24-variant25-variant32-variant33-variant37-variant39-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:85,9,0:0,0,2,1 chr2 109277239 . C T 865.51 PASS AC=2;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 1/1:0,48:48:99:1302,143,0:0,0,21,27 chr2 109278693 . A G 122.07 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=109;FS=7.497;FractionInformativeReads=1;MQ=46.15;MQRankSum=-1.781;QD=1.12;ReadPosRankSum=-2.781;SOR=2.136;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:96,13:109:99:150,0,2702:68,28,12,1 chr2 109278823 . T C 1151.83 PASS AC=1;AF=0.5;AN=2;DP=12425;set=variant2-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant16-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant36-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:323,95:418:99:1172,0,7631:155,168,44,51 chr2 109292280 . T C 4280.65 PASS AC=2;AF=0.943;AN=2;DP=8245;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,189:190:99:5433,543,0:0,1,111,78 chr2 109292979 . T C 160.38 PASS AC=2;AF=0.792;AN=2;DP=116;FractionInformativeReads=1;set=filterInvariant2-variant8-variant11-variant17-variant20-variant21-filterInvariant23-filterInvariant29-variant30-filterInvariant37-variant39-filterInvariant41 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:99,12,0:0,0,2,2 chr2 109294588 . A T 1412.03 PASS AC=2;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 1/1:0,92:92:99:2754,275,0:0,0,35,57 chr2 109296984 . C A 157.99 PASS AC=2;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 1/1:0,3:3:9:124,9,0:0,0,3,0 chr2 109297018 . AAAG A 713.21 PASS AC=2;AF=1;AN=2;DP=23;FS=0;FractionInformativeReads=1;MQ=50.81;QD=31.01;SOR=1.708;set=variant23 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:68:750,68,0:0,0,16,7 chr2 109301115 . T TA 2873.56 PASS AC=2;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 1/1:0,128:128:99:5179,385,0:0,0,61,67 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 1/1:0,428:428:99:13289,1284,0:0,0,208,220 chr2 109301841 . G A 4825.37 PASS AC=2;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 1/1:0,307:307:99:9158,919,0:0,0,143,164 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 0/1:9,13:22:99:354,0,212:6,3,9,4 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 0/1:20,29:49:99:620,0,507:5,15,12,17 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 0/1:25,25:50:99:656,0,676:20,5,19,6 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 0/1:13,7:20:99:195,0,343:11,2,7,0 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 0/1:30,12:42:99:284,0,807:22,8,12,0 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 0/1:32,39:71:99:1066,0,791:10,22,11,28 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 0/1:11,5:16:99:173,0,725:1,10,0,5 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 0/1:10,20:30:99:549,0,242:3,7,6,14 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 0/1:29,29:58:99:639,0,588:16,13,12,17 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 0/1:19,12:31:99:306,0,478:11,8,8,4 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 0/1:2,5:7:66:163,0,66:0,2,3,2 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 1/1:0,116:116:99:3342,347,0:0,0,51,65 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 1/1:0,33:33:99:1135,99,0:0,0,24,9 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 0/1:20,22:42:99:804,0,5810:4,16,3,19 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 0/1:19,19:38:99:804,0,5810:4,15,0,19 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 0/1:16,18:34:99:750,0,5592:3,13,0,18 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 0/1:14,17:31:99:672,0,5477:2,12,0,17 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 0/1:14,17:31:99:672,0,5477:2,12,0,17 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 0/1:14,17:31:99:672,0,5477:2,12,0,17 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 0/1:12,15:27:99:636,0,5095:1,11,0,15 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 0/1:11,14:25:99:552,0,5101:1,10,0,14 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 0/1:9,13:22:99:561,0,4297:1,8,0,13 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 0/1:8,13:21:99:522,0,3924:1,7,0,13 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 0/1:173,167:340:99:4029,0,4173:85,88,85,82 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 0/1:174,161:335:99:6333,0,8326:87,87,83,78 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 0/1:40,23:63:99:829,0,2288:24,16,14,9 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 0/1:46,27:73:99:964,0,2409:28,18,18,9 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 0/1:15,9:24:99:176,0,343:6,9,6,3 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 0/1:24,34:58:99:816,0,526:12,12,13,21 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 0/1:4,7:11:99:282,0,236:0,4,0,7 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 0/1:38,38:76:99:934,0,761:23,15,24,14 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 1/1:0,13:13:39:564,39,0:0,0,3,10 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 0/1:80,73:153:99:1715,0,1735:37,43,34,39 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 0/1:19,28:47:99:716,0,511:6,13,8,20 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 0/1:4,5:9:99:131,0,114:2,2,3,2 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 0/1:138,130:268:99:3243,0,3417:64,74,61,69 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 0/1:33,18:51:99:420,0,767:15,18,9,9 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 0/1:36,46:82:99:1253,0,855:17,19,22,24 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 0/1:52,41:93:99:876,0,1167:21,31,16,25 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 0/1:2,4:6:58:121,0,58:1,1,1,3 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 0/1:21,23:44:99:551,0,591:17,4,15,8 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 0/1:15,8:23:99:155,0,299:10,5,5,3 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 0/1:84,106:190:99:2442,0,1982:47,37,58,48 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 0/1:56,43:99:99:1145,0,1371:24,32,15,28 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 0/1:60,56:116:99:1385,0,1591:31,29,30,26 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 0/1:36,18:54:99:473,0,944:22,14,11,7 chr2 109556667 . G C 2367.13 PASS AC=1;AF=0.55;AN=2;DP=581;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant14-variant17-variant18-variant23-variant29-variant31-variant33-variant36 GT:AD:DP:GQ:PL:SB 0/1:12,44:56:99:1048,0,232:8,4,24,20 chr2 109556761 . C T 2109.91 PASS AC=1;AF=0.563;AN=2;DP=519;MQ=60;set=variant4-variant7-variant17-variant23-variant29-variant31-variant33-variant36 GT:AD:DP:GQ:PL:SB 0/1:27,46:73:99:1194,0,539:15,12,19,27 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 1/1:0,15:15:45:610,45,0:0,0,12,3 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 1/1:0,66:66:99:2984,209,0:0,0,28,38 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 0/1:4,8:12:96:225,0,96:1,3,3,5 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 0/1:32,36:68:99:926,0,820:19,13,20,16 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 1/1:0,59:59:99:2249,177,0:0,0,9,50 chr2 110303072 . C T 1064.05 PASS AC=1;AF=0.5;AN=2;DP=598;MQ=60;set=variant23-variant28-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:65,46:111:99:1092,0,1717:24,41,18,28 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 1/1:0,114:114:99:3658,342,0:0,0,67,47 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 1/1:0,76:76:99:2305,228,0:0,0,45,31 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 0/2:17:98:6,2,8,1 chr2 110552183 . G C 104.67 PASS AC=2;AF=0.889;AN=2;DP=106;FS=0;set=variant-variant2-variant4-variant9-variant10-variant12-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant31-variant32-variant33-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:223,15,0:0,0,2,3 chr2 110552184 . GC G 95.64 PASS AC=2;AF=0.912;AN=2;DP=96;FS=0;set=variant-variant2-variant4-variant9-variant10-variant12-variant16-variant18-variant19-variant21-variant23-variant24-variant25-variant31-variant32-variant33-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:223,15,0:0,0,2,3 chr2 110855123 . G T 1199.86 PASS AC=2;AF=0.966;AN=2;DP=5600;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:2648,289,0:0,0,55,42 chr2 110855270 . TG T 2393.96 PASS AC=1;AF=0.605;AN=2;DP=1393;MQ=60;set=variant3-variant4-variant5-variant8-variant10-variant11-variant15-variant16-variant18-variant20-variant21-variant23-variant25-variant28-variant29-variant30-variant32-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:30,37:67:99:1074,0,769:12,18,14,23 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 0/1:105:99:34,32,23,16 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 1/1:0,70:70:99:2036,210,0:0,0,43,27 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 0/1:15,37:52:99:987,0,381:12,3,25,12 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 0/1:25,19:44:99:722,0,2416:16,9,10,9 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 0/1:5,5:10:99:143,0,199:5,0,4,1 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 0/1:10,21:31:99:557,0,266:2,8,7,14 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 0/1:10,9:19:99:267,0,258:7,3,7,2 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 0/1:15,10:25:99:245,0,430:4,11,3,7 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 0/1:71,52:123:99:1034,0,1588:35,36,24,28 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 0/1:105,121:226:99:3068,0,2472:46,59,54,67 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 0/1:39,40:79:99:1127,0,971:25,14,25,15 chr2 111058854 . G A 515.77 PASS AC=2;AF=0.984;AN=2;DP=820;FS=0;MQRankSum=4.4;ReadPosRankSum=1.156;set=filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-variant8-filterInvariant9-filterInvariant10-filterInvariant11-filterInvariant12-filterInvariant13-filterInvariant14-filterInvariant15-filterInvariant18-filterInvariant19-filterInvariant20-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant25-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant34-filterInvariant36-filterInvariant37-filterInvariant38-filterInvariant39-filterInvariant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:949,116,0:0,0,19,20 chr2 111526092 . A T 226.5 PASS AC=1;AF=0.5;AN=2;DP=74;MQ=60;set=variant11-variant23 GT:AD:DP:GQ:PL:SB 0/1:13,12:25:99:280,0,348:1,12,3,9 chr2 111562875 . C T 1544.36 PASS AC=1;AF=0.5;AN=2;DP=147;FS=2.082;FractionInformativeReads=1;MQ=60;MQRankSum=0.064;QD=10.51;ReadPosRankSum=-0.754;SOR=0.866;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:81,66:147:99:1573,0,1886:41,40,30,36 chr2 111644475 . C T 1383.01 PASS AC=1;AF=0.63;AN=2;DP=2340;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant17-variant19-variant22-variant23-variant25-variant29-variant31-variant32-variant36-variant37-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:40,44:84:99:1151,0,1096:16,24,20,24 chr2 111644491 . TA T 1164.58 PASS AC=1;AF=0.615;AN=2;DP=2405;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant17-variant19-variant21-variant22-variant23-variant25-variant29-variant31-variant32-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,38:77:99:1174,0,1223:16,23,18,20 chr2 111644595 . C T 294.44 PASS AC=1;AF=0.615;AN=2;DP=1544;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant13-variant14-variant17-variant19-variant21-variant22-variant23-variant25-variant29-variant31-variant32-variant36-variant37-variant38-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,23:45:99:616,0,535:10,12,9,14 chr2 111721142 . ATGTGTGTGTGTGTGTGTGTG ATGTGTGTGTGTGTG,ATGTGTGTGTGTGTGTG,A,ATGTGTGTGTGTGTGTGTGTGTGTG,ATGTGTGTGTGTGTGTGTG,ATGTGTGTGTGTG 1279.5 PASS AC=1,0,0,0,0,0;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 0/1:65:99:25,8,19,13 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 0/1:4,9:13:66:285,0,66:3,1,6,3 chr2 111851212 . C T 121.23 PASS AC=1;AF=0.531;AN=2;DP=311;FractionInformativeReads=1;set=variant-variant4-variant5-variant10-variant12-variant14-variant15-variant20-variant23-variant24-variant30-variant32-variant34-variant36-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:9,3:12:58:58,0,292:3,6,1,2 chr2 111851499 . A G 8467.19 PASS AC=1;AF=0.586;AN=2;DP=7215;MQ=60;set=variant-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant25-variant27-variant30-variant32-variant34-variant36-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:97,108:205:99:2824,0,2507:62,35,68,40 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 0/1:6,4:10:81:81,0,130:3,3,2,2 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 3/1:110:99:0,0,58,52 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 0/1:51,55:106:99:2098,0,1978:30,21,26,29 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 0/1:72,52:124:99:1960,0,2760:36,36,31,21 chr2 111881870 . CT C,CTT 178.95 PASS AC=1,0;AF=0.417,0.083;AN=2;DP=969;MQ=60;set=filterInvariant-filterInvariant2-filterInvariant3-variant10-filterInvariant22-variant23-filterInvariant24-filterInvariant26-filterInvariant29-filterInvariant32-filterInvariant43-filterInvariant44 GT:DP:GQ:SB 0/1:56:99:20,22,4,10 chr2 111886180 . CTT CT,CTTT,CTTTT,C 229.91 PASS AC=1,0,0,0;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 0/1:33:87:17,8,5,3 chr2 111909610 . A G 1454.07 PASS AC=1;AF=0.556;AN=2;DP=1082;MQ=60;set=variant3-variant4-variant17-variant18-variant19-variant23-variant25-variant31-variant37 GT:AD:DP:GQ:PL:SB 0/1:67,61:128:99:1454,0,1664:30,37,26,35 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 1/1:0,3:3:9:111,9,0:0,0,3,0 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 0/1:35,26:61:99:602,0,841:20,15,14,12 chr2 112588751 . C T 303.14 PASS AC=1;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 0/1:10,5:15:99:170,0,286:7,3,4,1 chr2 112590989 . A T 311.09 PASS AC=1;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 0/1:15,14:29:99:390,0,463:4,11,5,9 chr2 112605302 . C T 270.87 PASS AC=1;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 0/1:8,7:15:99:223,0,182:5,3,7,0 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 1/1:0,39:39:99:1174,117,0:0,0,15,24 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 1/1:0,4:4:12:170,12,0:0,0,0,4 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 1/1:0,3:3:9:135,9,0:0,0,0,3 chr2 112614598 . T C 49.73 PASS AC=2;AF=0.868;AN=2;DP=67;FS=0;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant7-variant9-variant11-variant14-variant19-variant22-variant23-variant27-variant31-variant34-variant37-variant38-variant39-variant40-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,0,3 chr2 112622593 . C A 284.61 PASS AC=1;AF=0.556;AN=2;DP=554;FractionInformativeReads=1;set=variant2-variant4-variant5-variant6-variant7-variant10-variant11-variant18-variant23-variant27-variant28-variant30-variant31-variant33-variant34-variant36-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,19:39:99:397,0,418:9,11,9,10 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 0/1:6,7:13:99:276,0,369:1,5,2,5 chr2 112622643 . A G 293.15 PASS AC=1;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 0/1:6,7:13:99:276,0,369:1,5,2,5 chr2 112622650 . T C 166.67 PASS AC=1;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 0/1:4,7:11:99:279,0,313:1,3,2,5 chr2 112625575 . T C 159.5 PASS AC=1;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 0/1:6,3:9:67:67,0,162:3,3,1,2 chr2 112630412 . A C 241.5 PASS AC=1;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 0/1:4,4:8:76:76,0,109:0,4,1,3 chr2 112636685 . G A 209.71 PASS AC=1;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 0/1:1,3:4:34:99,0,34:0,1,0,3 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 1/1:0,33:33:99:1301,99,0:0,0,10,23 chr2 112641257 . A G 422.73 PASS AC=1;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 0/1:15,17:32:99:428,0,439:3,12,6,11 chr2 112641283 . A G 362.35 PASS AC=1;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 0/1:9,8:17:99:257,0,305:1,8,2,6 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 0/1:24,24:48:99:571,0,610:11,13,12,12 chr2 112641854 . C T 1095.53 PASS AC=1;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 0/1:60,62:122:99:1409,0,1502:31,29,30,32 chr2 112641909 . C T 1108.61 PASS AC=1;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 0/1:69,55:124:99:1342,0,1701:37,32,27,28 chr2 112687157 . A ATATTTATTTATTTATT,ATATTTATTTATT,ATATTTATTTATTTATTTATTTATTTATT,ATATTTATTTATTTATTTATTTATT 159.23 PASS AC=0,2,0,0;AF=0.119,0.381,0.167,0.167;AN=2;DP=300;MQ=60;set=variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant13-variant15-variant17-variant19-variant21-variant23-variant24-variant26-variant29-variant30-variant33-variant37-variant43-variant44 GT:DP:GQ:SB 2/2:9:26:0,0,2,7 chr2 112704862 . A G,C 180.71 PASS AC=2,0;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 1/1:14:39:0,0,5,9 chr2 112705157 . T C 360.92 PASS AC=2;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 1/1:0,20:20:59:754,59,0:0,0,2,18 chr2 112705185 . G T 225.34 PASS AC=2;AF=0.743;AN=2;DP=830;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant29-variant30-variant32-variant33-variant34-variant37-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:424,30,0:0,0,0,10 chr2 112725684 . A ATGTGTG 1432.82 PASS AC=2;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 1/1:0,104:104:99:4720,324,0:0,0,68,36 chr2 112740373 . G A 309.33 PASS AC=2;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 1/1:0,19:19:57:674,57,0:0,0,14,5 chr2 112740596 . GA G 2496.4 PASS AC=2;AF=0.618;AN=2;DP=2454;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant11-variant12-variant17-variant19-variant20-variant22-variant23-variant30-variant33-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,124:124:99:5568,379,0:0,0,65,59 chr2 112740598 . T G 2505.45 PASS AC=2;AF=0.618;AN=2;DP=2446;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant11-variant12-variant17-variant19-variant20-variant22-variant23-variant30-variant33-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:5568,379,0:0,0,65,61 chr2 112751928 . G A 1279.96 PASS AC=2;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 1/1:0,147:147:99:4104,438,0:0,0,80,67 chr2 112752142 . A C 246.31 PASS AC=2;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 1/1:0,36:36:99:1261,107,0:0,0,7,29 chr2 112752880 . G A 1422.91 PASS AC=2;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 1/1:0,74:74:99:2228,221,0:0,0,40,34 chr2 112753020 . A G 2521.04 PASS AC=2;AF=0.618;AN=2;DP=2734;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant11-variant12-variant17-variant19-variant20-variant22-variant23-variant30-variant33-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,131:131:99:4035,392,0:0,0,64,67 chr2 112753097 . A C 1716.33 PASS AC=2;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 1/1:0,113:113:99:3439,339,0:0,0,44,69 chr2 112753781 . TA T 1610.55 PASS AC=2;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 1/1:0,67:67:99:2390,202,0:0,0,32,35 chr2 112753883 . C T 998.7 PASS AC=2;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 1/1:0,42:42:99:1467,126,0:0,0,20,22 chr2 112754828 . G T 1567.78 PASS AC=2;AF=0.618;AN=2;DP=1638;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant11-variant12-variant17-variant19-variant20-variant22-variant23-variant30-variant33-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2225,209,0:0,0,45,25 chr2 112755001 . A G 1207.29 PASS AC=2;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 1/1:0,102:102:99:3254,306,0:0,0,36,66 chr2 112758559 . T A 461.51 PASS AC=2;AF=0.588;AN=2;DP=334;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant11-variant12-variant17-variant19-variant20-variant22-variant23-variant30-variant33-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:807,72,0:0,0,17,7 chr2 112761653 . C G 582.43 PASS AC=2;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 1/1:0,27:27:81:1044,81,0:0,0,6,21 chr2 112765973 . A G 1065.66 PASS AC=2;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 1/1:0,73:73:99:2164,218,0:0,0,42,31 chr2 112766262 . A G 659.15 PASS AC=2;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 1/1:0,48:48:99:1526,143,0:0,0,24,24 chr2 112766304 . G C 634.52 PASS AC=2;AF=0.618;AN=2;DP=945;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant11-variant12-variant17-variant19-variant20-variant22-variant23-variant30-variant33-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,51:51:99:1566,152,0:0,0,25,26 chr2 112766319 . T C 556.48 PASS AC=2;AF=0.618;AN=2;DP=980;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant11-variant12-variant17-variant19-variant20-variant22-variant23-variant30-variant33-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1537,150,0:0,0,25,25 chr2 112767406 . A G 559.16 PASS AC=2;AF=0.618;AN=2;DP=383;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant11-variant12-variant17-variant19-variant20-variant22-variant23-variant30-variant33-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:366,30,0:0,0,8,2 chr2 112767483 . A G 1105.61 PASS AC=2;AF=0.618;AN=2;DP=1123;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant11-variant12-variant17-variant19-variant20-variant22-variant23-variant30-variant33-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,50:50:99:1534,150,0:0,0,31,19 chr2 112767739 . A G 1966.71 PASS AC=2;AF=0.625;AN=2;DP=2332;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant11-variant12-variant17-variant19-variant20-variant22-variant23-variant30-variant33-variant37-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,110:111:99:3324,297,0:1,0,51,59 chr2 112767824 . A G 1549.12 PASS AC=2;AF=0.618;AN=2;DP=1740;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant11-variant12-variant17-variant19-variant20-variant22-variant23-variant30-variant33-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,76:76:99:2250,228,0:0,0,33,43 chr2 112767941 . A G 859.71 PASS AC=2;AF=0.618;AN=2;DP=723;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant11-variant12-variant17-variant19-variant20-variant22-variant23-variant30-variant33-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1088,105,0:0,0,16,19 chr2 112770770 . A G 503.26 PASS AC=2;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 1/1:0,49:49:99:1519,147,0:0,0,27,22 chr2 112770798 . T C 1007.34 PASS AC=2;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 1/1:0,46:46:99:2048,138,0:0,0,23,23 chr2 112770799 . G A 1007.34 PASS AC=2;AF=0.567;AN=2;DP=1101;MQ=60;set=variant-variant4-variant5-variant7-variant11-variant12-variant17-variant19-variant20-variant22-variant23-variant30-variant33-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,46:46:99:2048,138,0:0,0,23,23 chr2 112773366 . A G 813.81 PASS AC=2;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 1/1:0,60:60:99:1819,180,0:0,0,32,28 chr2 112773500 . A G 1302.71 PASS AC=2;AF=0.625;AN=2;DP=1173;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant11-variant12-variant17-variant19-variant20-variant22-variant23-variant30-variant33-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,58:58:99:1676,174,0:0,0,29,29 chr2 112773528 . TCTTGTAC T 1456.67 PASS AC=2;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 1/1:0,44:44:99:1948,133,0:0,0,16,28 chr2 112776913 . T TC 631.67 PASS AC=2;AF=0.6;AN=2;DP=763;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant11-variant12-variant17-variant19-variant20-variant22-variant23-variant30-variant33-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1375,144,0:0,0,30,18 chr2 112776979 . C A 1147.38 PASS AC=2;AF=0.594;AN=2;DP=1308;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant11-variant12-variant17-variant19-variant20-variant22-variant23-variant30-variant33-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2165,202,0:0,0,35,33 chr2 112779286 . A ATC 407.07 PASS AC=2;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 1/1:0,11:11:33:448,33,0:0,0,1,10 chr2 112785770 . A G 151.64 PASS AC=2;AF=0.643;AN=2;DP=230;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant7-variant11-variant12-variant17-variant19-variant20-variant22-variant23-variant30-variant33-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:500,42,0:0,0,11,3 chr2 112786523 . A AT 1931.08 PASS AC=2;AF=0.633;AN=2;DP=2197;MQ=60;set=variant-variant3-variant4-variant5-variant7-variant11-variant12-variant17-variant19-variant20-variant22-variant23-variant30-variant33-variant43 GT:AD:DP:GQ:PL:SB 1/1:2,112:114:99:3679,274,0:1,1,43,69 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 1/1:0,14:14:42:496,42,0:0,0,2,12 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 1/1:0,75:75:99:2212,225,0:0,0,33,42 chr2 112874268 . T TTCCC,TC 107.5 PASS AC=0,1;AF=0.071,0.429;AN=2;DP=860;MQ=60;set=filterInvariant10-variant11-filterInvariant14-filterInvariant19-filterInvariant23-filterInvariant36-filterInvariant41 GT:DP:GQ:SB 0/2:80:99:0,54,26,0 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 0/1:57,16:73:99:341,0,3223:2,55,16,0 chr2 112896112 . C T 666.94 PASS AC=1;AF=0.5;AN=2;DP=202;FractionInformativeReads=1;MQ=60;set=variant-variant16-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:13,33:46:99:841,0,269:9,4,20,13 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 0/1:12,15:27:99:392,0,282:8,4,10,5 chr2 112933125 . T C 208.63 PASS AC=1;AF=0.5;AN=2;DP=83;FractionInformativeReads=1;MQ=60;set=variant-variant16-variant23-variant40 GT:AD:DP:GQ:PL:SB 0/1:7,7:14:99:260,0,188:4,3,7,0 chr2 112945188 . T A 978.94 PASS AC=1;AF=0.808;AN=2;DP=4320;MQ=60;set=variant-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-variant36-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,47:109:99:1090,0,1605:27,35,21,26 chr2 112945220 . G A 1329.53 PASS AC=1;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 0/1:51,54:105:99:1424,0,1204:25,26,24,30 chr2 112973924 . C T 182.39 PASS AC=1;AF=0.5;AN=2;DP=667;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant12-variant13-variant16-variant18-variant19-variant22-variant23-variant33-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:14,16:30:99:427,0,336:8,6,8,8 chr2 112990804 . T TATAAAGA 109.62 PASS AC=1;AF=0.5;AN=2;DP=165;MQ=60;set=variant-variant2-variant4-variant8-variant12-variant13-variant16-variant18-variant19-variant22-variant23-variant33-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:99:269,0,425:5,0,3,1 chr2 112991609 . TA T 118.31 PASS AC=1;AF=0.5;AN=2;DP=128;MQ=60;set=variant-variant4-variant8-variant12-variant16-variant18-variant19-variant22-variant23-variant33-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:80:80,0,80:3,0,3,0 chr2 112995810 . A G 214.45 PASS AC=1;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 0/1:4,3:7:99:103,0,158:4,0,3,0 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 0/1:34:99:9,7,13,5 chr2 113079576 . C A 36.43 PASS AC=1;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 0/1:2,3:5:72:92,0,72:1,1,2,1 chr2 113082250 . CT C 950.89 PASS AC=1;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 0/1:35,35:70:99:904,0,893:11,24,13,22 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 1/1:0,57:57:99:1793,171,0:0,0,31,26 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 1/1:3,204:207:99:5704,560,0:2,1,104,100 chr2 113091340 . A G 3849.67 PASS AC=1;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 0/1:114,125:239:99:2834,0,2657:58,56,67,58 chr2 113091685 . T G 3580.08 PASS AC=1;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 0/1:60,67:127:99:1758,0,1625:24,36,26,41 chr2 113092433 . C A 5841.61 PASS AC=1;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 0/1:162,127:289:99:2819,0,3988:87,75,72,55 chr2 113093928 . C T 1120.65 PASS AC=1;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 0/1:39,31:70:99:789,0,991:19,20,13,18 chr2 113094793 . G A 1574.45 PASS AC=1;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 0/1:49,48:97:99:1025,0,1161:19,30,21,27 chr2 113094921 . A G 283.47 PASS AC=1;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 0/1:1,7:8:22:225,0,22:0,1,1,6 chr2 113096857 . G C 2270.29 PASS AC=1;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 0/1:74,61:135:99:1531,0,1866:41,33,35,26 chr2 113097699 . T G 397.85 PASS AC=1;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 0/1:17,10:27:99:266,0,473:5,12,2,8 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 1/1:0,3:3:9:115,9,0:0,0,0,3 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 1/1:0,34:34:99:864,102,0:0,0,21,13 chr2 113147159 . G A 1680.82 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=13290;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:185,146:331:99:2670,0,3687:79,106,57,89 chr2 113147238 . A G 201.83 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=1657;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:32,19:51:99:359,0,674:8,24,0,19 chr2 113191010 . A C 1012.12 PASS AC=1;AF=0.5;AN=2;DP=2166;set=variant-variant2-variant4-variant6-variant8-variant12-variant13-variant16-variant19-variant22-variant23-variant33-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:78,53:131:99:1221,0,1804:31,47,20,33 chr2 113192136 . G A 172.37 PASS AC=1;AF=0.5;AN=2;DP=249;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant12-variant13-variant16-variant19-variant22-variant23-variant33-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:13,6:19:99:191,0,362:4,9,0,6 chr2 113240183 . T C 626.25 PASS AC=1;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 0/1:18,19:37:99:673,0,484:4,14,1,18 chr2 113243799 . T A 222.14 PASS AC=1;AF=0.5;AN=2;DP=207;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant12-variant16-variant22-variant23-variant33-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:9,7:16:99:267,0,270:2,7,1,6 chr2 113258671 . G A 63.87 PASS AC=2;AF=0.586;AN=2;DP=402;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant27-variant28-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,7:7:21:258,21,0:0,0,6,1 chr2 113258916 . C T 305.42 PASS AC=2;AF=0.593;AN=2;DP=894;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant16-variant17-variant19-variant20-variant22-variant23-variant27-variant28-variant31-variant33-variant34-variant36-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:770,75,0:0,0,8,17 chr2 113277949 . T C 2705.21 PASS AC=1;AF=0.545;AN=2;DP=1747;FractionInformativeReads=1;MQ=60;set=variant3-variant7-variant13-variant20-variant23-variant28-variant31-variant34-variant36-variant37-variant39 GT:AD:DP:GQ:PL:SB 0/1:64,80:144:99:2350,0,1520:28,36,31,49 chr2 113278190 . T TTGTA 505.4 PASS AC=2;AF=0.586;AN=2;DP=626;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant27-variant28-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,20:20:60:857,60,0:0,0,4,16 chr2 113278191 . AGG A 505.4 PASS AC=2;AF=0.586;AN=2;DP=586;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant11-variant12-variant13-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant27-variant28-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,16:16:60:857,60,0:0,0,3,13 chr2 113286492 . T A 362.42 PASS AC=1;AF=0.5;AN=2;DP=877;MQ=60;set=variant-variant2-variant4-variant6-variant12-variant16-variant22-variant23-variant33-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:37,27:64:99:765,0,1102:16,21,13,14 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 1/1:0,83:83:99:2492,249,0:0,0,48,35 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 1/1:0,22:22:66:680,66,0:0,0,14,8 chr2 113287964 . A G 237.91 PASS AC=1;AF=0.83;AN=2;DP=1218;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:17,8:25:99:192,0,485:9,8,5,3 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 1/1:0,2:2:6:87,6,0:0,0,1,1 chr2 113289032 . A G 1121.51 PASS AC=1;AF=0.55;AN=2;DP=973;set=variant3-variant5-variant7-variant8-variant11-variant13-variant15-variant17-variant20-variant22-variant23-variant27-variant28-variant31-variant33-variant34-variant36-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:13,15:28:99:385,0,363:9,4,8,7 chr2 113289701 . T G 2268.96 PASS AC=2;AF=0.977;AN=2;DP=3347;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,63:65:99:2045,146,0:1,1,21,42 chr2 113300001 . TTCCGGCGTGTACCGAGAGACTGGCG T 3017.1 PASS AC=1;AF=0.5;AN=2;DP=5403;set=variant5-variant8-variant11-variant15-variant16-variant22-variant23-variant27-variant30-variant33-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:233,144:377:99:3223,0,10242:129,104,88,56 chr2 113300283 . C G 871.33 PASS AC=1;AF=0.5;AN=2;DP=856;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant11-variant15-variant16-variant22-variant23-variant27-variant30-variant33-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:34,44:78:99:1445,0,1089:3,31,5,39 chr2 113300330 . G A 827.87 PASS AC=1;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 0/1:8,15:23:99:560,0,297:0,8,0,15 chr2 113306827 . A G 605.23 PASS AC=1;AF=0.5;AN=2;DP=1147;MQ=60;set=variant5-variant8-variant11-variant15-variant16-variant22-variant23-variant27-variant30-variant33-variant37-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:32,48:80:99:1330,0,694:19,13,31,17 chr2 113310197 . CT C 1061.63 PASS AC=1;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 0/1:23,17:40:99:336,0,479:15,8,13,4 chr2 113326281 . C G 1264.6 PASS AC=1;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 0/1:14,35:49:99:877,0,284:8,6,22,13 chr2 113326502 . C T 2296.48 PASS AC=1;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 0/1:30,39:69:99:903,0,684:12,18,15,24 chr2 113332421 . T C 730.52 PASS AC=1;AF=0.5;AN=2;DP=615;MQ=60;set=variant5-variant8-variant11-variant15-variant16-variant22-variant23-variant27-variant30-variant33-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:17,15:32:99:421,0,470:13,4,13,2 chr2 113333410 . C T 4090.78 PASS AC=1;AF=0.5;AN=2;DP=4348;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant11-variant15-variant16-variant22-variant23-variant27-variant30-variant33-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:192,152:344:99:3687,0,4526:102,90,78,74 chr2 113333892 . TTTG T 7124.63 PASS AC=1;AF=0.5;AN=2;DP=4702;MQ=60;set=variant5-variant8-variant11-variant15-variant16-variant22-variant23-variant27-variant30-variant33-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:150,157:307:99:6041,0,7089:72,78,68,89 chr2 113342051 . G T 431.75 PASS AC=1;AF=0.5;AN=2;DP=429;FractionInformativeReads=1;MQ=60;set=variant5-variant8-variant11-variant15-variant16-variant22-variant23-variant27-variant30-variant33-variant37-variant40 GT:AD:DP:GQ:PL:SB 0/1:28,12:40:99:239,0,703:15,13,9,3 chr2 113344047 . T C 5181.59 PASS AC=1;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 0/1:89,89:178:99:2236,0,2018:40,49,38,51 chr2 113346512 . A C 1090.52 PASS AC=1;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 0/1:27,22:49:99:512,0,661:14,13,11,11 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 1/1:0,82:82:99:2659,246,0:0,0,33,49 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 1/1:0,144:144:99:4515,431,0:0,0,53,91 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 1/1:0,9:9:27:405,27,0:0,0,1,8 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 1/1:0,9:9:27:405,27,0:0,0,1,8 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 1/1:0,22:22:66:657,66,0:0,0,8,14 chr2 113479614 . G A 4281.42 PASS AC=2;AF=0.694;AN=2;DP=6088;MQ=60;set=variant-variant2-variant3-variant4-variant6-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant34-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,148:148:99:4320,441,0:0,0,70,78 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 1/1:0,97:97:99:3067,292,0:0,0,41,56 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 1/1:0,11:11:33:485,33,0:0,0,4,7 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 1/1:0,10:10:36:530,36,0:0,0,4,6 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 1/1:0,10:10:33:495,33,0:0,0,5,5 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 1/1:0,10:10:39:585,39,0:0,0,5,5 chr2 113480938 . G GCACACA,GCACACACACACA,GCACACACA,GCACACACACACACA,GCACACACACACACACACA,GCACACACACA,GCACACACACACACACA,GCA,GCACA 330.45 PASS AC=1,0,1,0,0,0,0,0,0;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 1/3:10:75:0,0,6,4 chr2 113481439 . T A 1600.04 PASS AC=2;AF=0.682;AN=2;DP=3348;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant31-variant33-variant34-variant36-variant37-variant38-variant39-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,85:85:99:2629,249,0:0,0,45,40 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 1/1:0,75:75:99:2542,225,0:0,0,37,38 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 1/1:1,148:149:99:4401,400,0:0,1,71,77 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 1/1:0,123:123:99:3540,367,0:0,0,55,68 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 1/1:0,85:85:99:2728,254,0:0,0,31,54 chr2 113484441 . T G 291.71 PASS AC=2;AF=0.661;AN=2;DP=637;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant10-variant11-variant12-variant13-variant15-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant31-variant33-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,24:24:72:957,72,0:0,0,4,20 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 1/1:0,256:256:99:7644,766,0:0,0,99,157 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 1/1:0,88:88:99:2746,264,0:0,0,52,36 chr2 113498566 . A G 197.62 PASS AC=1;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 0/1:20,19:39:99:436,0,462:8,12,7,12 chr2 113513825 . T C 5415.05 PASS AC=2;AF=0.977;AN=2;DP=6127;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:4187,384,0:0,0,66,62 chr2 113514883 . AT A 59.91 PASS AC=1;AF=0.813;AN=2;DP=104;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant12-variant13-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant25-variant37-variant39-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:3,3:6:97:97,0,103:0,3,1,2 chr2 113520129 . G A 1057.98 PASS AC=1;AF=0.5;AN=2;DP=465;FractionInformativeReads=1;MQ=60;set=variant11-variant23-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:48,52:100:99:1167,0,1137:20,28,21,31 chr2 113531715 . T TTGAA 7611.35 PASS AC=2;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 1/1:0,135:135:99:5964,406,0:0,0,54,81 chr2 113532083 . A G 2765.06 PASS AC=2;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 1/1:0,88:88:99:2606,263,0:0,0,57,31 chr2 113532236 . T C 6650.48 PASS AC=2;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 1/1:0,200:200:99:6177,600,0:0,0,105,95 chr2 113532885 . G T 2732.22 PASS AC=2;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 1/1:0,103:103:99:3179,309,0:0,0,38,65 chr2 113535395 . G T 652.2 PASS AC=2;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 1/1:0,12:12:35:425,35,0:0,0,11,1 chr2 113535438 . C T 719.71 PASS AC=2;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 1/1:0,27:27:79:855,79,0:0,0,19,8 chr2 113537223 . C A 1712.87 PASS AC=2;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 1/1:1,49:50:99:1583,104,0:0,1,14,35 chr2 113540084 . G A 743.66 PASS AC=2;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 1/1:0,14:14:42:427,42,0:0,0,8,6 chr2 113540177 . C T 1380.42 PASS AC=2;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 1/1:0,48:48:99:1474,144,0:0,0,31,17 chr2 113540205 . G T 2531.26 PASS AC=2;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 1/1:0,63:63:99:1829,188,0:0,0,39,24 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 1/1:0,7:7:21:226,21,0:0,0,5,2 chr2 113587433 . C G 2744.34 PASS AC=2;AF=0.588;AN=2;DP=4029;MQ=60;set=variant2-variant9-variant11-variant12-variant18-variant20-variant22-variant23-variant24-variant25-variant28-variant30-variant32-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,235:235:99:7212,703,0:0,0,144,91 chr2 113588755 . CAA C 271.56 PASS AC=2;AF=0.588;AN=2;DP=370;MQ=60;set=variant2-variant9-variant11-variant12-variant18-variant20-variant22-variant23-variant24-variant25-variant28-variant30-variant32-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:1027,69,0:0,0,21,2 chr2 113588793 . C T 412 PASS AC=2;AF=0.588;AN=2;DP=721;MQ=60;set=variant2-variant9-variant11-variant12-variant18-variant20-variant22-variant23-variant24-variant25-variant28-variant30-variant32-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,46:47:99:1375,113,0:1,0,34,12 chr2 113590390 . G A 1443.27 PASS AC=2;AF=0.583;AN=2;DP=2139;MQ=60;set=variant2-variant9-variant11-variant12-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant30-variant32-variant38-variant39-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,100:100:99:3106,300,0:0,0,40,60 chr2 113594387 . G A 357.73 PASS AC=2;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 1/1:0,26:26:78:749,78,0:0,0,10,16 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 1/1:0,7:7:21:261,21,0:0,0,5,2 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 1/1:0,49:49:99:1696,147,0:0,0,11,38 chr2 113742734 . G A 1034.35 PASS AC=2;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 1/1:0,26:26:78:954,78,0:0,0,12,14 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 0/1:83,77:160:99:1743,0,2024:45,38,38,39 chr2 113763575 . A G 3801.07 PASS AC=2;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 1/1:0,135:135:99:4043,404,0:0,0,61,74 chr2 113763676 . C T 702.53 PASS AC=1;AF=0.5;AN=2;DP=48;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-2.415;QD=14.64;ReadPosRankSum=2.043;SOR=0.596;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:23,25:48:99:731,0,684:5,18,6,19 chr2 113764419 . T C 516.91 PASS AC=1;AF=0.542;AN=2;DP=288;MQ=60;set=variant2-variant9-variant11-variant15-variant18-variant23-variant24-variant25-variant26-variant30-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:10,5:15:99:156,0,267:3,7,0,5 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 0/1:83,92:175:99:2289,0,2033:48,35,49,43 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 0/1:8,12:20:99:431,0,297:8,0,11,1 chr2 113783909 . A T 1677.15 PASS AC=2;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 1/1:0,37:37:99:1150,110,0:0,0,12,25 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 0/1:96,109:205:99:2947,0,2427:58,38,71,38 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 0/1:103,114:217:99:2811,0,2582:39,64,46,68 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 1/1:0,24:24:72:778,72,0:0,0,8,16 chr2 113786833 . C G 344.41 PASS AC=2;AF=0.782;AN=2;DP=547;MQ=60;set=variant-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-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,13:13:39:523,39,0:0,0,3,10 chr2 113788590 . C G 794.83 PASS AC=1;AF=0.5;AN=2;DP=169;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:31,29:60:99:823,0,852:21,10,20,9 chr2 113789169 . C A 106.77 PASS AC=2;AF=1;AN=2;DP=3;FS=0;FractionInformativeReads=1;MQ=60;QD=26.22;SOR=2.833;set=variant23 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,3,0 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 0/1:22,15:37:99:280,0,550:11,11,8,7 chr2 113810286 . G A 125.48 PASS AC=1;AF=0.5;AN=2;DP=89;FractionInformativeReads=1;MQ=60;set=variant9-variant10-variant12-variant20-variant22-variant23-variant24-variant38 GT:AD:DP:GQ:PL:SB 0/1:9,3:12:58:58,0,330:8,1,2,1 chr2 113810413 . G A 423.23 PASS AC=1;AF=0.5;AN=2;DP=318;MQ=60;set=variant9-variant10-variant12-variant20-variant22-variant23-variant24-variant38 GT:AD:DP:GQ:PL:SB 0/1:20,18:38:99:409,0,564:8,12,9,9 chr2 113816090 . T A 45.95 PASS AC=2;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 1/1:0,9:9:27:288,27,0:0,0,7,2 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 0/1:38,30:68:99:1142,0,1879:19,19,14,16 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 0/1:39,30:69:99:1142,0,1879:19,20,14,16 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 0/1:18,17:35:99:494,0,556:3,15,6,11 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 0/1:3,14:17:84:357,0,84:0,3,5,9 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 0/1:37,29:66:99:646,0,963:23,14,17,12 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 0/1:21,14:35:99:387,0,605:14,7,7,7 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 0/1:31,21:52:99:559,0,922:23,8,12,9 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 0/1:36,18:54:99:411,0,941:20,16,11,7 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 0/1:43,38:81:99:854,0,1069:19,24,21,17 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 0/1:41,42:83:99:989,0,1077:15,26,24,18 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 0/1:45,54:99:99:1389,0,1085:24,21,30,24 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 0/1:55,48:103:99:1178,0,1549:35,20,25,23 chr2 113821117 . C T 1314.13 PASS AC=2;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 1/1:0,153:153:99:4247,459,0:0,0,78,75 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 0/1:70,70:140:99:1855,0,1798:38,32,34,36 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 0/1:24,10:34:99:186,0,669:10,14,3,7 chr2 113825386 . C A 41.46 PASS AC=2;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 1/1:0,7:7:21:263,21,0:0,0,5,2 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 0/1:2,4:6:69:121,0,69:1,1,3,1 chr2 113830201 . T G 1912.71 PASS AC=2;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 1/1:0,77:77:99:2711,231,0:0,0,53,24 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 0/1:33,18:51:99:451,0,882:12,21,5,13 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 0/1:24,14:38:99:376,0,727:5,19,3,11 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 0/1:5,4:9:99:112,0,160:1,4,1,3 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 0/1:52,68:120:99:1653,0,1318:19,33,32,36 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 0/1:47,54:101:99:1281,0,1140:16,31,25,29 chr2 113870663 . G A 386.59 PASS AC=1;AF=0.5;AN=2;DP=344;FractionInformativeReads=1;MQ=60;set=variant9-variant10-variant12-variant20-variant22-variant23-variant24-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,12:23:99:267,0,264:4,7,5,7 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 0/1:8,8:16:99:230,0,264:2,6,1,7 chr2 113875513 . G A 433.78 PASS AC=1;AF=0.5;AN=2;DP=47;FS=0;FractionInformativeReads=0.979;MQ=60;MQRankSum=-0.979;QD=9.23;ReadPosRankSum=-3.391;SOR=0.562;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:29,17:46:99:462,0,765:18,11,10,7 chr2 113877495 . G T 584.72 PASS AC=1;AF=0.886;AN=2;DP=1149;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:8,7:15:99:174,0,275:6,2,5,2 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 0/1:14,14:28:99:462,0,449:2,12,2,12 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 0/1:58,39:97:99:985,0,1549:34,24,22,17 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 0/1:46,36:82:99:919,0,1306:22,24,15,21 chr2 113940681 . T C 1697.15 PASS AC=1;AF=0.6;AN=2;DP=2138;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant33-variant34-variant36-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,21:68:99:592,0,1344:25,22,10,11 chr2 113940839 . G C 3058.34 PASS AC=1;AF=0.6;AN=2;DP=5958;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant33-variant34-variant36-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:100,93:193:99:2315,0,2597:55,45,51,42 chr2 113942903 . A C 939 PASS AC=1;AF=0.6;AN=2;DP=1519;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant33-variant34-variant36-variant38-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,38:63:99:985,0,621:11,14,20,18 chr2 113943063 . T G 796.21 PASS AC=1;AF=0.5;AN=2;DP=820;FractionInformativeReads=1;MQ=60;set=variant5-variant11-variant16-variant21-variant23-variant27-variant37-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,44:93:99:1086,0,1187:26,23,24,20 chr2 113943470 . A G 4001.09 PASS AC=1;AF=0.597;AN=2;DP=4758;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant30-variant33-variant34-variant36-variant38-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:72,74:146:99:1679,0,1609:41,31,39,35 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 1/1:0,76:76:99:2346,228,0:0,0,33,43 chr2 113953508 . G A 672.71 PASS AC=1;AF=0.533;AN=2;DP=833;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant12-variant16-variant23-variant24-variant25-variant26-variant32-variant34-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:16,27:43:99:778,0,389:5,11,12,15 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 0/1:73,47:120:99:963,0,1795:42,31,26,21 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 0/1:16,24:40:99:614,0,388:6,10,8,16 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 0/1:14,17:31:99:646,0,514:5,9,4,13 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 0/1:14,16:30:99:646,0,514:5,9,3,13 chr2 113953984 . G A 335.95 PASS AC=1;AF=0.533;AN=2;DP=330;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant8-variant12-variant16-variant23-variant24-variant25-variant26-variant32-variant34-variant37-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:264,0,510:3,9,4,8 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 0/1:9,12:21:99:343,0,217:3,6,3,9 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 0/1:38,50:88:99:1229,0,929:22,16,30,20 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 0/1:66,58:124:99:1417,0,1691:31,35,29,29 chr2 113955233 . C T 1410.4 PASS AC=1;AF=0.5;AN=2;DP=928;MQ=60;set=variant7-variant8-variant12-variant23-variant25-variant26-variant32 GT:AD:DP:GQ:PL:SB 0/1:60,55:115:99:1443,0,1581:30,30,26,29 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 0/1:110,82:192:99:1931,0,2909:58,52,38,44 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 0/1:63,54:117:99:1260,0,1562:21,42,22,32 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 1/1:0,68:68:99:2233,204,0:0,0,44,24 chr2 113960305 . G A 793.6 PASS AC=1;AF=0.5;AN=2;DP=275;MQ=60;set=variant6-variant20-variant23-variant38 GT:AD:DP:GQ:PL:SB 0/1:33,33:66:99:990,0,917:14,19,19,14 chr2 113973467 . T C 211.67 PASS AC=1;AF=0.529;AN=2;DP=165;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant10-variant16-variant17-variant19-variant23-variant24-variant25-variant26-variant30-variant32-variant34-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:1,5:6:19:163,0,19:1,0,2,3 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 0/1:21,8:29:99:175,0,537:13,8,5,3 chr2 113973801 . T C 1286.45 PASS AC=2;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 1/1:0,51:51:99:1549,153,0:0,0,26,25 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 0/1:21,38:59:99:1022,0,515:8,13,21,17 chr2 113974196 . G C 597.27 PASS AC=1;AF=0.526;AN=2;DP=734;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant10-variant12-variant14-variant16-variant17-variant19-variant23-variant24-variant25-variant26-variant30-variant32-variant34-variant37-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,15:40:99:324,0,690:12,13,7,8 chr2 113975066 . T G 347.12 PASS AC=1;AF=0.577;AN=2;DP=589;MQ=60;set=variant2-variant7-variant12-variant14-variant16-variant23-variant24-variant25-variant26-variant32-variant34-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,23:45:99:520,0,413:11,11,11,12 chr2 113975104 . T G 402.03 PASS AC=1;AF=0.542;AN=2;DP=519;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant12-variant14-variant16-variant23-variant24-variant26-variant32-variant34-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:21,23:44:99:561,0,470:10,11,13,10 chr2 113975923 . T C 426.81 PASS AC=1;AF=0.5;AN=2;DP=160;FractionInformativeReads=1;MQ=60;set=variant6-variant20-variant23-variant38 GT:AD:DP:GQ:PL:SB 0/1:26,13:39:99:287,0,753:11,15,4,9 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 1/1:0,15:15:45:470,45,0:0,0,4,11 chr2 113984594 . T C 2075.67 PASS AC=1;AF=0.5;AN=2;DP=800;FractionInformativeReads=1;MQ=60;set=variant7-variant12-variant23-variant25-variant26-variant32 GT:AD:DP:GQ:PL:SB 0/1:54,75:129:99:1857,0,1289:38,16,45,30 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 0/1:27,31:58:99:680,0,626:11,16,9,22 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 0/1:98:97:33,49,6,10 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 1/1:0,34:34:99:1173,102,0:0,0,9,25 chr2 114017029 . A G 1045.89 PASS AC=1;AF=0.591;AN=2;DP=3506;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:51,34:85:99:733,0,1233:25,26,17,17 chr2 114017282 . C CATTA 175.27 PASS AC=1;AF=0.597;AN=2;DP=496;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant32-variant34-variant36-variant37-variant39-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,5:10:99:186,0,258:0,5,1,4 chr2 114020828 . G T 615.61 PASS AC=1;AF=0.583;AN=2;DP=1469;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant34-variant37-variant39-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:20,15:35:99:361,0,859:14,6,8,7 chr2 114020848 . T G 916.27 PASS AC=1;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 0/1:20,29:49:99:771,0,661:11,9,19,10 chr2 114020911 . C G,T 1039.94 PASS AC=1,0;AF=0.333,0.25;AN=2;DP=1176;MQ=60;set=variant2-variant6-variant7-variant12-variant14-variant21-variant23-variant24-variant25-variant26-variant32-variant34 GT:DP:GQ:SB 0/1:82:99:25,25,20,12 chr2 114021118 . G A 252.97 PASS AC=1;AF=0.5;AN=2;DP=176;FractionInformativeReads=1;MQ=60;set=variant2-variant7-variant12-variant21-variant23-variant25-variant26-variant32 GT:AD:DP:GQ:PL:SB 0/1:6,14:20:99:469,0,130:2,4,3,11 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 1/1:0,99:99:99:2780,297,0:0,0,53,46 chr2 114196739 . T G 401.2 PASS AC=1;AF=0.667;AN=2;DP=78;FS=0;FractionInformativeReads=1;set=variant20-variant23-variant38 GT:AD:DP:GQ:PL:SB 0/1:14,9:23:99:225,0,311:6,8,3,6 chr2 114257319 . C G 2068.95 PASS AC=1;AF=0.536;AN=2;DP=2194;set=variant3-variant7-variant8-variant9-variant12-variant15-variant16-variant17-variant23-variant26-variant32-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:84,53:137:99:1088,0,1964:36,48,25,28 chr2 114335868 . C T 53.49 PASS AC=1;AF=0.5;AN=2;DP=274;set=filterInvariant4-filterInvariant16-filterInvariant22-filterInvariant23-filterInvariant25-variant27-filterInvariant36-filterInvariant37-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:29,7:36:73:73,0,780:11,18,5,2 chr2 114335961 . G T 73.21 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=270;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:13,9:22:99:152,0,264:5,8,4,5 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 0/1:5,12:17:99:331,0,134:3,2,10,2 chr2 114340454 . G A 187.17 PASS AC=1;AF=0.5;AN=2;DP=268;FractionInformativeReads=1;set=variant7-filterInvariant8-variant9-variant16-variant17-variant23-variant27-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:26,9:35:99:184,0,735:15,11,8,1 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 0/1:41,18:59:99:346,0,930:22,19,10,8 chr2 114340628 . C T 131.75 PASS AC=1;AF=0.5;AN=2;DP=1378;FractionInformativeReads=1;set=variant4-variant6-variant7-variant8-variant9-filterInvariant10-variant14-filterInvariant15-variant16-filterInvariant17-filterInvariant22-variant23-variant25-variant27-variant28-filterInvariant32-filterInvariant33-filterInvariant34-filterInvariant36-variant38-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:57,20:77:99:332,0,1520:25,32,7,13 chr2 114340631 . A G 37.48 PASS AC=1;AF=0.5;AN=2;DP=166;FractionInformativeReads=1;set=filterInvariant17-filterInvariant23-variant29 GT:AD:DP:GQ:PL:SB 0/1:65,11:76:90:90,0,1905:28,37,4,7 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 0/1:30,35:65:99:1240,0,1172:15,15,13,22 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 0/1:27,27:54:99:1038,0,1128:12,15,9,18 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 0/1:18,13:31:99:290,0,415:8,10,4,9 chr2 114346484 . C T 80.75 DRAGENHardSNP AC=1;AF=0.654;AN=2;DP=583;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:129,0,233:8,3,6,1 chr2 114346531 . A G 358.79 DRAGENHardSNP AC=1;AF=0.602;AN=2;DP=1769;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:26,18:44:99:323,0,540:17,9,11,7 chr2 114346567 . G A 382.72 DRAGENHardSNP AC=1;AF=0.535;AN=2;DP=2778;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:39,31:70:99:562,0,775:23,16,16,15 chr2 114346582 . A G 822.49 DRAGENHardSNP AC=1;AF=0.602;AN=2;DP=3232;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:47,31:78:99:524,0,930:27,20,16,15 chr2 114346668 . ACC A 1177.76 PASS AC=1;AF=0.602;AN=2;DP=2213;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:30,16:46:99:582,0,1211:14,16,6,10 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 0/1:32,10:42:99:121,0,773:19,13,5,5 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 0/1:45,8:53:99:201,0,1933:25,20,3,5 chr2 114352820 . C T 193.62 PASS AC=1;AF=0.5;AN=2;DP=877;FractionInformativeReads=1;set=filterInvariant-variant2-variant3-filterInvariant4-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant16-variant17-variant19-variant21-variant22-variant23-variant28-variant30-variant32-variant33-variant34-variant37-variant38-variant40-variant41-filterInvariant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,8:52:99:201,0,1983:23,21,3,5 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 0/1:23,6:29:61:61,0,536:11,12,3,3 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 0/1:61,22:83:99:335,0,1413:32,29,15,7 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 0/1:42,12:54:99:201,0,1259:30,12,12,0 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 0/1:17,12:29:99:398,0,599:7,10,5,7 chr2 114369935 . T G 193.67 PASS AC=2;AF=0.8;AN=2;DP=136;FS=0;FractionInformativeReads=1;set=variant2-variant3-variant4-variant6-variant7-variant8-variant10-variant11-filterInvariant13-variant15-variant17-variant19-filterInvariant23-variant26-variant27-variant28-variant29-variant30-variant31-variant36-variant37-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:95,9,0:0,0,0,3 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 0/1:7,6:13:99:175,0,221:1,6,6,0 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 0/1:86,92:178:99:2311,0,2135:32,54,33,59 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 0/1:46,50:96:99:1559,0,1261:12,34,12,38 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 0/1:45,38:83:99:902,0,1083:16,29,10,28 chr2 114426090 . C T 2209.38 PASS AC=1;AF=0.545;AN=2;DP=1332;FractionInformativeReads=1;set=variant3-variant4-variant7-variant12-variant16-variant17-variant23-variant24-variant32-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,71:130:99:1729,0,1356:36,23,40,31 chr2 114429542 . G A 1921.45 PASS AC=1;AF=0.5;AN=2;DP=1721;set=variant3-variant11-variant15-variant20-variant23-variant27-variant29-variant31-variant32-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:65,40:105:99:752,0,1646:35,30,20,20 chr2 114429576 . T C 2010.2 PASS AC=1;AF=0.5;AN=2;DP=1657;set=variant3-variant11-variant15-variant20-variant23-variant27-variant29-variant31-variant32-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:73,35:108:99:584,0,1780:35,38,15,20 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 0/1:119,90:209:99:1848,0,2856:54,65,44,46 chr2 114471326 . TA T,TAA 130.95 PASS AC=1,0;AF=0.375,0.125;AN=2;DP=722;set=filterInvariant3-variant14-filterInvariant17-filterInvariant23-filterInvariant24-filterInvariant28-filterInvariant29-variant38 GT:DP:GQ:SB 0/1:43:99:8,16,7,12 chr2 114471921 . A G 1042.8 PASS AC=1;AF=0.583;AN=2;DP=1276;MQ=60;set=variant3-variant4-variant7-variant12-variant15-variant16-variant17-variant23-variant24-variant28-variant29-variant32-variant33-variant36-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:44,15:59:99:404,0,1104:24,20,8,7 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 0/1:13,11:24:99:423,0,633:6,7,3,8 chr2 114493509 . CT C 1026.11 PASS AC=1;AF=0.583;AN=2;DP=1333;MQ=60;set=variant3-variant4-variant7-variant12-variant15-variant16-variant17-variant23-variant24-variant28-variant29-variant32-variant33-variant36-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,30:49:99:809,0,440:7,12,14,16 chr2 114501112 . C T 276.84 PASS AC=1;AF=0.588;AN=2;DP=412;FractionInformativeReads=1;MQ=60;set=variant4-variant7-variant12-variant15-variant16-variant17-variant23-variant24-variant28-variant29-variant32-variant33-variant36-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,14:26:99:347,0,216:7,5,9,5 chr2 114503630 . T G 232.42 PASS AC=1;AF=0.588;AN=2;DP=186;FractionInformativeReads=1;MQ=60;set=variant3-variant4-variant7-variant12-variant15-variant16-variant17-variant23-variant24-variant28-variant29-variant32-variant33-variant36-variant38-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:156,0,120:4,0,4,0 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 1/1:0,165:165:99:5069,494,0:0,0,95,70 chr2 114513901 . C T 2710.65 PASS AC=1;AF=0.583;AN=2;DP=3900;MQ=60;set=variant3-variant4-variant7-variant12-variant15-variant16-variant17-variant23-variant24-variant28-variant29-variant32-variant33-variant36-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:87,92:179:99:2266,0,2187:44,43,38,54 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 0/1:50,44:94:99:994,0,1080:23,27,20,24 chr2 114684848 . T C 215.9 PASS AC=1;AF=0.5;AN=2;DP=31;FS=0;FractionInformativeReads=1;MQ=60;set=variant3-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:6,5:11:99:111,0,157:4,2,3,2 chr2 114697516 . A G 142.39 PASS AC=1;AF=0.5;AN=2;DP=52;FractionInformativeReads=1;MQ=60;set=variant3-variant23-variant27-variant38 GT:AD:DP:GQ:PL:SB 0/1:3,7:10:61:248,0,61:2,1,7,0 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 0/1:16,18:34:99:465,0,396:6,10,9,9 chr2 114716178 . GT G,GTT 109.7 PASS AC=0,1;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 0/2:20:99:7,2,6,5 chr2 114718893 . C G 4168.48 PASS AC=1;AF=0.5;AN=2;DP=1050;MQ=60;set=variant3-variant23-variant27-variant38 GT:AD:DP:GQ:PL:SB 0/1:97,125:222:99:3174,0,2435:37,60,56,69 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 0/1:145,153:298:99:4018,0,3882:72,73,77,76 chr2 114720132 . A AT 2632.96 PASS AC=1;AF=0.5;AN=2;DP=612;MQ=60;set=variant3-variant23-variant27-variant38 GT:AD:DP:GQ:PL:SB 0/1:62,46:108:99:1314,0,1888:29,33,18,28 chr2 115919301 . G A 666.15 PASS AC=1;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 0/1:20,22:42:99:415,0,454:9,11,10,12 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 1/1:0,63:63:99:2837,193,0:0,0,34,29 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 1/1:0,63:63:99:2837,193,0:0,0,35,28 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 1/1:0,44:44:99:1377,131,0:0,0,15,29 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 1/1:0,120:120:99:3479,359,0:0,0,48,72 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 0/1:20,15:35:99:314,0,490:13,7,9,6 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 0/1:22,20:42:99:524,0,572:6,16,7,13 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 1/1:0,78:78:99:2516,233,0:0,0,29,49 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 1/1:0,30:30:90:1172,90,0:0,0,6,24 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 0/1:62,48:110:99:1061,0,1439:31,31,29,19 chr2 116510817 . G C 1184.04 PASS AC=1;AF=0.776;AN=2;DP=1995;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:33,25:58:99:565,0,789:17,16,15,10 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 1/1:0,103:103:99:3150,309,0:0,0,53,50 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 1/1:0,9:9:27:358,27,0:0,0,2,7 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 0/1:37,40:77:99:1006,0,1034:24,13,23,17 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 0/1:9,7:16:99:224,0,179:6,3,6,1 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 0/1:38,36:74:99:949,0,966:18,20,15,21 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 1/1:0,4:4:12:131,12,0:0,0,1,3 chr2 116594221 . G C 920.62 PASS AC=1;AF=0.605;AN=2;DP=1549;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant11-variant12-variant20-variant23-variant29-variant32-variant34-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:53,35:88:99:739,0,1423:25,28,19,16 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 0/1:39,42:81:99:901,0,822:17,22,18,24 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 1/1:0,13:13:39:416,39,0:0,0,4,9 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 1/1:0,28:28:84:1020,84,0:0,0,20,8 chr2 116599927 . T C 11398.5 PASS AC=2;AF=0.989;AN=2;DP=14420;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,305:305:99:9526,914,0:0,0,161,144 chr2 116600388 . A G 986.64 PASS AC=1;AF=0.579;AN=2;DP=1498;MQ=60;set=variant-variant2-variant3-variant5-variant6-variant9-variant11-variant12-variant20-variant23-variant29-variant32-variant34-variant37-variant38-variant39-variant40-variant42-variant43 GT:AD:DP:GQ:PL:SB 0/1:39,45:84:99:1257,0,1211:29,10,31,14 chr2 116601631 . C T 7122.02 PASS AC=1;AF=0.731;AN=2;DP=7621;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,108:186:99:2629,0,1896:35,43,54,54 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 0/1:75,68:143:99:1433,0,1738:35,40,31,37 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 1/1:0,137:137:99:4712,410,0:0,0,62,75 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 0/1:198,170:368:99:3852,0,4970:99,99,76,94 chr2 118572471 . A C,T 3108.6 PASS AC=2,0;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 1/1:317:99:0,0,130,187 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 1/1:0,32:32:96:939,96,0:0,0,18,14 chr2 118578824 . A G 1266.99 PASS AC=1;AF=0.5;AN=2;DP=102;FS=1.606;FractionInformativeReads=1;MQ=60;MQRankSum=-0.862;QD=12.42;ReadPosRankSum=-1.311;SOR=0.922;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:48,54:102:99:1295,0,1050:25,23,31,23 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 1/1:0,110:110:99:5027,343,0:0,0,48,62 chr2 118583940 . C T 669.38 PASS AC=2;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 1/1:0,30:30:90:886,90,0:0,0,19,11 chr2 118588640 . C T 1931.52 PASS AC=2;AF=0.898;AN=2;DP=5976;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,109:109:99:3733,326,0:0,0,31,78 chr2 118673663 . T C 11096.6 PASS AC=1;AF=0.667;AN=2;DP=7370;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant33-variant34-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:120,111:231:99:3090,0,3262:46,74,44,67 chr2 118673738 . G A 3493.04 PASS AC=1;AF=0.575;AN=2;DP=4103;MQ=60;set=variant3-variant6-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant33-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:81,84:165:99:2222,0,2188:38,43,42,42 chr2 118673912 . TA T 9730.96 PASS AC=1;AF=0.672;AN=2;DP=7763;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant33-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:94,122:216:99:2781,0,1946:44,50,59,63 chr2 118674716 . G GATC 4869.86 PASS AC=1;AF=0.667;AN=2;DP=2631;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant33-variant34-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:47,36:83:99:1404,0,2168:26,21,20,16 chr2 118675578 . C T 1721.22 PASS AC=1;AF=0.667;AN=2;DP=1284;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant33-variant34-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:22,23:45:99:559,0,532:9,13,10,13 chr2 118675615 . ATGTC A 1165.4 PASS AC=1;AF=0.575;AN=2;DP=793;MQ=60;set=variant3-variant6-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant33-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,18:47:99:669,0,1423:14,15,8,10 chr2 118675743 . G A 1964.61 PASS AC=1;AF=0.667;AN=2;DP=1357;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant33-variant34-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,16:33:99:415,0,540:10,7,8,8 chr2 118676111 . T C 1130.68 PASS AC=1;AF=0.575;AN=2;DP=1423;MQ=60;set=variant3-variant6-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant33-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:41,29:70:99:829,0,1235:14,27,13,16 chr2 118676836 . T C 1532.02 PASS AC=1;AF=0.667;AN=2;DP=1132;FractionInformativeReads=1;MQ=60;set=variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant33-variant34-variant37-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,18:39:99:434,0,569:12,9,8,10 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 1/1:0,46:46:99:1631,138,0:0,0,15,31 chr2 118692929 . G A 417.92 PASS AC=1;AF=0.575;AN=2;DP=590;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant33-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:17,13:30:99:350,0,534:12,5,10,3 chr2 118694393 . C G 1397.14 PASS AC=1;AF=0.575;AN=2;DP=1244;MQ=60;set=variant3-variant6-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant33-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:29,32:61:99:768,0,660:13,16,13,19 chr2 118698699 . A G 391.76 PASS AC=1;AF=0.5;AN=2;DP=372;FractionInformativeReads=1;MQ=60;set=variant3-variant6-variant10-variant20-variant21-variant22-variant23-variant30-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:12,13:25:99:307,0,373:9,3,8,5 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 1/1:0,37:37:99:1335,111,0:0,0,8,29 chr2 118704503 . A G 1391.48 PASS AC=1;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 0/1:12,11:23:99:330,0,334:4,8,2,9 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 1/1:0,69:69:99:2062,207,0:0,0,42,27 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 1/1:2,52:54:99:1549,112,0:1,1,31,21 chr2 118716166 . C T 481.93 PASS AC=1;AF=0.575;AN=2;DP=1026;MQ=60;set=variant3-variant6-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant33-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,29:53:99:751,0,594:9,15,10,19 chr2 118731573 . G A 2247.44 PASS AC=1;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 0/1:53,55:108:99:1250,0,1291:27,26,26,29 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 1/1:1,60:61:99:2035,173,0:1,0,21,39 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 1/1:0,22:22:66:724,66,0:0,0,15,7 chr2 118752903 . T A 450.84 PASS AC=1;AF=0.5;AN=2;DP=71;FractionInformativeReads=1;MQ=60;set=variant23-variant36 GT:AD:DP:GQ:PL:SB 0/1:9,18:27:99:479,0,186:6,3,10,8 chr2 118753097 . C T 464.73 PASS AC=1;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 0/1:31,25:56:99:556,0,637:16,15,9,16 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 1/1:0,29:29:87:1305,87,0:0,0,7,22 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 0/1:39,25:64:99:742,0,1268:23,16,16,9 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 1/1:0,46:46:99:1579,137,0:0,0,36,10 chr2 118771566 . C A 2403.28 PASS AC=1;AF=0.575;AN=2;DP=3518;MQ=60;set=variant3-variant6-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant33-variant38-variant39-variant43 GT:AD:DP:GQ:PL:SB 0/1:96,94:190:99:2142,0,2297:50,46,47,47 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 1/1:1,139:140:99:4168,402,0:1,0,60,79 chr2 118771682 . TGCCGCCGCC TGCCGCC,T,TGCC 2400.9 PASS AC=1,0,0;AF=0.26,0.12,0.24;AN=2;DP=3189;set=variant3-variant6-variant8-variant9-variant10-variant12-variant14-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant30-variant31-variant33-variant37-variant38-variant39-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:81:99:14,26,16,25 chr2 118850459 . T G 1358.36 PASS AC=1;AF=0.583;AN=2;DP=1111;set=variant6-variant9-variant10-variant19-variant20-variant21-variant22-variant23-variant26-variant30-variant38-variant43 GT:AD:DP:GQ:PL:SB 0/1:49,30:79:99:779,0,1146:29,20,17,13 chr2 118850591 . T G 195 PASS AC=1;AF=0.5;AN=2;DP=582;set=variant12-variant16-variant18-variant23-filterInvariant30-variant31 GT:AD:DP:GQ:PL:SB 0/1:30,43:73:99:989,0,709:12,18,23,20 chr2 118850785 . AGATGATGATGAT A,AGATGAT,AGATGATGATGATGAT,AGATGATGATGATGATGAT,AGATGATGAT 554.02 PASS AC=0,0,0,0,1;AF=0.237,0.105,0.053,0.053,0.263;AN=2;DP=844;set=variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant26-variant29-variant33-variant36-variant43 GT:DP:GQ:SB 0/5:22:99:3,4,7,8 chr2 118850939 . AGATGAT AGAT,A 186.04 PASS AC=2,0;AF=0.367,0.567;AN=2;DP=670;set=variant5-variant6-variant8-variant10-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant26-variant31-variant38-variant40 GT:DP:GQ:SB 1/1:10:30:0,0,2,8 chr2 118851073 . AGATGATGATGATGAT AGAT,AGATGATGAT,A,AGATGATGATGATGATGATGAT 516.41 PASS AC=1,0,0,0;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 0/1:8:36:1,0,7,0 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 1/1:1,33:34:77:1146,77,0:1,0,25,8 chr2 118851809 . AGAT AGATGAT,AGATGATGAT,AGATGATGATGAT,AGATGATGATGATGAT,A 1256.93 PASS AC=1,1,0,0,0;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 1/2:70:99:1,2,34,33 chr2 118866033 . G GA 778.04 PASS AC=1;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 0/1:22,15:37:99:449,0,713:6,16,5,10 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 1/1:0,169:169:99:4936,506,0:0,0,93,76 chr2 119599735 . A G 444.15 PASS AC=1;AF=0.708;AN=2;DP=813;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant29-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,10:17:99:243,0,156:5,2,6,4 chr2 119600067 . C CT 639.55 PASS AC=2;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 1/1:0,9:9:27:350,27,0:0,0,3,6 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 0/1:2,4:6:29:58,0,29:0,2,0,4 chr2 119700096 . T C 1538.16 PASS AC=1;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 0/1:15,19:34:99:622,0,466:2,13,3,16 chr2 119727550 . T C 258.48 PASS AC=1;AF=0.5;AN=2;DP=278;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant7-variant21-variant23-variant26-variant29-variant34-variant37-variant43 GT:AD:DP:GQ:PL:SB 0/1:6,10:16:99:281,0,128:4,2,7,3 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 0/1:76,67:143:99:1801,0,1965:33,43,23,44 chr2 119739269 . C T 996.43 PASS AC=2;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 1/1:0,79:79:99:2421,237,0:0,0,31,48 chr2 119739400 . C T 62.96 PASS AC=1;AF=0.5;AN=2;DP=15;FS=2.447;FractionInformativeReads=1;MQ=60;MQRankSum=-0.849;QD=4.2;ReadPosRankSum=-0.326;SOR=1.555;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:11,4:15:91:91,0,328:6,5,1,3 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 1/1:0,6:6:18:229,18,0:0,0,1,5 chr2 119749477 . T G 2231.23 PASS AC=1;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 0/1:76,67:143:99:1558,0,1797:35,41,31,36 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 0/1:17,14:31:99:402,0,536:4,13,3,11 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 0/1:11:99:4,0,7,0 chr2 119751860 . G A 883.67 PASS AC=1;AF=0.5;AN=2;DP=62;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-2.371;QD=14.25;ReadPosRankSum=0;SOR=0.789;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:27,35:62:99:912,0,653:18,9,24,11 chr2 119914101 . T G 1210.36 PASS AC=1;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 0/1:36,36:72:99:935,0,951:18,18,21,15 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 1/1:1,37:38:82:1177,82,0:1,0,27,10 chr2 119915249 . T C 793.2 PASS AC=1;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 0/1:71,83:154:99:2010,0,1574:37,34,44,39 chr2 119915509 . G T 947.02 PASS AC=1;AF=0.571;AN=2;DP=687;MQ=60;set=variant-variant4-variant13-variant14-variant15-variant16-variant19-variant20-variant23-variant26-variant27-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:15,19:34:99:482,0,425:7,8,10,9 chr2 119915988 . A G 492.14 PASS AC=1;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 0/1:16,36:52:99:938,0,359:10,6,19,17 chr2 119916308 . C G 1674.15 PASS AC=1;AF=0.5;AN=2;DP=511;FractionInformativeReads=1;MQ=60;set=variant23-variant25-variant33-variant42 GT:AD:DP:GQ:PL:SB 0/1:67,73:140:99:1702,0,2505:33,34,38,35 chr2 119916313 . T A 2112.52 PASS AC=1;AF=0.571;AN=2;DP=2010;MQ=60;set=variant-variant4-variant13-variant14-variant15-variant16-variant19-variant20-variant23-variant26-variant27-variant37-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:76,67:143:99:1471,0,2846:40,36,33,34 chr2 119916340 . C A 1473.5 PASS AC=1;AF=0.5;AN=2;DP=513;FractionInformativeReads=1;MQ=60;set=variant23-variant25-variant33-variant42 GT:AD:DP:GQ:PL:SB 0/1:65,69:134:99:1502,0,1566:33,32,35,34 chr2 119981523 . G T 358.59 PASS AC=2;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 1/1:0,23:23:68:557,68,0:0,0,11,12 chr2 119988565 . G A 1181.34 PASS AC=2;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 1/1:0,130:130:99:3673,387,0:0,0,68,62 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 1/1:0,56:56:99:1802,168,0:0,0,23,33 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 0/1:93:99:19,26,15,33 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 1/1:0,22:22:66:884,66,0:0,0,19,3 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 1/1:0,101:101:99:3340,302,0:0,0,40,61 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 1/1:0,40:40:99:1296,120,0:0,0,16,24 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 1/1:0,26:26:77:838,77,0:0,0,10,16 chr2 120023188 . A G 5296.53 PASS AC=2;AF=0.943;AN=2;DP=7004;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,113:113:99:3456,338,0:0,0,57,56 chr2 120023260 . C T 1269.29 PASS AC=1;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 0/1:51,31:82:99:730,0,1388:19,32,11,20 chr2 120059895 . G GGAAA 984.77 PASS AC=2;AF=0.735;AN=2;DP=2559;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-variant28-variant30-variant31-variant32-variant34-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:2392,168,0:0,0,29,20 chr2 120059921 . C A 1040.52 PASS AC=1;AF=0.533;AN=2;DP=1382;MQ=60;set=variant-variant4-variant7-variant10-variant13-variant15-variant17-variant18-variant20-variant23-variant24-variant25-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,41:77:99:947,0,899:23,13,23,18 chr2 120059988 . T C 1398.69 PASS AC=2;AF=0.735;AN=2;DP=4140;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-variant28-variant30-variant31-variant32-variant34-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,98:98:99:2832,292,0:0,0,49,49 chr2 120060082 . T C 926.72 PASS AC=2;AF=0.735;AN=2;DP=2578;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-variant28-variant30-variant31-variant32-variant34-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1453,145,0:0,0,21,28 chr2 120069155 . C T 121.72 PASS AC=1;AF=0.5;AN=2;DP=33;FractionInformativeReads=1;MQ=60;set=variant19-variant23 GT:AD:DP:GQ:PL:SB 0/1:12,11:23:99:379,0,255:7,5,10,1 chr2 120075163 . C T 603.9 PASS AC=1;AF=0.5;AN=2;DP=64;FractionInformativeReads=1;MQ=60;set=variant19-variant23 GT:AD:DP:GQ:PL:SB 0/1:16,14:30:99:378,0,438:5,11,4,10 chr2 120078689 . T C 148.12 PASS AC=1;AF=0.571;AN=2;DP=198;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant7-variant10-variant13-variant15-variant17-variant20-variant23-variant24-variant25-variant36-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,4:13:60:60,0,219:6,3,2,2 chr2 120078778 . T C 990.43 PASS AC=2;AF=0.735;AN=2;DP=2618;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-variant28-variant30-variant31-variant32-variant34-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2576,275,0:0,0,51,41 chr2 120097851 . A G 142.88 PASS AC=1;AF=0.639;AN=2;DP=2066;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,28:52:99:658,0,596:9,15,12,16 chr2 120125029 . A G 4838.05 PASS AC=1;AF=0.841;AN=2;DP=6894;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:66,63:129:99:1553,0,1623:40,26,39,24 chr2 120125936 . T C 1156.15 PASS AC=1;AF=0.83;AN=2;DP=3117;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:33,34:67:99:748,0,719:14,19,15,19 chr2 120125973 . G C 271.55 PASS AC=1;AF=0.528;AN=2;DP=883;MQ=60;set=variant-variant3-variant4-variant7-variant9-variant13-variant15-variant17-variant19-variant20-variant23-variant25-variant29-variant31-variant36-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:25,19:44:99:507,0,601:10,15,6,13 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 0/1:13,16:29:99:493,0,340:8,5,12,4 chr2 120189404 . A G 538.86 PASS AC=1;AF=0.864;AN=2;DP=643;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:4,6:10:69:169,0,69:2,2,3,3 chr2 120189433 . G C 787.34 PASS AC=1;AF=0.864;AN=2;DP=838;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:5,9:14:99:241,0,102:3,2,5,4 chr2 120194651 . A AGTGTGC 5059.99 PASS AC=1;AF=0.909;AN=2;DP=7932;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:106,76:182:99:2789,0,5459:53,53,36,40 chr2 120195182 . C G 1424.6 PASS AC=1;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 0/1:25,12:37:99:345,0,714:10,15,2,10 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 0/1:25,30:55:99:1174,0,1835:12,13,16,14 chr2 120195699 . T TC 2469.1 PASS AC=1;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 0/1:30,33:63:99:861,0,738:16,14,18,15 chr2 120195700 . G C,GC 2325.77 PASS AC=1,1;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 1/2:64:99:0,0,34,30 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 0/1:55,52:107:99:1221,0,1233:28,27,28,24 chr2 120199140 . A G 809.26 PASS AC=1;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 0/1:25,40:65:99:976,0,518:11,14,20,20 chr2 120209689 . A G 1841.72 PASS AC=1;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 0/1:56,66:122:99:1567,0,1242:25,31,30,36 chr2 120219287 . CAAAAA CAA,CA,CAAAA,CAAA,C 217.24 PASS AC=1,0,0,0,0;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 0/1:10:97:3,2,5,0 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 0/1:12,9:21:99:316,0,410:10,2,9,0 chr2 120221984 . A C 463.53 PASS AC=1;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 0/1:9,8:17:99:221,0,304:1,8,3,5 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 1/1:2,88:90:99:2579,246,0:0,2,59,29 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 1/1:2,192:194:99:5716,532,0:1,1,84,108 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 1/1:0,53:53:99:1642,159,0:0,0,19,34 chr2 120282015 . C T 257.82 PASS AC=1;AF=0.583;AN=2;DP=551;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant10-variant12-variant13-variant14-variant17-variant19-variant21-variant22-variant23-variant24-variant28-variant30-variant31-variant33-variant34-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,9:20:99:197,0,267:5,6,3,6 chr2 120282026 . T G 247.81 PASS AC=1;AF=0.596;AN=2;DP=608;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant17-variant19-variant21-variant22-variant23-variant24-variant28-variant30-variant31-variant33-variant34-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,8:20:99:161,0,287:6,6,4,4 chr2 120303820 . A T 319.36 PASS AC=1;AF=0.625;AN=2;DP=775;MQ=60;set=variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant28-variant30-variant31-variant33-variant34-variant37-variant39-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:19,7:26:99:155,0,598:4,15,2,5 chr2 120317621 . CTT CT,CTTT,CTTTT,C 167.59 PASS AC=0,1,0,0;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 0/2:66:99:12,26,12,16 chr2 120362407 . C T 3828.3 PASS AC=2;AF=0.955;AN=2;DP=6083;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,92:92:99:2831,274,0:0,0,43,49 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 1/1:0,52:52:99:1743,156,0:0,0,16,36 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 1/1:29:33:1,1,19,8 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 1/1:0,83:83:99:2298,248,0:0,0,41,42 chr2 120383138 . CATT C 403.53 PASS AC=1;AF=0.571;AN=2;DP=732;MQ=60;set=variant7-variant8-variant11-variant13-variant15-variant18-variant21-variant22-variant23-variant30-variant33-variant37-variant39-variant40 GT:AD:DP:GQ:PL:SB 0/1:20,25:45:99:990,0,975:17,3,19,6 chr2 120385094 . GATATATATAT GATAT,GAT,GATATAT,G,GATATATAT 341.69 PASS AC=2,0,0,0,0;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 1/1:8:23:0,0,6,2 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 1/1:0,5:5:15:184,15,0:0,0,1,4 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 1/1:0,171:171:99:5167,510,0:0,0,90,81 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 1/1:1,74:75:99:1910,216,0:0,1,36,38 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 1/1:0,39:39:99:1246,117,0:0,0,27,12 chr2 120414083 . C T 581.38 PASS AC=2;AF=0.662;AN=2;DP=2003;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant28-variant30-variant31-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:1892,183,0:0,0,27,34 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 1/1:0,24:24:72:937,72,0:0,0,22,2 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 1/1:0,151:151:99:4585,453,0:0,0,84,67 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 1/1:0,186:186:99:5953,557,0:0,0,95,91 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 1/1:0,99:99:99:2968,296,0:0,0,55,44 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 1/1:0,54:54:99:1711,162,0:0,0,25,29 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 1/1:1,76:77:99:2277,200,0:1,0,32,44 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 1/1:0,23:23:69:750,69,0:0,0,12,11 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 1/1:0,14:14:42:421,42,0:0,0,6,8 chr2 120517250 . C A 270.71 PASS AC=1;AF=0.529;AN=2;DP=757;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant6-variant7-variant12-variant14-variant17-variant18-variant19-variant22-variant23-variant24-variant25-variant28-variant29-variant31-variant41 GT:AD:DP:GQ:PL:SB 0/1:28,19:47:99:447,0,744:18,10,13,6 chr2 120517593 . C T 3242.44 PASS AC=1;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 0/1:60,77:137:99:1732,0,1443:24,36,36,41 chr2 120620092 . AT A,ATT 93.18 DRAGENHardINDEL AC=0,1;AF=0.333,0.167;AN=2;DP=535;set=FilteredInAll GT:DP:GQ:SB 0/2:70:85:33,25,7,5 chr2 120635205 . G A 54.21 PASS AC=1;AF=0.538;AN=2;DP=107;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant12-variant14-variant17-variant19-variant22-variant23-variant24-variant25-variant29-variant31-variant33 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:67:239,0,67:0,2,0,6 chr2 120689905 . A G 417.99 PASS AC=1;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 0/1:3,8:11:95:238,0,95:3,0,6,2 chr2 120703842 . A G 357.65 PASS AC=1;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 0/1:2,5:7:71:169,0,71:2,0,5,0 chr2 120704164 . A AT 7975.92 PASS AC=1;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 0/1:108,76:184:99:2815,0,6216:51,57,34,42 chr2 120704166 . G T 7984.96 PASS AC=1;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 0/1:110,77:187:99:2815,0,6216:52,58,35,42 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 0/1:71:99:27,27,9,8 chr2 120718322 . A G 644.69 PASS AC=1;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 0/1:6,16:22:99:514,0,166:5,1,13,3 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 1/1:0,12:12:36:434,36,0:0,0,2,10 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 1/1:0,8:8:24:357,24,0:0,0,0,8 chr2 120734737 . C CA 2053.18 PASS AC=2;AF=0.575;AN=2;DP=3458;MQ=60;set=variant2-variant4-variant6-variant7-variant12-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant31-variant32-variant33-variant41 GT:AD:DP:GQ:PL:SB 1/1:5,118:123:99:3268,245,0:3,2,82,36 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 1/1:0,30:30:90:938,90,0:0,0,13,17 chr2 120736882 . T C 5755.12 PASS AC=2;AF=0.579;AN=2;DP=9104;MQ=60;set=variant2-variant4-variant6-variant7-variant12-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant31-variant33-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,413:413:99:12575,1236,0:0,0,208,205 chr2 120737825 . C A 3192.13 PASS AC=1;AF=0.525;AN=2;DP=6565;MQ=60;set=variant2-variant4-variant6-variant7-variant12-variant14-variant17-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant31-variant32-variant33-variant41 GT:AD:DP:GQ:PL:SB 0/1:147,158:305:99:3652,0,3662:62,85,73,85 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 1/1:0,88:88:99:2891,264,0:0,0,37,51 chr2 120739236 . T C 9108.99 PASS AC=1;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 0/1:93,111:204:99:2749,0,2396:52,41,67,44 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 1/1:0,102:102:99:4642,313,0:0,0,53,49 chr2 120741083 . T C 12659.3 PASS AC=1;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 0/1:175,168:343:99:3711,0,4082:82,93,75,93 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 1/1:0,63:63:99:1910,189,0:0,0,34,29 chr2 120770857 . G A 733.06 PASS AC=2;AF=0.571;AN=2;DP=924;MQ=60;set=variant2-variant4-variant6-variant7-variant14-variant16-variant18-variant21-variant22-variant23-variant25-variant29-variant33-variant37 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:1776,199,0:0,0,36,32 chr2 120831654 . CT CTT,C 408.5 PASS AC=0,1;AF=0.25,0.25;AN=2;DP=82;FractionInformativeReads=1;MQ=60;set=variant3-filterInvariant23 GT:DP:GQ:SB 0/2:31:74:20,5,4,2 chr2 120900736 . T C 1207.1 PASS AC=2;AF=0.577;AN=2;DP=1137;MQ=60;set=variant2-variant4-variant6-variant7-variant14-variant18-variant21-variant22-variant23-variant25-variant29-variant33-variant37 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2197,215,0:0,0,35,37 chr2 120932615 . C T 1666.57 PASS AC=1;AF=0.5;AN=2;DP=279;MQ=60;set=variant23-variant25 GT:AD:DP:GQ:PL:SB 0/1:69,64:133:99:1695,0,1844:31,38,31,33 chr2 120979322 . T C 1944.98 PASS AC=1;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 0/1:30,37:67:99:972,0,668:16,14,19,18 chr2 120979463 . A G 1091.27 PASS AC=1;AF=0.5;AN=2;DP=427;FractionInformativeReads=1;MQ=60;set=variant4-variant17-variant20-variant23-variant28-variant32-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:18,22:40:99:731,0,446:10,8,16,6 chr2 120980701 . A G 1653.78 PASS AC=1;AF=0.5;AN=2;DP=915;FractionInformativeReads=1;MQ=60;set=variant4-variant17-variant20-variant23-variant28-variant32-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:63,49:112:99:1349,0,1575:33,30,23,26 chr2 120997856 . T A 1265.44 PASS AC=1;AF=0.5;AN=2;DP=403;set=variant4-variant17-variant20-variant23-variant28-variant32-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,17:33:99:592,0,1097:6,10,4,13 chr2 120997857 . A T 1265.36 PASS AC=1;AF=0.5;AN=2;DP=438;FractionInformativeReads=1;set=variant4-variant10-variant17-variant20-variant23-variant28-variant32-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:16,16:32:99:592,0,1097:6,10,4,12 chr2 121010443 . A T 2301.4 PASS AC=1;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 0/1:23,50:73:99:1083,0,505:10,13,25,25 chr2 121036025 . G C 710.3 PASS AC=1;AF=0.5;AN=2;DP=608;FractionInformativeReads=1;MQ=60;set=variant4-variant11-variant17-variant20-variant23-variant28-variant31-variant32-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:34,23:57:99:573,0,987:24,10,15,8 chr2 121036333 . G A 930 PASS AC=1;AF=0.5;AN=2;DP=518;MQ=60;set=variant4-variant17-variant20-variant23-variant28-variant32-variant38-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:35,26:61:99:613,0,931:14,21,8,18 chr2 121036385 . T G 728.03 PASS AC=1;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 0/1:28,19:47:99:714,0,1460:8,20,5,14 chr2 121036386 . T A 728.03 PASS AC=1;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 0/1:28,19:47:99:714,0,1460:8,20,5,14 chr2 121038290 . GA G 692.39 PASS AC=1;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 0/1:6,6:12:99:123,0,122:5,1,4,2 chr2 121038558 . G GT 144.11 PASS AC=1;AF=0.5;AN=2;DP=254;MQ=60;set=variant4-variant11-variant13-variant17-variant18-variant20-variant23-filterInvariant28-variant31-variant32-variant34-variant38-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:7,10:17:99:233,0,159:1,6,3,7 chr2 121043403 . G A 932.48 PASS AC=1;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 0/1:14,10:24:99:329,0,442:11,3,7,3 chr2 121050989 . T A 4768.32 PASS AC=1;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 0/1:70,77:147:99:1965,0,1890:36,34,42,35 chr2 121052268 . A T 915.9 PASS AC=1;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 0/1:10,9:19:99:236,0,306:2,8,2,7 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 0/1:29,19:48:99:446,0,649:17,12,12,7 chr2 121108218 . G T 578.74 PASS AC=1;AF=0.5;AN=2;DP=95;FractionInformativeReads=1;MQ=60;set=variant5-variant23 GT:AD:DP:GQ:PL:SB 0/1:19,30:49:99:720,0,458:12,7,13,17 chr2 121108974 . CAA CA,C,CAAA 110.07 PASS AC=1,0,0;AF=0.458,0.028,0.028;AN=2;DP=1706;set=variant-variant2-variant3-variant4-variant5-filterInvariant9-variant10-variant11-variant12-filterInvariant13-variant14-filterInvariant15-filterInvariant16-filterInvariant17-variant20-variant21-variant22-variant23-variant24-filterInvariant25-variant26-filterInvariant27-variant28-filterInvariant29-variant30-filterInvariant31-variant32-filterInvariant34-filterInvariant36-filterInvariant37-variant38-filterInvariant39-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 0/1:32:99:5,4,11,12 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 1/1:0,10:10:30:400,30,0:0,0,9,1 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 1/1:0,36:36:99:1085,108,0:0,0,22,14 chr2 121708663 . A G 1570.95 PASS AC=2;AF=0.898;AN=2;DP=1847;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,30:30:89:1082,89,0:0,0,24,6 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 0/1:6,8:14:55:70,0,55:4,2,7,1 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 1/1:0,35:35:99:1500,105,0:0,0,8,27 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 1/1:0,31:31:99:1450,99,0:0,0,6,25 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 1/1:0,24:24:72:937,72,0:0,0,4,20 chr2 121726447 . G A 6330.34 PASS AC=2;AF=0.932;AN=2;DP=14278;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,293:294:99:8684,848,0:1,0,129,164 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 1/1:0,29:29:87:1091,87,0:0,0,25,4 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 1/1:0,55:55:99:1832,165,0:0,0,39,16 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 1/1:0,191:191:99:5552,570,0:0,0,96,95 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 1/1:0,33:33:99:1056,99,0:0,0,10,23 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 1/1:0,61:61:99:2070,183,0:0,0,43,18 chr2 121732710 . C T 746.77 PASS AC=1;AF=0.5;AN=2;DP=179;FractionInformativeReads=1;MQ=60;set=variant19-variant23-variant27 GT:AD:DP:GQ:PL:SB 0/1:27,38:65:99:947,0,676:9,18,14,24 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 1/1:0,24:24:72:1080,72,0:0,0,18,6 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 1/1:0,24:24:72:1080,72,0:0,0,18,6 chr2 121740505 . C T 507.89 PASS AC=1;AF=0.898;AN=2;DP=3243;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:25,37:62:99:921,0,613:9,16,15,22 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 1/1:0,59:59:99:1832,177,0:0,0,25,34 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 1/1:0,203:203:99:6368,608,0:0,0,96,107 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 1/1:0,143:143:99:4606,428,0:0,0,68,75 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 1/1:0,126:126:99:3982,377,0:0,0,63,63 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 1/1:0,49:49:99:1623,147,0:0,0,25,24 chr2 121749242 . C T 1083.27 PASS AC=1;AF=0.5;AN=2;DP=110;FS=0.719;FractionInformativeReads=1;MQ=60;MQRankSum=-1.335;QD=9.85;ReadPosRankSum=-0.883;SOR=0.816;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:62,48:110:99:1112,0,1545:33,29,27,21 chr2 121749583 . TACACACACACACACACACAC T,TACACACACACACACACACACACAC,TACACACACACACACACAC,TACACACACACACACACACACACACAC,TACACACACACACACACACACAC,TACACACACACACAC,TACACACACACACACACACACACACACAC,TACACACACAC 283.97 PASS AC=0,0,0,2,0,0,0,0;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 4/4:8:31:0,0,4,4 chr2 121976642 . G A 1158.49 PASS AC=2;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 1/1:0,128:128:99:3923,384,0:0,0,55,73 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 1/1:0,104:104:99:3324,311,0:0,0,46,58 chr2 121978882 . T C 940.01 PASS AC=1;AF=0.5;AN=2;DP=258;MQ=60;set=variant8-variant22-variant23-variant37 GT:AD:DP:GQ:PL:SB 0/1:19,38:57:99:992,0,459:8,11,17,21 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 1/1:0,21:21:63:533,63,0:0,0,8,13 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 1/1:0,164:164:99:7381,497,0:0,0,87,77 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 1/1:0,164:164:99:7478,506,0:0,0,86,78 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 1/1:1,93:94:99:2590,255,0:0,1,34,59 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 1/1:0,51:51:99:1906,154,0:0,0,29,22 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 1/1:0,59:59:99:1912,177,0:0,0,31,28 chr2 121980857 . ATAGT A 316.68 PASS AC=2;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 1/1:0,35:35:99:1540,105,0:0,0,17,18 chr2 121982011 . T A 691.27 PASS AC=2;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 1/1:2,79:81:99:2338,193,0:1,1,36,43 chr2 121989489 . G A 629.34 PASS AC=2;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 1/1:1,93:94:99:2735,236,0:1,0,54,39 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 0/1:28,38:66:99:900,0,714:11,17,15,23 chr2 122007378 . A C 527.38 PASS AC=2;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 1/1:0,32:32:96:1065,96,0:0,0,9,23 chr2 122042759 . C T 2254.37 PASS AC=1;AF=0.5;AN=2;DP=166;FS=0;FractionInformativeReads=0.994;MQ=60;MQRankSum=-1.018;QD=13.58;ReadPosRankSum=0.368;SOR=0.685;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:76,89:165:99:2283,0,1871:28,48,33,56 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 0/1:116,111:227:99:4119,0,4563:55,61,50,61 chr2 122095519 . GCC GC,G 1667.15 PASS AC=2,0;AF=0.795,0.159;AN=2;DP=3348;MQ=60;set=Intersection GT:DP:GQ:SB 1/1:61:99:0,1,21,39 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 0/1:17,16:33:99:418,0,488:8,9,7,9 chr2 122095855 . C T 839.45 PASS AC=1;AF=0.5;AN=2;DP=231;FractionInformativeReads=1;MQ=60;set=variant9-variant23-variant24-variant28 GT:AD:DP:GQ:PL:SB 0/1:33,16:49:99:418,0,840:18,15,7,9 chr2 122096162 . G A 1340.52 PASS AC=1;AF=0.5;AN=2;DP=121;FS=3.332;FractionInformativeReads=0.992;MQ=60;MQRankSum=-1.349;QD=11.08;ReadPosRankSum=-1.197;SOR=0.489;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:61,59:120:99:1369,0,1342:35,26,29,30 chr2 122273475 . T C 106.14 PASS AC=1;AF=0.5;AN=2;DP=56;FS=0;FractionInformativeReads=1;MQ=60;set=variant10-variant17-variant23 GT:AD:DP:GQ:PL:SB 0/1:6,12:18:99:343,0,202:1,5,2,10 chr2 122520713 . GTT GTTT,GTTTT,GT,G 137 PASS AC=0,0,0,1;AF=0.283,0.022,0.174,0.043;AN=2;DP=1404;set=filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-variant7-variant8-filterInvariant9-filterInvariant10-filterInvariant13-variant15-filterInvariant16-filterInvariant19-filterInvariant20-filterInvariant22-variant23-filterInvariant24-filterInvariant26-variant27-filterInvariant31-filterInvariant33-variant34-variant36-variant38 GT:DP:GQ:SB 0/4:16:99:3,4,2,7 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 1/1:0,128:128:99:4030,384,0:0,0,68,60 chr2 125204192 . A G 624.5 PASS AC=1;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 0/1:13,15:28:99:358,0,339:8,5,9,6 chr2 125204769 . AT A 128.16 PASS AC=1;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 0/1:9,13:22:99:301,0,177:3,6,3,10 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 1/1:0,71:71:99:2376,213,0:0,0,23,48 chr2 125405302 . C T 1123.53 PASS AC=2;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 1/1:0,125:125:99:4007,375,0:0,0,83,42 chr2 125504906 . C T 1246.52 PASS AC=1;AF=0.5;AN=2;DP=104;FS=0.727;FractionInformativeReads=1;MQ=60;MQRankSum=-1.06;QD=11.99;ReadPosRankSum=-0.995;SOR=0.613;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:51,53:104:99:1275,0,1308:22,29,24,29 chr2 127413616 . G A 667.41 PASS AC=2;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 1/1:0,38:38:99:1056,114,0:0,0,23,15 chr2 127447763 . G A 732.66 PASS AC=2;AF=0.662;AN=2;DP=2397;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:2079,188,0:0,0,45,18 chr2 127453664 . A C 1395.74 PASS AC=2;AF=0.662;AN=2;DP=5943;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant33-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,179:181:99:5453,493,0:1,1,96,83 chr2 127657221 . C T 1009.57 PASS AC=2;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 1/1:0,27:27:81:953,81,0:0,0,12,15 chr2 127808226 . A T 1095.09 PASS AC=1;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 0/1:32,47:79:99:1249,0,913:11,21,17,30 chr2 127808532 . G A 1514.64 PASS AC=1;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 0/1:48,38:86:99:884,0,1291:18,30,16,22 chr2 127808909 . G A 2564.79 PASS AC=1;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 0/1:65,66:131:99:1568,0,1660:30,35,30,36 chr2 127811712 . G GCA 466.36 PASS AC=1;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 0/1:13,13:26:99:506,0,516:5,8,4,9 chr2 127814835 . T C 222.69 PASS AC=1;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 0/1:5,3:8:99:108,0,154:4,1,3,0 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 0/1:60,48:108:99:1193,0,1606:37,23,30,18 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 1/1:19:58:0,0,8,11 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 0/1:18,17:35:99:492,0,346:10,8,11,6 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 0/1:71,55:126:99:1304,0,1964:41,30,31,24 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 0/1:126,100:226:99:2251,0,3081:73,53,52,48 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 0/1:43,31:74:99:662,0,1109:19,24,13,18 chr2 127833963 . C T 202.71 PASS AC=1;AF=0.583;AN=2;DP=97;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant20-variant23-variant25-variant27-variant28-variant34-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,6:8:55:226,0,55:1,1,5,1 chr2 127834136 . T C 4956.17 PASS AC=1;AF=0.567;AN=2;DP=2419;MQ=60;set=variant-variant2-variant3-variant4-variant20-variant23-variant25-variant27-variant28-variant31-variant34-variant36-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:69,78:147:99:2064,0,1533:37,32,42,36 chr2 127834369 . C T 941.49 PASS AC=1;AF=0.567;AN=2;DP=542;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant20-variant23-variant25-variant27-variant28-variant31-variant34-variant36-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,17:28:99:637,0,486:1,10,1,16 chr2 127834384 . T C 858.53 PASS AC=1;AF=0.567;AN=2;DP=391;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant20-variant23-variant25-variant27-variant28-variant31-variant34-variant36-variant38-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,12:16:99:531,0,258:0,4,0,12 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 0/1:50,57:107:99:1211,0,1090:24,26,23,34 chr2 127839513 . G A 1357.85 PASS AC=1;AF=0.571;AN=2;DP=880;MQ=60;set=variant-variant2-variant3-variant4-variant20-variant23-variant25-variant27-variant28-variant31-variant34-variant36-variant38-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,41:68:99:1063,0,677:7,20,15,26 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 0/1:34,14:48:99:425,0,941:11,23,2,12 chr2 127864200 . C A 140.3 PASS AC=1;AF=0.625;AN=2;DP=64;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant23-variant25-variant26-variant31-variant36-variant44 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:107,0,117:3,1,3,1 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 0/1:216,168:384:99:3685,0,4930:107,109,80,88 chr2 127941798 . T C 4502.86 PASS AC=2;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 1/1:0,229:229:99:7091,685,0:0,0,102,127 chr2 127942231 . G A 380.65 PASS AC=2;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 1/1:0,33:33:98:926,98,0:0,0,19,14 chr2 127942334 . C T 907.59 PASS AC=2;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 1/1:0,47:47:99:1372,141,0:0,0,24,23 chr2 127944781 . A AC 2858.62 PASS AC=2;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 1/1:0,61:61:99:2458,184,0:0,0,30,31 chr2 127950904 . A T 284.84 PASS AC=2;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 1/1:0,36:36:99:1277,108,0:0,0,9,27 chr2 127951458 . G A 735.07 PASS AC=2;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 1/1:0,62:62:99:2758,187,0:0,0,28,34 chr2 127951459 . C T 735.07 PASS AC=2;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 1/1:0,62:62:99:2758,187,0:0,0,28,34 chr2 127963423 . TC T 111.13 PASS AC=2;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 1/1:0,15:15:45:490,45,0:0,0,4,11 chr2 127977550 . G C,A 3539.37 PASS AC=2,0;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 1/1:109:99:0,0,57,52 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 1/1:0,8:8:24:223,24,0:0,0,3,5 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 1/1:0,67:67:99:2213,201,0:0,0,39,28 chr2 128050000 . A G 341.84 PASS AC=2;AF=0.897;AN=2;DP=232;set=variant3-variant5-variant6-variant7-variant8-variant12-variant14-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant31-variant32-variant33-variant36-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,6:6:18:189,18,0:0,0,4,2 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 1/1:0,39:39:99:1234,117,0:0,0,26,13 chr2 128051726 . G A 1846.82 PASS AC=1;AF=0.5;AN=2;DP=341;MQ=60;set=variant23-variant30 GT:AD:DP:GQ:PL:SB 0/1:100,88:188:99:1875,0,2363:49,51,38,50 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 0/1:27,29:56:99:690,0,604:13,14,10,19 chr2 128056879 . G A 3127.86 PASS AC=1;AF=0.5;AN=2;DP=439;MQ=60;set=variant12-variant23 GT:AD:DP:GQ:PL:SB 0/1:112,106:218:99:2705,0,2894:61,51,54,52 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 1/1:0,192:192:99:8680,584,0:0,0,98,94 chr2 128060017 . CCA C 1937.9 PASS AC=1;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 0/1:19,19:38:99:542,0,552:15,4,13,6 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 0/1:51,60:111:99:1724,0,1556:40,11,43,17 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 0/1:169,162:331:99:3702,0,3942:89,80,87,75 chr2 128060902 . GA GAA,G 266.36 PASS AC=1,0;AF=0.52,0.04;AN=2;DP=640;set=variant-variant3-variant5-variant7-variant9-variant12-filterInvariant13-variant14-variant16-variant18-variant19-variant22-variant23-variant24-variant26-variant29-variant31-variant32-variant34-variant36-filterInvariant37-variant38-variant39-variant42-variant43 GT:DP:GQ:SB 0/1:20:99:8,3,6,3 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 0/1:51,54:105:99:1281,0,1136:27,24,29,25 chr2 128061173 . CAG C 3932.28 PASS AC=1;AF=0.5;AN=2;DP=305;MQ=60;set=variant23-variant30 GT:AD:DP:GQ:PL:SB 0/1:77,102:179:99:3970,0,2964:41,36,58,44 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 0/1:64,85:149:99:2143,0,1476:30,34,39,46 chr2 128062656 . G GA 1348.05 PASS AC=1;AF=0.5;AN=2;DP=268;MQ=60;set=variant23-variant30 GT:AD:DP:GQ:PL:SB 0/1:72,62:134:99:1385,0,1652:31,41,27,35 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 1/2:140:99:17,5,63,55 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 1/1:0,47:47:99:1836,141,0:0,0,27,20 chr2 128064423 . CGTGTGT C,CGT,CGTGT,CGTGTGTGTGTGT 7846.14 PASS AC=0,1,0,0;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 0/2:144:99:37,31,38,38 chr2 128076022 . T C 227.92 PASS AC=2;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 1/1:0,10:10:30:406,30,0:0,0,1,9 chr2 128079806 . A G 359.07 PASS AC=1;AF=0.607;AN=2;DP=678;MQ=60;set=variant2-variant4-variant10-variant13-variant15-variant20-variant21-variant23-variant26-variant30-variant31-variant33-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:32,22:54:99:524,0,784:11,21,8,14 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 0/1:6,9:15:99:230,0,169:4,2,4,5 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 0/1:52,49:101:99:1251,0,1381:35,17,30,19 chr2 128175875 . G A 3391.4 PASS AC=1;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 0/1:57,60:117:99:1399,0,1432:39,18,35,25 chr2 128176040 . A T 2459.89 PASS AC=1;AF=0.593;AN=2;DP=5032;MQ=60;set=variant2-variant4-variant5-variant10-variant11-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant30-variant31-variant32-variant33-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:73,79:152:99:1818,0,1655:35,38,38,41 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 1/1:0,24:24:72:955,72,0:0,0,2,22 chr2 128177377 . C T 4533.43 PASS AC=1;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 0/1:97,82:179:99:1920,0,2352:49,48,46,36 chr2 128180872 . G T 3825.58 PASS AC=2;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 1/1:1,108:109:99:3334,316,0:1,0,60,48 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 1/1:0,123:123:99:4017,367,0:0,0,66,57 chr2 128181234 . GC G 2537.49 PASS AC=2;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 1/1:0,64:64:99:2089,193,0:0,0,31,33 chr2 128184770 . T C 165.67 PASS AC=1;AF=0.559;AN=2;DP=597;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant10-variant13-variant15-variant19-variant20-variant21-variant22-variant23-variant24-variant26-variant30-variant31-variant33-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,15:29:99:406,0,382:4,10,5,10 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 1/1:0,5:5:15:186,15,0:0,0,5,0 chr2 128271958 . C T 1065.9 PASS AC=2;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 1/1:0,102:102:99:3237,306,0:0,0,36,66 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 1/1:0,30:30:90:1153,90,0:0,0,3,27 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 0/1:34,24:58:99:538,0,772:17,17,11,13 chr2 128334355 . C T 475.42 PASS AC=1;AF=0.5;AN=2;DP=35;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.743;QD=13.58;ReadPosRankSum=2.195;SOR=0.631;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:18,17:35:99:504,0,581:3,15,3,14 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 0/1:27,21:48:99:509,0,680:9,18,7,14 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 0/1:23,14:37:99:345,0,576:12,11,10,4 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 0/1:17,13:30:99:468,0,568:10,7,7,6 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 1/1:0,67:67:99:2243,201,0:0,0,18,49 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 0/1:32,30:62:99:623,0,727:17,15,19,11 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 1/1:0,11:11:33:470,33,0:0,0,0,11 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 0/1:64,88:152:99:2340,0,1625:20,44,27,61 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 1/1:0,73:73:99:2585,220,0:0,0,17,56 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 0/1:8,13:21:99:422,0,297:2,6,2,11 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 1/1:0,39:39:99:1361,117,0:0,0,15,24 chr2 128366272 . G A 587.73 PASS AC=1;AF=0.5;AN=2;DP=521;FractionInformativeReads=1;MQ=60;set=variant-variant19-variant22-variant23-variant24-variant26-variant30-variant31-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:19,23:42:99:697,0,461:14,5,16,7 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 0/1:57,43:100:99:988,0,1355:29,28,21,22 chr2 128367359 . G A 1265.69 PASS AC=1;AF=0.5;AN=2;DP=1473;MQ=60;set=variant-variant19-variant23-variant24-variant26-variant30-variant31-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:54,85:139:99:2101,0,1319:23,31,33,52 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 0/1:60,36:96:99:828,0,1566:35,25,21,15 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 0/1:50,44:94:99:1682,0,2819:25,25,27,17 chr2 128377842 . T C 1064.22 PASS AC=1;AF=0.5;AN=2;DP=888;FractionInformativeReads=1;MQ=60;set=variant-variant19-variant23-variant24-variant26-variant30-variant31-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:54,46:100:99:1733,0,2874:27,27,29,17 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 0/1:13,4:17:81:81,0,357:5,8,1,3 chr2 128379563 . C G 2087.53 PASS AC=1;AF=0.5;AN=2;DP=1795;MQ=60;set=variant-variant19-variant23-variant24-variant26-variant30-variant31-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:87,92:179:99:2134,0,2006:43,44,45,47 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 0/1:7,7:14:99:220,0,191:4,3,7,0 chr2 128383174 . T C 464.13 PASS AC=1;AF=0.5;AN=2;DP=489;FractionInformativeReads=1;MQ=60;set=variant-variant19-variant23-variant24-variant26-variant30-variant31-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:20,27:47:99:732,0,613:5,15,9,18 chr2 128383366 . T C 129.16 PASS AC=1;AF=0.5;AN=2;DP=118;FractionInformativeReads=1;MQ=60;set=variant6-variant19-variant23-variant24-variant26-variant30-variant31-variant32-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:4,4:8:99:149,0,159:1,3,0,4 chr2 128384965 . A G 137.52 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=957;MQ=60;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:68,23:91:99:206,0,1413:55,13,0,23 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 0/1:64,51:115:99:1341,0,1738:32,32,27,24 chr2 128385244 . T C 1857.69 PASS AC=1;AF=0.5;AN=2;DP=2032;MQ=60;set=variant-variant6-variant10-variant19-variant20-variant23-variant24-variant26-variant30-variant31-variant32-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:59,47:106:99:1209,0,1600:32,27,22,25 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 0/1:44,41:85:99:1096,0,1087:16,28,9,32 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 0/1:14,5:19:99:158,0,428:3,11,2,3 chr2 128392647 . G T 1083.19 PASS AC=1;AF=0.55;AN=2;DP=627;FractionInformativeReads=1;MQ=60;set=variant6-variant8-variant11-variant23-variant25-variant27-variant31-variant32-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:15,31:46:99:866,0,413:10,5,20,11 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 0/1:20,17:37:99:461,0,488:13,7,12,5 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 0/1:30,23:53:99:550,0,678:19,11,16,7 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 0/1:52,51:103:99:1408,0,1481:32,20,32,19 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 0/1:90,89:179:99:3520,0,5183:49,41,49,40 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 0/2:185:99:51,43,50,41 chr2 128395885 . A C 285.1 PASS AC=1;AF=0.5;AN=2;DP=18;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.272;QD=15.84;ReadPosRankSum=1.087;SOR=0.346;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:7,11:18:99:313,0,216:6,1,8,3 chr2 128397517 . C T 335.31 PASS AC=1;AF=0.5;AN=2;DP=81;FractionInformativeReads=1;MQ=60;set=variant23-variant31 GT:AD:DP:GQ:PL:SB 0/1:17,11:28:99:364,0,483:14,3,7,4 chr2 128397728 . G C 1476.85 PASS AC=1;AF=0.5;AN=2;DP=272;MQ=60;set=variant23-variant31 GT:AD:DP:GQ:PL:SB 0/1:71,63:134:99:1505,0,1931:36,35,33,30 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 0/1:56,49:105:99:1110,0,1446:27,29,21,28 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 0/1:18,17:35:99:449,0,453:6,12,7,10 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 0/1:28,28:56:99:738,0,752:13,15,14,14 chr2 128401695 . T A 1237.52 PASS AC=1;AF=0.5;AN=2;DP=142;FractionInformativeReads=1;MQ=60;set=variant23-variant31 GT:AD:DP:GQ:PL:SB 0/1:19,43:62:99:1266,0,463:5,14,15,28 chr2 128401742 . A G 512.88 PASS AC=1;AF=0.5;AN=2;DP=384;FractionInformativeReads=1;MQ=60;set=variant8-variant10-variant11-variant23-variant25-variant27-variant31-variant39 GT:AD:DP:GQ:PL:SB 0/1:11,26:37:99:734,0,325:1,10,9,17 chr2 128401755 . C G 654.38 PASS AC=1;AF=0.5;AN=2;DP=83;FractionInformativeReads=1;MQ=60;set=variant23-variant31 GT:AD:DP:GQ:PL:SB 0/1:10,24:34:99:683,0,295:1,9,8,16 chr2 128403762 . G A 618 PASS AC=1;AF=0.5;AN=2;DP=118;FS=0;FractionInformativeReads=1;MQ=60;set=variant23-variant31 GT:AD:DP:GQ:PL:SB 0/1:23,28:51:99:646,0,614:10,13,12,16 chr2 128403882 . G A 165.59 PASS AC=1;AF=0.5;AN=2;DP=35;FractionInformativeReads=1;MQ=60;set=variant23-variant31 GT:AD:DP:GQ:PL:SB 0/1:8,8:16:99:194,0,181:3,5,2,6 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 0/1:28,25:53:99:628,0,596:14,14,12,13 chr2 128405745 . A C 610.06 PASS AC=1;AF=0.5;AN=2;DP=54;FS=1.05;FractionInformativeReads=1;MQ=60;MQRankSum=1.648;QD=11.3;ReadPosRankSum=0.954;SOR=0.609;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:29,25:54:99:638,0,620:16,13,12,13 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 1/1:0,62:62:99:2533,190,0:0,0,42,20 chr2 128409905 . A G 1319.31 PASS AC=2;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 1/1:0,94:94:99:2872,282,0:0,0,44,50 chr2 128411934 . A G 630.86 PASS AC=2;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 1/1:0,36:36:99:1219,108,0:0,0,27,9 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 1/1:0,49:49:99:1484,147,0:0,0,32,17 chr2 128421829 . G A 314.98 PASS AC=2;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 1/1:0,14:14:42:446,42,0:0,0,10,4 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 1/1:0,42:42:99:1368,126,0:0,0,20,22 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 2/3:51:99:1,0,13,37 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 0/1:45,18:63:99:153,0,815:26,19,11,7 chr2 128620372 . T C 772.07 PASS AC=2;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 1/1:0,19:19:56:610,56,0:0,0,4,15 chr2 128699833 . C T 1431.88 PASS AC=2;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 1/1:0,25:25:75:967,75,0:0,0,16,9 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 1/1:0,64:64:99:2024,192,0:0,0,29,35 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 1/1:0,70:70:99:2012,209,0:0,0,28,42 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 1/1:0,56:56:99:1651,168,0:0,0,33,23 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 1/1:0,61:61:99:2060,182,0:0,0,33,28 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 1/1:0,11:11:33:330,33,0:0,0,6,5 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 1/1:0,85:85:99:2588,255,0:0,0,33,52 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 1/1:0,52:52:99:1768,156,0:0,0,13,39 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 1/1:0,37:37:99:1025,111,0:0,0,15,22 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 1/1:0,21:21:63:799,63,0:0,0,4,17 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 1/1:0,9:9:27:389,27,0:0,0,9,0 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 1/1:0,70:70:99:2112,210,0:0,0,32,38 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 1/1:0,14:14:42:461,42,0:0,0,10,4 chr2 128878979 . C CT,CTT,CTTT 213.99 PASS AC=0,0,1;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 0/3:13:25:0,3,3,7 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 1/1:0,4:4:12:180,12,0:0,0,0,4 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 1/1:0,35:35:99:1071,105,0:0,0,14,21 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 1/1:0,5:5:15:154,15,0:0,0,1,4 chr2 128890878 . T TG 2426.19 PASS AC=2;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 1/1:0,115:115:99:4244,346,0:0,0,43,72 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 0/1:116:99:48,32,17,19 chr2 129025705 . C G 734.74 PASS AC=1;AF=0.5;AN=2;DP=546;FractionInformativeReads=1;set=variant-variant5-variant6-variant10-variant18-variant20-variant21-variant23-variant26-variant28-variant34-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:17,12:29:99:328,0,505:10,7,9,3 chr2 129075961 . T C 1553.55 PASS AC=1;AF=0.706;AN=2;DP=6027;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant12-variant14-variant17-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant33-variant34-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:129,76:205:99:1527,0,3051:58,71,44,32 chr2 130681407 . G C 331.77 PASS AC=2;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 1/1:0,21:21:63:716,63,0:0,0,5,16 chr2 130681447 . G A 151.77 PASS AC=2;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 1/1:0,10:10:30:369,30,0:0,0,2,8 chr2 130737221 . T C 769.03 PASS AC=1;AF=0.5;AN=2;DP=1028;FractionInformativeReads=1;set=variant4-variant7-variant11-variant20-variant23-variant30-variant36-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:41,38:79:99:785,0,1115:27,14,22,16 chr2 130737303 . C G 1787.79 PASS AC=1;AF=0.5;AN=2;DP=422;FractionInformativeReads=1;set=variant6-variant9-variant23 GT:AD:DP:GQ:PL:SB 0/1:78,54:132:99:2023,0,3182:44,34,25,29 chr2 130737320 . T C 1876.91 PASS AC=1;AF=0.5;AN=2;DP=694;FractionInformativeReads=1;set=variant6-variant9-variant23-variant34-variant41 GT:AD:DP:GQ:PL:SB 0/1:76,54:130:99:2032,0,3124:39,37,25,29 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 0/1:11,5:16:99:155,0,333:5,6,4,1 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 0/1:8,8:16:99:201,0,223:4,4,5,3 chr2 130737610 . C T 138.32 PASS AC=1;AF=0.5;AN=2;DP=22;FS=0;FractionInformativeReads=1;MQ=45.04;MQRankSum=3.059;QD=6.29;ReadPosRankSum=1.069;SOR=0.495;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:16,6:22:99:167,0,654:7,9,3,3 chr2 130737632 . G C 110.81 PASS AC=1;AF=0.5;AN=2;DP=25;FS=2.072;FractionInformativeReads=1;MQ=43.11;MQRankSum=2.616;QD=4.43;ReadPosRankSum=-1.325;SOR=1.385;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:20,5:25:99:139,0,742:8,12,1,4 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 0/1:77,88:165:99:2020,0,1752:32,45,36,52 chr2 130738329 . C A 818.41 PASS AC=1;AF=0.5;AN=2;DP=182;FractionInformativeReads=1;set=variant6-variant9-variant23 GT:AD:DP:GQ:PL:SB 0/1:34,17:51:99:428,0,981:22,12,11,6 chr2 130832185 . G A 215.45 DRAGENHardSNP AC=2;AF=0.989;AN=2;DP=2109;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:917,107,0:0,0,23,13 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 0/1:17,53:70:99:1092,0,333:14,3,24,29 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 0/1:95,13:108:99:128,0,2739:61,34,13,0 chr2 130832479 . C T 3770.47 PASS AC=1;AF=0.5;AN=2;DP=176;FS=27.08;FractionInformativeReads=1;MQ=50.73;MQRankSum=7.63;QD=21.42;ReadPosRankSum=0.927;SOR=0.068;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:41,135:176:99:3799,0,957:36,5,84,51 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 0/1:216,122:338:99:2609,0,5368:118,98,74,48 chr2 130832873 . G A 311.83 PASS AC=1;AF=0.5;AN=2;DP=4654;set=variant2-filterInvariant3-filterInvariant4-filterInvariant5-filterInvariant6-filterInvariant7-filterInvariant9-filterInvariant12-filterInvariant14-filterInvariant15-filterInvariant16-filterInvariant17-filterInvariant18-filterInvariant19-filterInvariant21-filterInvariant22-filterInvariant23-filterInvariant24-variant25-filterInvariant26-filterInvariant27-filterInvariant28-filterInvariant29-filterInvariant30-filterInvariant31-filterInvariant33-filterInvariant36-filterInvariant37-filterInvariant38-variant39-filterInvariant40-variant41-filterInvariant42-filterInvariant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:153,26:179:99:106,0,3947:76,77,13,13 chr2 130872658 . A T 649.82 DRAGENHardSNP AC=1;AF=0.679;AN=2;DP=2663;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:32,32:64:99:713,0,714:23,9,23,9 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 0/1:123,39:162:99:543,0,3429:73,50,20,19 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 1/1:0,98:98:99:3257,293,0:0,0,70,28 chr2 130897218 . T C 4787.35 PASS AC=1;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 0/1:146,122:268:99:3079,0,3547:72,74,61,61 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 1/1:0,15:15:45:540,45,0:0,0,0,15 chr2 130912778 . A G 248.15 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=381;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:184,21:205:99:276,0,8531:84,100,9,12 chr2 130912789 . A C 223.16 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=369;FractionInformativeReads=1;QD=1.15;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:175,19:194:99:251,0,8397:79,96,8,11 chr2 130941065 . T C 1317.48 PASS AC=2;AF=0.909;AN=2;DP=3170;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,74:74:99:2410,222,0:0,0,49,25 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 1/1:0,124:124:99:3854,370,0:0,0,78,46 chr2 130951548 . G A 2349.83 PASS AC=2;AF=0.898;AN=2;DP=6778;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,117:117:99:4036,350,0:0,0,55,62 chr2 130951566 . G A 2468.97 PASS AC=2;AF=0.83;AN=2;DP=6538;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:1,117:118:99:4029,342,0:1,0,58,59 chr2 130959832 . G A 38.01 PASS AC=1;AF=0.5;AN=2;DP=11;FS=0;FractionInformativeReads=1;MQ=52.76;MQRankSum=-2.262;QD=3.46;ReadPosRankSum=-0.566;SOR=1.371;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:8,3:11:66:66,0,249:6,2,3,0 chr2 130959859 . G T 79.69 PASS AC=1;AF=0.5;AN=2;DP=26;FS=2.556;FractionInformativeReads=1;MQ=54.96;MQRankSum=-3.448;QD=3.07;ReadPosRankSum=0.325;SOR=1.329;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:21,5:26:99:108,0,669:17,4,5,0 chr2 130960023 . T C 1377.47 PASS AC=1;AF=0.685;AN=2;DP=3971;set=variant-variant2-variant3-variant6-variant7-variant8-variant9-variant11-variant12-variant14-variant17-variant18-variant20-variant21-variant23-variant25-variant27-variant28-variant32-variant33-variant34-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,57:135:99:1208,0,2025:36,42,30,27 chr2 130987919 . G A 3652.26 PASS AC=1;AF=0.5;AN=2;DP=280;FS=0.435;FractionInformativeReads=1;MQ=58.68;MQRankSum=-1.534;QD=13.04;ReadPosRankSum=2.883;SOR=0.741;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:134,146:280:99:3680,0,3573:70,64,78,68 chr2 131096892 . G C 1047.51 PASS AC=1;AF=0.5;AN=2;DP=103;FS=1.628;FractionInformativeReads=1;MQ=60;MQRankSum=-1.448;QD=10.17;ReadPosRankSum=-0.679;SOR=0.882;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:60,43:103:99:1076,0,1392:25,35,16,27 chr2 131097236 . G A 1694.16 PASS AC=1;AF=0.5;AN=2;DP=153;FS=3.801;FractionInformativeReads=1;MQ=60;MQRankSum=1.319;QD=11.07;ReadPosRankSum=-2.566;SOR=1.004;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:82,71:153:99:1722,0,1796:38,44,28,43 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 0/1:66,83:149:99:3210,0,2355:27,39,38,45 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 0/1:57,79:136:99:3079,0,2174:23,34,36,43 chr2 131099375 . C G 36.85 PASS AC=1;AF=0.5;AN=2;DP=9;FS=13.222;FractionInformativeReads=1;MQ=60;MQRankSum=0.573;QD=4.09;ReadPosRankSum=-1.203;SOR=2.78;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:65:65,0,263:1,5,3,0 chr2 131099378 . G C 55.5 PASS AC=1;AF=0.5;AN=2;DP=68;FractionInformativeReads=1;MQ=60;set=variant15-variant22-variant23-variant30-variant33-variant34 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:65:65,0,263:1,5,3,0 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 0/1:100,69:169:99:1587,0,2500:43,57,30,39 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 0/1:58,67:125:99:1594,0,1196:31,27,37,30 chr2 131100997 . T C 638.72 PASS AC=1;AF=0.5;AN=2;DP=59;FS=3.245;FractionInformativeReads=1;MQ=60;MQRankSum=-0.406;QD=10.83;ReadPosRankSum=1.726;SOR=0.277;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:34,25:59:99:667,0,1218:4,30,5,20 chr2 131113540 . G A 203.12 PASS AC=1;AF=0.5;AN=2;DP=23;FS=1.674;FractionInformativeReads=1;MQ=60;MQRankSum=-0.775;QD=8.83;ReadPosRankSum=0.465;SOR=1.003;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:13,10:23:99:231,0,259:6,7,6,4 chr2 131113698 . C T 645.99 PASS AC=1;AF=0.5;AN=2;DP=71;FS=6.477;FractionInformativeReads=1;MQ=60;MQRankSum=-1.82;QD=9.1;ReadPosRankSum=-1.993;SOR=0.238;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:39,32:71:99:674,0,957:26,13,16,16 chr2 131114010 . G A 778.46 PASS AC=1;AF=0.545;AN=2;DP=390;MQ=60;set=variant4-variant9-variant14-variant15-variant18-variant23-variant25-variant26-variant31-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,20:38:99:618,0,696:11,7,5,15 chr2 131114028 . G C 505.43 PASS AC=1;AF=0.5;AN=2;DP=36;FS=10.409;FractionInformativeReads=1;MQ=60;MQRankSum=0.844;QD=14.04;ReadPosRankSum=1.64;SOR=1.609;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:16,20:36:99:534,0,612:6,10,14,6 chr2 131114042 . G T 525.39 PASS AC=1;AF=0.533;AN=2;DP=604;MQ=60;set=variant2-variant4-variant9-variant11-variant14-variant15-variant18-variant23-variant25-variant26-variant31-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:22,11:33:99:342,0,888:16,6,7,4 chr2 131116404 . T C 1354.99 PASS AC=2;AF=0.559;AN=2;DP=2451;MQ=60;set=variant2-variant4-variant9-variant10-variant11-variant14-variant15-variant17-variant18-variant23-variant25-variant26-variant31-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:3611,354,0:0,0,68,51 chr2 131119567 . C CT 125.8 PASS AC=1;AF=0.5;AN=2;DP=213;MQ=60;set=variant5-variant11-variant16-variant19-variant23-variant39-variant44 GT:AD:DP:GQ:PL:SB 0/1:17,15:32:99:274,0,325:12,5,8,7 chr2 131119642 . A G 486.71 PASS AC=1;AF=0.5;AN=2;DP=103;FractionInformativeReads=1;MQ=60;set=variant10-variant23 GT:AD:DP:GQ:PL:SB 0/1:32,26:58:99:614,0,702:17,15,11,15 chr2 131128207 . G A 1592.64 PASS AC=1;AF=0.5;AN=2;DP=150;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.937;QD=10.62;ReadPosRankSum=-2.427;SOR=0.743;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:85,65:150:99:1621,0,2210:46,39,36,29 chr2 131129928 . AGACGGG A 1055.16 PASS AC=2;AF=0.563;AN=2;DP=1468;MQ=60;set=variant2-variant4-variant9-variant10-variant11-variant14-variant15-variant18-variant23-variant25-variant26-variant31-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,65:65:99:2906,197,0:0,0,40,25 chr2 131130678 . T C 512.57 PASS AC=2;AF=0.563;AN=2;DP=1331;MQ=60;set=variant2-variant4-variant9-variant10-variant11-variant14-variant15-variant18-variant23-variant25-variant26-variant31-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,73:73:99:2370,219,0:0,0,37,36 chr2 131130830 . T G 2246.45 PASS AC=1;AF=0.5;AN=2;DP=227;FS=1.015;FractionInformativeReads=0.996;MQ=60;MQRankSum=0.141;QD=9.9;ReadPosRankSum=0.317;SOR=0.769;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:116,110:226:99:2275,0,2594:57,59,52,58 chr2 131131424 . G C 918.92 PASS AC=1;AF=0.533;AN=2;DP=1002;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant9-variant11-variant14-variant15-variant18-variant23-variant25-variant26-variant31-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,25:51:99:607,0,737:9,17,11,14 chr2 131131481 . T TAGTC 1285.32 PASS AC=2;AF=0.563;AN=2;DP=987;MQ=60;set=variant2-variant4-variant9-variant10-variant11-variant14-variant15-variant18-variant23-variant25-variant26-variant31-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:2229,150,0:0,0,22,27 chr2 131131525 . C T 648.79 PASS AC=1;AF=0.533;AN=2;DP=1046;MQ=60;set=variant2-variant4-variant9-variant11-variant14-variant15-variant18-variant23-variant25-variant26-variant31-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:25,18:43:99:440,0,722:13,12,11,7 chr2 131131866 . A G 743.13 PASS AC=1;AF=0.533;AN=2;DP=735;MQ=60;set=variant2-variant4-variant9-variant11-variant14-variant15-variant18-variant23-variant25-variant26-variant31-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:27,18:45:99:651,0,1477:10,17,4,14 chr2 131131869 . A G 743.13 PASS AC=1;AF=0.533;AN=2;DP=713;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant9-variant11-variant14-variant15-variant18-variant23-variant25-variant26-variant31-variant36-variant37-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:26,16:42:99:629,0,1480:9,17,3,13 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 1/1:0,29:29:87:855,87,0:0,0,24,5 chr2 131221170 . C T 2296.48 DRAGENHardSNP AC=2;AF=0.895;AN=2;DP=7370;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:1,90:91:99:2265,261,0:1,0,52,38 chr2 131266530 . C A 2870.96 PASS AC=2;AF=0.875;AN=2;DP=11532;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:2,98:100:99:2824,277,0:1,1,46,52 chr2 131369330 . C T 1085.13 PASS AC=1;AF=0.5;AN=2;DP=237;FS=1.851;FractionInformativeReads=0.996;MQ=49.2;MQRankSum=-1.71;QD=4.58;ReadPosRankSum=3.195;SOR=0.833;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:175,61:236:99:1113,0,4370:72,103,23,38 chr2 131377707 . A G 30.86 DRAGENHardSNP AC=2;AF=1;AN=2;DP=2;FS=0;FractionInformativeReads=1;MQ=25.18;QD=15.43;SOR=2.303;set=FilteredInAll GT:AD:DP:GQ:PL:SB 1/1:0,2:2:6:59,6,0:0,0,0,2 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 0/1:7,5:12:99:176,0,233:6,1,5,0 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 0/1:13,16:29:99:412,0,291:2,11,3,13 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 0/1:18,7:25:99:202,0,644:16,2,7,0 chr2 131414073 . T A 142.1 PASS AC=1;AF=0.511;AN=2;DP=1012;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:21,11:32:99:358,0,722:18,3,11,0 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 0/1:79,67:146:99:1403,0,1795:45,34,40,27 chr2 131414394 . C T 130.59 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=4635;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:112,20:132:99:178,0,2715:56,56,4,16 chr2 131414737 . A G 48.35 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=63;FS=0;FractionInformativeReads=1;MQ=27.71;MQRankSum=-2.838;QD=0.77;ReadPosRankSum=1.267;SOR=0.793;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:54,9:63:77:77,0,1398:10,44,1,8 chr2 131414951 . G A 1061.59 PASS AC=1;AF=0.5;AN=2;DP=128;FS=0;FractionInformativeReads=1;MQ=34.84;MQRankSum=-1.655;QD=8.29;ReadPosRankSum=1.703;SOR=0.674;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:72,56:128:99:1090,0,1671:44,28,34,22 chr2 131415082 . T C 437.29 PASS AC=1;AF=0.5;AN=2;DP=106;FS=7.717;FractionInformativeReads=1;MQ=40.57;MQRankSum=-4.575;QD=4.13;ReadPosRankSum=0.218;SOR=1.607;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:79,27:106:99:466,0,1802:34,45,7,20 chr2 131487673 . A C 3726.13 PASS AC=1;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 0/1:77,67:144:99:1704,0,2110:41,36,39,28 chr2 131520663 . T C 6108.01 PASS AC=2;AF=0.943;AN=2;DP=9706;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,232:232:99:6730,695,0:0,0,101,131 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 1/1:0,8:8:24:295,24,0:0,0,6,2 chr2 131594958 . A C 2016.82 PASS AC=1;AF=0.533;AN=2;DP=1071;set=variant2-variant6-variant8-variant10-variant14-variant17-variant23-variant24-variant25-variant26-variant27-variant29-variant33-variant36-variant43 GT:AD:DP:GQ:PL:SB 0/1:31,24:55:99:533,0,764:20,11,12,12 chr2 131672101 . T C 2093 PASS AC=2;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 1/1:0,81:81:99:2691,243,0:0,0,36,45 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 1/1:0,71:71:99:2168,211,0:0,0,36,35 chr2 131672950 . A G 1734.45 PASS AC=2;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 1/1:0,115:115:99:3736,345,0:0,0,54,61 chr2 131673316 . C T 2647.56 PASS AC=2;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 1/1:0,132:132:99:4123,393,0:0,0,66,66 chr2 131674285 . A G 1600.1 PASS AC=2;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 1/1:0,69:69:99:2041,207,0:0,0,34,35 chr2 131769237 . G A 1172.17 PASS AC=1;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 0/1:27,32:59:99:854,0,588:13,14,20,12 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 0/1:5,1:6:69:69,0,321:4,1,1,0 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 0/1:5,4:9:99:130,0,315:4,1,4,0 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 0/1:49,44:93:99:1051,0,1336:28,21,26,18 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 0/1:34,37:71:99:945,0,844:14,20,14,23 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 0/1:21,17:38:99:507,0,772:19,2,14,3 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 0/1:74,89:163:99:2156,0,1774:33,41,37,52 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 0/1:36,36:72:99:812,0,883:13,23,17,19 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 0/1:153:99:33,41,39,40 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 0/1:107,110:217:99:2678,0,2668:58,49,57,53 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 0/1:14,7:21:99:158,0,433:10,4,4,3 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 0/1:32,36:68:99:955,0,822:22,10,25,11 chr2 131812777 . C T 1561.75 PASS AC=1;AF=0.5;AN=2;DP=113;FS=0.737;FractionInformativeReads=1;MQ=60;MQRankSum=0.147;QD=13.82;ReadPosRankSum=0.21;SOR=0.809;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:53,60:113:99:1590,0,1259:34,19,40,20 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 1/1:0,7:7:21:312,21,0:0,0,0,7 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 0/1:35,32:67:99:1261,0,2208:14,21,14,18 chr2 131862700 . A T 51.54 PASS AC=1;AF=0.625;AN=2;DP=68;MQ=60;set=variant23-variant29-variant37-variant41 GT:AD:DP:GQ:PL:SB 0/1:16,5:21:80:80,0,390:9,7,0,5 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 0/1:42,42:84:99:1225,0,1127:31,11,33,9 chr2 131865115 . G A 2294.09 PASS AC=1;AF=0.5;AN=2;DP=387;FractionInformativeReads=1;MQ=60;set=variant19-variant23 GT:AD:DP:GQ:PL:SB 0/1:94,94:188:99:1936,0,2059:53,41,48,46 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 0/1:3,7:10:98:268,0,98:1,2,0,7 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 0/1:91,81:172:99:2003,0,2443:49,42,42,39 chr2 132009959 . T A 52.02 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=5;FS=0;FractionInformativeReads=1;MQ=25.85;MQRankSum=1.231;QD=10.4;ReadPosRankSum=1.231;SOR=1.022;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:2,3:5:42:80,0,42:2,0,3,0 chr2 132021078 . A G 642.9 PASS AC=1;AF=0.5;AN=2;DP=78;FS=3.141;FractionInformativeReads=1;MQ=31.19;MQRankSum=1.153;QD=8.24;ReadPosRankSum=-1.79;SOR=1.104;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:45,33:78:99:671,0,964:19,26,11,22 chr2 132021908 . G A 712.15 PASS AC=1;AF=0.5;AN=2;DP=1505;set=variant3-filterInvariant4-filterInvariant5-filterInvariant13-variant16-filterInvariant19-filterInvariant23-variant25-filterInvariant26-variant30-filterInvariant31-filterInvariant36-filterInvariant39-filterInvariant41-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:75,21:96:99:396,0,2041:14,61,4,17 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 0/1:22,9:31:99:203,0,588:2,20,0,9 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 0/1:39,11:50:99:338,0,1713:24,15,4,7 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 0/1:43,11:54:99:329,0,1799:27,16,4,7 chr2 132044842 . G A 388.22 PASS AC=1;AF=0.5;AN=2;DP=1342;set=variant2-variant4-variant8-variant9-filterInvariant12-variant13-filterInvariant14-variant17-variant18-variant20-filterInvariant21-variant22-variant23-filterInvariant25-variant26-variant28-variant33-filterInvariant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:47,11:58:99:320,0,1909:28,19,4,7 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 0/1:46,11:57:99:320,0,1909:27,19,4,7 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 0/1:42,9:51:99:222,0,1783:22,20,4,5 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 0/1:44,8:52:99:201,0,1786:21,23,3,5 chr2 132044903 . G A 116.03 PASS AC=1;AF=0.5;AN=2;DP=514;set=filterInvariant6-filterInvariant10-variant18-variant19-variant23-filterInvariant27-filterInvariant36-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:36,6:42:99:123,0,1429:15,21,2,4 chr2 132044904 . GTACC G 100.92 PASS AC=1;AF=0.5;AN=2;DP=479;FractionInformativeReads=1;set=filterInvariant6-variant18-variant19-filterInvariant23-filterInvariant27-filterInvariant36-variant43-filterInvariant44 GT:AD:DP:GQ:PL:SB 0/1:37,6:43:99:120,0,1471:16,21,2,4 chr2 132044916 . C T 92.07 DRAGENHardSNP AC=1;AF=0.5;AN=2;DP=130;FractionInformativeReads=1;set=FilteredInAll GT:AD:DP:GQ:PL:SB 0/1:31,3:34:72:72,0,1332:12,19,0,3 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 1/1:0,12:12:36:456,36,0:0,0,1,11 chr2 132248584 . T C 8230.81 PASS AC=2;AF=1;AN=2;DP=12870;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,268:268:99:7925,803,0:0,0,137,131 chr2 132249372 . C T 1076.75 PASS AC=2;AF=0.989;AN=2;DP=1585;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,28:28:84:926,84,0:0,0,20,8 chr2 132258259 . C T 430.48 PASS AC=2;AF=0.583;AN=2;DP=237;set=variant13-variant23-variant27-variant28-variant32-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,28:28:83:930,83,0:0,0,5,23 chr2 132272384 . TG T 174.35 PASS AC=1;AF=0.5;AN=2;DP=26;FS=0;FractionInformativeReads=0.962;MQ=60;MQRankSum=-0.903;QD=6.71;ReadPosRankSum=1.019;SOR=0.784;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:17,8:25:99:212,0,559:7,10,3,5 chr2 132275366 . A G 794.56 PASS AC=2;AF=0.571;AN=2;DP=840;set=variant5-variant13-variant23-variant27-variant28-variant32-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2555,239,0:0,0,36,44 chr2 132275384 . T C 766.04 PASS AC=2;AF=0.571;AN=2;DP=812;set=variant5-variant13-variant23-variant27-variant28-variant32-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,70:70:99:2235,209,0:0,0,31,39 chr2 132275396 . T C 1476.03 PASS AC=2;AF=0.672;AN=2;DP=5375;set=variant-variant2-variant3-variant5-variant6-variant9-variant10-variant12-variant13-variant14-variant15-variant17-variant18-variant20-variant23-variant24-variant25-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,64:64:99:2746,196,0:0,0,28,36 chr2 132275403 . C A 1037.1 PASS AC=2;AF=0.571;AN=2;DP=733;set=variant5-variant13-variant23-variant27-variant28-variant32-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,56:56:99:2583,181,0:0,0,23,33 chr2 132287569 . G A 2319.1 PASS AC=2;AF=0.571;AN=2;DP=1002;set=variant5-variant13-variant23-variant27-variant28-variant32-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:3690,355,0:0,0,65,54 chr2 132354365 . G C 4213.77 PASS AC=2;AF=1;AN=2;DP=6881;FS=0;MQRankSum=0.469;ReadPosRankSum=1.498;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,119:119:99:3559,357,0:0,0,65,54 chr2 132354479 . C A 5919.73 PASS AC=2;AF=1;AN=2;DP=9507;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,181:181:99:5468,543,0:0,0,99,82 chr2 132354586 . A G 5834.78 PASS AC=2;AF=1;AN=2;DP=9011;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,175:175:99:6071,525,0:0,0,107,68 chr2 132354807 . C T 3946.51 PASS AC=2;AF=1;AN=2;DP=5820;FS=0;MQRankSum=1.435;ReadPosRankSum=0.718;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,110:110:99:3668,330,0:0,0,31,79 chr2 132354853 . C G 2121.15 PASS AC=2;AF=1;AN=2;DP=2504;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,48:48:99:1686,144,0:0,0,9,39 chr2 132357474 . C T 314.83 PASS AC=2;AF=1;AN=2;DP=894;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-filterInvariant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:404,33,0:0,0,10,1 chr2 132357667 . A G 1153.34 PASS AC=2;AF=1;AN=2;DP=1662;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:972,105,0:0,0,15,20 chr2 132361518 . G A 446.49 PASS AC=2;AF=1;AN=2;DP=622;FS=0;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:447,30,0:0,0,8,2 chr2 132361543 . A G 741.71 PASS AC=2;AF=1;AN=2;DP=1025;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,15:15:45:634,45,0:0,0,11,4 chr2 132384137 . A C,G 2784.81 PASS AC=1,0;AF=0.4,0.15;AN=2;DP=3624;set=variant-variant6-variant10-variant16-variant23-variant28-variant32-variant35-variant36-variant41 GT:DP:GQ:SB 0/1:353:99:83,99,81,90 chr2 132384339 . C T 1462.47 PASS AC=1;AF=0.895;AN=2;DP=9776;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 0/1:112,86:198:99:2240,0,3007:51,61,46,40 chr2 132384682 . T C 4003.27 PASS AC=2;AF=1;AN=2;DP=7005;FS=0;FractionInformativeReads=1;MQRankSum=-0.129;ReadPosRankSum=1.62;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,135:135:99:6048,409,0:0,0,58,77 chr2 132384683 . T G 4003.27 PASS AC=2;AF=1;AN=2;DP=6897;FS=0;FractionInformativeReads=1;MQRankSum=-0.572;ReadPosRankSum=0.853;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,131:131:99:6048,409,0:0,0,57,74 chr2 132517068 . A G 268.36 PASS AC=1;AF=0.708;AN=2;DP=968;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant11-variant12-variant13-variant14-variant15-variant17-variant20-variant21-variant22-variant23-variant24-variant25-variant27-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:11,8:19:99:141,0,266:7,4,4,4 chr2 132591648 . C T 234.51 PASS AC=1;AF=0.526;AN=2;DP=1013;set=variant-variant6-variant7-variant10-variant13-variant16-variant17-variant23-variant26-variant28-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:24,18:42:99:542,0,681:18,6,11,7 chr2 132591808 . T G 1459.61 PASS AC=1;AF=0.538;AN=2;DP=3080;set=variant-variant7-variant16-variant17-variant23-variant26-variant28-variant32-variant36-variant37-variant38-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:109,98:207:99:2378,0,2825:60,49,52,46 chr2 132592178 . T C 1927.88 PASS AC=1;AF=0.661;AN=2;DP=7513;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant16-variant17-variant21-variant23-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:131,126:257:99:3158,0,2905:60,71,58,68 chr2 132593636 . C T 1376.93 PASS AC=1;AF=0.62;AN=2;DP=3705;set=variant-variant2-variant5-variant7-variant9-variant12-variant13-variant16-variant17-variant21-variant23-variant26-variant28-variant29-variant30-variant31-variant32-variant34-variant36-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:62,68:130:99:1799,0,1610:39,23,40,28 chr2 132594079 . C A 1188.74 PASS AC=1;AF=0.737;AN=2;DP=5125;set=variant-variant2-variant4-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-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 0/1:41,75:116:99:1827,0,942:17,24,32,43 chr2 132905626 . A G 116.28 PASS AC=1;AF=0.5;AN=2;DP=661;set=variant3-variant5-variant7-variant8-variant10-filterInvariant12-variant15-variant16-variant18-variant19-filterInvariant20-variant22-variant23-variant24-variant26-variant27-variant29-variant32-variant33-variant36-variant37-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,7:34:99:165,0,916:23,4,7,0 chr2 132905664 . G T 838.04 PASS AC=1;AF=0.5;AN=2;DP=2354;FractionInformativeReads=1;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-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 0/1:44,29:73:99:1079,0,1844:30,14,14,15 chr2 132905682 . T C 975.9 PASS AC=1;AF=0.5;AN=2;DP=3128;FractionInformativeReads=1;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-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 0/1:52,36:88:99:1391,0,2156:31,21,18,18 chr2 132905693 . T C 957.84 PASS AC=1;AF=0.5;AN=2;DP=3545;FractionInformativeReads=1;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-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 0/1:57,44:101:99:1673,0,2303:32,25,21,23 chr2 132905703 . C G 945.8 PASS AC=1;AF=0.5;AN=2;DP=3851;FractionInformativeReads=1;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-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 0/1:62,44:106:99:1658,0,2513:35,27,21,23 chr2 132905706 . A G 939.81 PASS AC=1;AF=0.5;AN=2;DP=3933;FractionInformativeReads=1;set=variant-variant3-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-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 0/1:63,43:106:99:1610,0,2600:35,28,20,23 chr2 132905741 . G A 872.33 PASS AC=1;AF=0.5;AN=2;DP=4631;set=variant-variant3-variant5-variant6-variant7-filterInvariant8-variant9-variant10-variant11-variant12-variant13-variant15-filterInvariant16-variant18-variant19-variant20-variant21-variant22-variant23-filterInvariant24-variant25-variant26-filterInvariant27-filterInvariant28-variant29-variant30-variant31-variant32-variant33-filterInvariant34-variant35-variant36-variant37-variant38-filterInvariant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:78,41:119:99:1481,0,3006:40,38,18,23 chr2 132905792 . G C 401.57 PASS AC=1;AF=0.5;AN=2;DP=3910;set=variant-variant2-variant3-filterInvariant4-filterInvariant5-variant6-variant7-filterInvariant8-variant9-variant10-variant12-variant13-variant14-variant15-variant18-variant19-variant20-filterInvariant21-variant22-variant23-filterInvariant24-variant25-variant26-filterInvariant27-variant29-variant30-filterInvariant31-variant32-filterInvariant34-variant35-variant37-filterInvariant38-filterInvariant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:75,29:104:99:727,0,2980:30,45,11,18 chr2 132905814 . G C 52.14 PASS AC=1;AF=0.5;AN=2;DP=2019;FractionInformativeReads=1;set=filterInvariant-filterInvariant2-filterInvariant3-filterInvariant4-filterInvariant6-filterInvariant7-filterInvariant9-variant10-variant13-variant14-variant15-variant18-filterInvariant19-filterInvariant20-variant23-variant25-variant26-filterInvariant30-filterInvariant35-variant37-filterInvariant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:66,13:79:99:344,0,2774:25,41,6,7 chr2 132905819 . T A 31.05 PASS AC=1;AF=0.5;AN=2;DP=1504;FractionInformativeReads=1;set=filterInvariant2-filterInvariant4-filterInvariant6-filterInvariant9-variant10-variant14-variant15-variant18-filterInvariant19-filterInvariant20-variant23-filterInvariant25-variant26-filterInvariant30-variant35-variant37-filterInvariant38-variant40-filterInvariant41-variant44 GT:AD:DP:GQ:PL:SB 0/1:64,12:76:99:353,0,2648:25,39,6,6 chr2 132914561 . G A 1013.9 PASS AC=1;AF=0.5;AN=2;DP=6910;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:84,61:145:99:1059,0,2183:49,35,31,30 chr2 132919171 . A G 70.55 PASS AC=1;AF=0.5;AN=2;DP=168;FractionInformativeReads=1;set=variant2-variant8-variant23-filterInvariant31-filterInvariant36 GT:AD:DP:GQ:PL:SB 0/1:23,4:27:96:96,0,1012:10,13,2,2 chr2 132919192 . G A 79.54 PASS AC=1;AF=0.5;AN=2;DP=184;FractionInformativeReads=1;set=variant2-variant8-filterInvariant16-variant23-filterInvariant31-filterInvariant36 GT:AD:DP:GQ:PL:SB 0/1:22,4:26:96:96,0,1000:10,12,2,2 chr2 133014493 . G A 340.74 PASS AC=1;AF=0.5;AN=2;DP=3050;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant12-variant13-filterInvariant14-variant15-variant16-variant17-variant20-filterInvariant21-variant23-variant24-variant25-variant28-variant30-filterInvariant31-filterInvariant32-variant33-filterInvariant35-variant36-variant37-variant38-variant39-variant40-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:66,16:82:99:466,0,3461:42,24,12,4 chr2 133014494 . C T 337.75 PASS AC=1;AF=0.5;AN=2;DP=3098;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant20-filterInvariant21-variant23-variant24-variant25-variant28-variant30-filterInvariant31-filterInvariant32-variant33-filterInvariant35-variant36-variant37-variant38-variant39-variant40-filterInvariant42 GT:AD:DP:GQ:PL:SB 0/1:69,16:85:99:457,0,3578:44,25,12,4 chr2 133014497 . G C 607.18 PASS AC=1;AF=0.5;AN=2;DP=4478;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:73,19:92:99:566,0,3816:49,24,12,7 chr2 133014504 . G T 631.11 PASS AC=1;AF=0.5;AN=2;DP=4810;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:85,19:104:99:534,0,4208:57,28,13,6 chr2 133014510 . T C 638.29 PASS AC=1;AF=0.5;AN=2;DP=5173;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:75,33:108:99:1059,0,3045:52,23,21,12 chr2 133014513 . G A 408.94 PASS AC=1;AF=0.5;AN=2;DP=4235;set=variant2-variant3-variant4-filterInvariant5-variant6-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant20-filterInvariant21-variant22-variant23-variant24-variant25-variant28-variant30-variant31-filterInvariant32-variant33-filterInvariant35-variant36-variant37-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:85,28:113:99:775,0,3465:56,29,20,8 chr2 133014552 . C T 165.34 PASS AC=1;AF=0.5;AN=2;DP=7442;set=filterInvariant-filterInvariant2-variant3-variant4-filterInvariant5-variant6-variant7-variant8-variant9-variant10-variant12-variant13-variant14-variant15-filterInvariant16-variant18-variant19-filterInvariant20-variant21-variant22-variant23-variant24-variant25-variant26-variant27-filterInvariant29-variant32-variant33-variant34-variant37-filterInvariant38-filterInvariant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:135,84:219:99:2074,0,3911:88,47,54,30 chr2 133014592 . G A 613.02 PASS AC=1;AF=0.5;AN=2;DP=13702;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-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-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:190,81:271:99:2312,0,7796:117,73,55,26 chr2 133014602 . G C 4820.71 PASS AC=1;AF=0.5;AN=2;DP=14938;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:113,196:309:99:7808,0,4131:64,49,123,73 chr2 133014612 . A C 5028.35 PASS AC=1;AF=0.5;AN=2;DP=16029;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:120,210:330:99:8502,0,4239:67,53,124,86 chr2 133014614 . C T 543.37 PASS AC=1;AF=0.5;AN=2;DP=3295;set=filterInvariant13-filterInvariant17-variant23-variant29-filterInvariant30-variant32-variant38-variant40-variant44 GT:AD:DP:GQ:PL:SB 0/1:248,73:321:99:1617,0,10217:142,106,45,28 chr2 133014619 . C T 1859.52 PASS AC=1;AF=0.5;AN=2;DP=16976;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:230,121:351:99:4614,0,9458:128,102,76,45 chr2 133014640 . C T 2539.17 PASS AC=1;AF=0.5;AN=2;DP=19084;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:258,140:398:99:5128,0,10467:142,116,82,58 chr2 133014651 . A AC 6280.36 PASS AC=1;AF=0.5;AN=2;DP=20068;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:127,260:387:99:9677,0,3298:66,61,143,117 chr2 133014657 . G A 2611.92 PASS AC=1;AF=0.5;AN=2;DP=20727;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:AD:DP:GQ:PL:SB 0/1:251,146:397:99:5060,0,10117:130,121,84,62 chr2 133014678 . A G 7409.48 PASS AC=1;AF=0.5;AN=2;DP=21102;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:119,272:391:99:10999,0,3818:56,63,131,141 chr2 133014703 . T C 7910.09 PASS AC=1;AF=0.5;AN=2;DP=21571;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:131,280:411:99:11592,0,4629:55,76,123,157 chr2 133014721 . T C 7339.97 PASS AC=1;AF=0.5;AN=2;DP=21946;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:127,280:407:99:11101,0,4437:52,75,114,166 chr2 133014751 . T C 2894.76 PASS AC=1;AF=0.5;AN=2;DP=20261;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:279,111:390:99:3688,0,10726:125,154,46,65 chr2 133014776 . C T 3094.95 PASS AC=1;AF=0.5;AN=2;DP=18499;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:252,101:353:99:3431,0,10293:105,147,41,60 chr2 133014777 . A G 3094.95 PASS AC=1;AF=0.5;AN=2;DP=18400;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:251,101:352:99:3431,0,10293:105,146,41,60 chr2 133014786 . G A 2727.12 PASS AC=1;AF=0.5;AN=2;DP=17554;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:196,129:325:99:4533,0,7890:83,113,49,80 chr2 133074745 . A T 1931.07 PASS AC=1;AF=0.5;AN=2;DP=3877;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:33,63:96:99:1629,0,745:19,14,36,27 chr2 133074759 . A C 1959.58 PASS AC=1;AF=0.5;AN=2;DP=3918;FractionInformativeReads=1;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:33,65:98:99:1713,0,687:20,13,36,29 chr2 133074851 . A T 1971.29 PASS AC=1;AF=0.5;AN=2;DP=4991;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:54,75:129:99:1794,0,1415:34,20,40,35 chr2 133074876 . A G 1920.16 PASS AC=1;AF=0.5;AN=2;DP=5751;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:59,68:127:99:1863,0,1473:35,24,34,34 chr2 133075027 . G A 2482.67 PASS AC=1;AF=0.5;AN=2;DP=8681;set=Intersection GT:AD:DP:GQ:PL:SB 0/1:94,92:186:99:2222,0,2271:45,49,46,46 chr2 133174764 . C T 2320.44 PASS AC=1;AF=0.583;AN=2;DP=4821;MQ=60;set=variant6-variant7-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant22-variant23-variant24-variant27-variant29-variant30-variant32-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:84,76:160:99:1916,0,2121:46,38,42,34 chr2 133174999 . A G 2569.14 PASS AC=1;AF=0.58;AN=2;DP=5421;MQ=60;set=variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant22-variant23-variant24-variant27-variant29-variant30-variant32-variant35-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:91,106:197:99:2892,0,2271:47,44,50,56 chr2 133175717 . T C 103.54 PASS AC=2;AF=0.786;AN=2;DP=43;FS=0;FractionInformativeReads=1;MQ=60;set=variant12-variant17-variant22-variant23-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:301,24,0:0,0,1,7 chr2 133404223 . C A 1318.72 PASS AC=2;AF=0.759;AN=2;DP=1336;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant10-variant11-variant12-variant14-variant15-variant17-variant19-variant20-variant23-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,43:43:99:1657,129,0:0,0,6,37 chr2 133425786 . TTAACTC T 995.61 PASS AC=2;AF=0.766;AN=2;DP=530;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:630,42,0:0,0,8,6 chr2 133425912 . C T 2510.9 PASS AC=2;AF=0.766;AN=2;DP=2952;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,75:75:99:2483,225,0:0,0,51,24 chr2 133426183 . G C 1336.64 PASS AC=2;AF=0.766;AN=2;DP=1574;MQ=60;set=variant-variant4-variant5-variant7-variant8-variant9-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant22-variant23-variant24-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant35-variant36-variant37-variant38-variant39-variant40-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1636,135,0:0,0,11,34 chr2 133539460 . A T 394.59 PASS AC=1;AF=0.714;AN=2;DP=551;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant21-variant22-variant23-variant24-variant25-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:7,8:15:99:199,0,180:5,2,6,2 chr2 133539566 . G A 2601.97 PASS AC=1;AF=0.708;AN=2;DP=2341;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-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:18,26:44:99:682,0,543:12,6,17,9 chr2 133540714 . G A 1773.79 PASS AC=1;AF=0.5;AN=2;DP=324;FractionInformativeReads=1;MQ=60;set=variant7-variant23 GT:AD:DP:GQ:PL:SB 0/1:98,79:177:99:1945,0,2463:48,50,41,38 chr2 133541444 . T C 6722.15 PASS AC=2;AF=0.718;AN=2;DP=6312;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-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,137:137:99:6064,415,0:0,0,72,65 chr2 133541454 . A G 6714.49 PASS AC=2;AF=0.711;AN=2;DP=6489;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-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,146:146:99:6336,442,0:0,0,75,71 chr2 133541575 . C T 4478.73 PASS AC=1;AF=0.571;AN=2;DP=4527;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant21-variant22-variant23-variant25-variant26-variant28-variant31-variant32-variant34-variant35-variant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:74,64:138:99:1581,0,1930:33,41,29,35 chr2 133542014 . T C 3129.64 PASS AC=2;AF=0.724;AN=2;DP=3317;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-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,77:77:99:2390,231,0:0,0,38,39 chr2 133542545 . G A 5358.01 PASS AC=1;AF=0.574;AN=2;DP=4496;MQ=60;set=variant-variant2-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant16-variant21-variant22-variant23-variant25-variant28-variant31-variant32-variant34-variant35-variant37-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:59,61:120:99:1515,0,1652:28,31,31,30 chr2 133554054 . A T 390.45 PASS AC=1;AF=0.5;AN=2;DP=24;FS=7.52;FractionInformativeReads=1;MQ=60;MQRankSum=-1.357;QD=16.27;ReadPosRankSum=-0.491;SOR=2.494;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:12,12:24:99:419,0,374:8,4,11,1 chr2 133554288 . A G 1943.11 PASS AC=2;AF=0.724;AN=2;DP=2525;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-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant37-variant38-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,44:44:99:1298,132,0:0,0,16,28 chr2 133618220 . A G 306.07 PASS AC=1;AF=0.579;AN=2;DP=612;MQ=60;set=variant5-variant8-variant9-variant11-variant12-variant13-variant14-variant16-variant18-variant19-variant22-variant23-variant24-variant30-variant33-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:12,21:33:99:620,0,353:2,10,5,16 chr2 133618246 . A G 414.03 PASS AC=1;AF=0.5;AN=2;DP=22;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=0.785;QD=18.82;ReadPosRankSum=-1.331;SOR=0.446;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:8,14:22:99:442,0,239:1,7,3,11 chr2 133626706 . T C 118.69 PASS AC=2;AF=0.768;AN=2;DP=293;FS=0;set=variant2-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant19-variant20-variant21-variant22-variant23-variant24-variant25-variant29-variant30-variant31-variant33-variant34-variant37-variant38-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:276,24,0:0,0,2,6 chr2 133683658 . G T 1187.68 PASS AC=1;AF=0.808;AN=2;DP=1965;FractionInformativeReads=1;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-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 0/1:17,9:26:99:246,0,460:9,8,4,5 chr2 134877946 . G C 1907.6 PASS AC=1;AF=0.5;AN=2;DP=1842;MQ=60;set=variant-variant2-variant7-variant14-variant15-variant19-variant20-variant23-variant24-variant25-variant26-variant32-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:66,73:139:99:1689,0,1420:28,38,26,47 chr2 134884700 . G A 981.64 PASS AC=2;AF=0.646;AN=2;DP=2772;MQ=60;set=variant-variant2-variant3-variant6-variant7-variant8-variant13-variant14-variant15-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant32-variant35-variant38-variant39-variant40-variant41-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:2785,287,0:0,0,51,45 chr2 135076111 . C G 471.22 PASS AC=2;AF=0.966;AN=2;DP=503;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:451,33,0:0,0,8,3 chr2 135096097 . T C 724.18 PASS AC=2;AF=0.966;AN=2;DP=930;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,22:22:66:763,66,0:0,0,5,17 chr2 135160755 . G A 1261.94 PASS AC=1;AF=0.63;AN=2;DP=3044;MQ=60;set=variant2-variant3-variant5-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant22-variant23-variant25-variant29-variant33-variant34-variant35-variant36-variant38-variant40-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:43,50:93:99:1368,0,1067:18,25,23,27 chr2 135206934 . C T 1332.75 PASS AC=1;AF=0.773;AN=2;DP=1507;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:24,23:47:99:480,0,560:12,12,13,10 chr2 135208077 . A G 562.32 PASS AC=1;AF=0.829;AN=2;DP=2498;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-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 0/1:24,23:47:99:644,0,570:12,12,14,9 chr2 135208213 . A G 524.38 PASS AC=1;AF=0.829;AN=2;DP=1528;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-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 0/1:11,23:34:99:631,0,244:6,5,7,16 chr2 135208354 . AGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT AGTGTGTGTGTGTGTGTGTGTGTGTGTGT,AGTGTGTGTGTGTGTGTGTGTGTGT,AGTGTGTGTGTGTGTGTGTGTGTGTGT,AGTGTGTGTGTGTGTGTGTGTGT,AGTGTGTGTGTGTGT,AGTGTGTGTGTGTGTGTGT,A,AGTGTGTGTGTGTGTGT,AGTGT,AGTGTGTGTGT 40.34 PASS AC=2,0,0,0,0,0,0,0,0,0;AF=0.159,0.366,0.085,0.037,0.012,0.049,0.061,0.012,0.012,0.012;AN=2;DP=1294;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-variant28-variant29-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:DP:GQ:SB 1/1:7:21:0,0,4,3 chr2 135209142 . G A 1234.59 PASS AC=1;AF=0.795;AN=2;DP=2642;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant20-variant21-variant22-variant23-variant25-variant27-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:36,30:66:99:777,0,1054:24,12,18,12 chr2 135209154 . A G 2489.29 PASS AC=1;AF=0.788;AN=2;DP=2495;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,31:71:99:835,0,1070:25,15,19,12 chr2 135209591 . C T 10418.6 PASS AC=1;AF=0.788;AN=2;DP=10248;set=variant2-variant3-variant4-variant5-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant21-variant22-variant23-variant25-variant27-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:134,154:288:99:4145,0,3655:43,91,56,98 chr2 135212242 . G C 78.41 PASS AC=1;AF=0.648;AN=2;DP=440;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant33-variant34-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:3,13:16:84:334,0,84:0,3,6,7 chr2 135212329 . G T 51.2 PASS AC=1;AF=0.75;AN=2;DP=149;FS=0;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant4-variant6-variant7-variant9-variant10-variant12-variant13-variant15-variant16-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant27-variant28-variant29-variant33-variant34-variant37-variant38-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:2,3:5:34:111,0,34:1,1,1,2 chr2 135213256 . G A 85.66 PASS AC=1;AF=0.654;AN=2;DP=285;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant33-variant34-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:8,3:11:99:99,0,207:4,4,3,0 chr2 135213413 . G A 913.17 PASS AC=1;AF=0.647;AN=2;DP=1238;FractionInformativeReads=1;MQ=60;set=variant2-variant4-variant5-variant6-variant9-variant14-variant18-variant21-variant22-variant23-variant27-variant29-variant33-variant34-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:40,45:85:99:1143,0,901:22,18,26,19 chr2 135213515 . AC A 1512.6 PASS AC=1;AF=0.643;AN=2;DP=3769;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant33-variant34-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:70,58:128:99:1678,0,2089:41,29,33,25 chr2 135213762 . T C 4533.27 PASS AC=1;AF=0.643;AN=2;DP=9024;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant9-variant10-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant20-variant21-variant22-variant23-variant26-variant27-variant28-variant29-variant33-variant34-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:146,135:281:99:3429,0,3643:62,84,60,75 chr2 135214418 . AT A,ATT 695.94 PASS AC=1,0;AF=0.575,0.05;AN=2;DP=1448;MQ=60;set=variant2-variant3-variant4-variant5-variant6-variant9-variant14-variant18-variant20-variant21-variant22-variant23-variant26-variant27-variant29-variant33-variant34-variant38-variant42-variant44 GT:DP:GQ:SB 0/1:57:99:18,16,8,15 chr2 135215941 . G A 107.68 PASS AC=1;AF=0.66;AN=2;DP=554;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant22-variant23-variant26-variant27-variant29-variant33-variant37-variant38-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:5,8:13:92:199,0,92:2,3,3,5 chr2 135260665 . A G 41 PASS AC=1;AF=0.5;AN=2;DP=622;set=filterInvariant2-variant6-variant7-filterInvariant14-filterInvariant17-variant18-filterInvariant20-variant23-variant27-variant34-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,6:45:99:135,0,2333:9,30,2,4 chr2 135260672 . T C 47.01 PASS AC=1;AF=0.5;AN=2;DP=563;FractionInformativeReads=1;set=filterInvariant2-variant6-variant7-filterInvariant14-filterInvariant17-variant18-filterInvariant20-variant23-variant27-variant34-variant44 GT:AD:DP:GQ:PL:SB 0/1:37,6:43:99:135,0,2333:9,28,2,4 chr2 135470735 . A T 502.26 PASS AC=1;AF=0.563;AN=2;DP=557;MQ=60;set=variant2-variant5-variant7-variant12-variant13-variant16-variant17-variant20-variant23-variant25-variant28-variant29-variant30-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:21,10:31:99:261,0,635:16,5,8,2 chr2 135471290 . T C 594.13 PASS AC=1;AF=0.594;AN=2;DP=633;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant7-variant12-variant13-variant16-variant17-variant20-variant23-variant25-variant28-variant29-variant30-variant35-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:23,15:38:99:480,0,877:1,22,2,13 chr2 135595968 . GTTTT G 40.69 PASS AC=1;AF=0.6;AN=2;DP=111;MQ=60;set=variant2-variant12-variant13-variant14-variant15-variant16-variant17-variant20-variant23-variant25-variant28-variant29-variant33-variant39-variant41 GT:AD:DP:GQ:PL:SB 0/1:6,3:9:99:108,0,318:5,1,3,0 chr2 135602601 . T A 471.95 PASS AC=2;AF=0.803;AN=2;DP=1728;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-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,49:49:99:1664,147,0:0,0,36,13 chr2 135629927 . C T 678.65 PASS AC=2;AF=0.803;AN=2;DP=2410;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-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2177,201,0:0,0,37,30 chr2 135677268 . G A 624.96 PASS AC=1;AF=0.672;AN=2;DP=1322;MQ=60;set=variant2-variant4-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant25-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:14,14:28:99:290,0,429:11,3,8,6 chr2 135677471 . A AGTTT 1181.98 PASS AC=1;AF=0.672;AN=2;DP=2199;MQ=60;set=variant2-variant4-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant25-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:38,36:74:99:1397,0,2230:15,23,17,19 chr2 135694354 . G C 485.96 PASS AC=1;AF=0.679;AN=2;DP=785;MQ=60;set=variant2-variant4-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant23-variant25-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:9,13:22:99:406,0,234:7,2,9,4 chr2 135694379 . C T 386.35 PASS AC=2;AF=0.803;AN=2;DP=1547;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-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,35:35:99:1165,105,0:0,0,20,15 chr2 135700151 . A T 588.7 PASS AC=1;AF=0.672;AN=2;DP=2910;MQ=60;set=variant2-variant4-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant25-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:50,56:106:99:1293,0,1213:28,22,30,26 chr2 135703338 . CT C 1295.87 PASS AC=1;AF=0.672;AN=2;DP=2244;MQ=60;set=variant2-variant4-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant25-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,30:51:99:705,0,405:15,6,20,10 chr2 135705558 . G A 823.62 PASS AC=2;AF=0.825;AN=2;DP=2746;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-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,68:68:99:2178,204,0:0,0,26,42 chr2 135710322 . A G 1391.38 PASS AC=2;AF=0.803;AN=2;DP=4437;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-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,103:103:99:3162,309,0:0,0,54,49 chr2 135711516 . C T 693.66 PASS AC=2;AF=0.803;AN=2;DP=2350;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-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,61:61:99:2074,183,0:0,0,37,24 chr2 135711657 . G A 902.82 PASS AC=2;AF=0.803;AN=2;DP=4490;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-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,80:80:99:2547,239,0:0,0,40,40 chr2 135713385 . TAAAA T 1235.29 PASS AC=1;AF=0.589;AN=2;DP=2541;MQ=60;set=variant2-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant25-variant28-variant29-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:39,36:75:99:1387,0,1897:12,27,9,27 chr2 135713703 . G A 3846.73 PASS AC=2;AF=0.803;AN=2;DP=9640;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-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,248:248:99:7664,741,0:0,0,135,113 chr2 135715169 . T G 3843.22 PASS AC=1;AF=0.587;AN=2;DP=4040;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant13-variant14-variant19-variant20-variant23-variant24-variant25-variant26-variant29-variant33-variant34-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:74,68:142:99:1836,0,2017:26,48,21,47 chr2 135715174 . TC T 3740.66 PASS AC=2;AF=0.803;AN=2;DP=6210;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-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,129:129:99:5577,397,0:0,0,41,88 chr2 135715465 . ATAAT A 4475.01 PASS AC=2;AF=0.803;AN=2;DP=9176;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-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,250:250:99:11203,753,0:0,0,135,115 chr2 135715957 . A G 1666.38 PASS AC=2;AF=0.803;AN=2;DP=4312;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-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:2,106:108:99:3584,249,0:2,0,29,77 chr2 135716598 . T C 2621.68 PASS AC=1;AF=0.587;AN=2;DP=5541;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant9-variant10-variant13-variant14-variant19-variant20-variant23-variant24-variant25-variant26-variant29-variant33-variant34-variant38-variant40-variant41 GT:AD:DP:GQ:PL:SB 0/1:106,117:223:99:3020,0,2526:53,53,57,60 chr2 135722143 . A C 1363.71 PASS AC=2;AF=0.789;AN=2;DP=4601;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-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,94:94:99:2853,282,0:0,0,51,43 chr2 135740876 . A G 1485.41 PASS AC=1;AF=0.58;AN=2;DP=2748;set=variant2-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant19-variant21-variant23-variant28-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:35,38:73:99:1094,0,865:13,22,16,22 chr2 135741061 . G A 394.47 PASS AC=1;AF=0.615;AN=2;DP=729;MQ=60;set=variant2-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant28-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:21,14:35:99:340,0,477:9,12,5,9 chr2 135745129 . G A 2184.9 PASS AC=1;AF=0.575;AN=2;DP=2898;MQ=60;set=variant-variant3-variant5-variant6-variant7-variant10-variant13-variant14-variant19-variant20-variant22-variant23-variant25-variant26-variant28-variant29-variant33-variant37-variant38-variant40 GT:AD:DP:GQ:PL:SB 0/1:73,57:130:99:1444,0,2019:34,39,30,27 chr2 135745392 . G A 1400.27 PASS AC=1;AF=0.577;AN=2;DP=1953;MQ=60;set=variant2-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant28-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:43,28:71:99:770,0,1181:19,24,11,17 chr2 135745545 . C T 1250.61 PASS AC=1;AF=0.615;AN=2;DP=2298;set=variant2-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant28-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:45,30:75:99:735,0,1420:31,14,18,12 chr2 135745722 . A G 1408.69 PASS AC=1;AF=0.615;AN=2;DP=3042;MQ=60;set=variant2-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant28-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:AD:DP:GQ:PL:SB 0/1:63,46:109:99:1079,0,1774:25,38,23,23 chr2 135748872 . AAAAAC A,AAAAACAAAACAAAAC,AAAAACAAAAC 507.93 PASS AC=1,0,0;AF=0.577,0.019,0.019;AN=2;DP=887;set=variant2-variant6-variant9-variant11-variant12-variant13-variant14-variant15-variant16-variant17-variant18-variant19-variant21-variant23-variant28-variant30-variant32-variant33-variant34-variant35-variant37-variant38-variant39-variant41-variant42-variant44 GT:DP:GQ:SB 0/1:31:99:10,4,11,6 chr2 135762980 . C T 642.09 PASS AC=2;AF=0.571;AN=2;DP=1487;FractionInformativeReads=1;MQ=60;set=variant2-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant30-variant32-variant33-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,79:79:99:2378,237,0:0,0,49,30 chr2 135893372 . A G 1699.55 PASS AC=2;AF=0.571;AN=2;DP=3430;MQ=60;set=variant2-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant19-variant22-variant23-variant24-variant25-variant30-variant32-variant33-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,142:142:99:4253,425,0:0,0,82,60 chr2 135911422 . T C 1360.96 PASS AC=2;AF=0.667;AN=2;DP=3413;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,78:78:99:2414,234,0:0,0,29,49 chr2 135954797 . T C 1359.31 PASS AC=2;AF=0.788;AN=2;DP=4417;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,132:132:99:4107,396,0:0,0,58,74 chr2 136070923 . CAA CA,C 130.69 PASS AC=1,0;AF=0.423,0.115;AN=2;DP=162;MQ=60;set=variant2-variant3-variant5-variant6-variant11-variant12-variant13-variant16-variant21-variant23-variant26-variant40-variant43 GT:DP:GQ:SB 0/1:16:99:7,0,8,1 chr2 136148394 . GAAA GAA,G,GA 46.47 PASS AC=1,0,1;AF=0.357,0.071,0.143;AN=2;DP=241;set=variant3-variant8-variant11-variant13-variant19-variant22-variant23-variant25-variant27-filterInvariant29-variant31-filterInvariant33-variant35-variant38 GT:DP:GQ:SB 3/1:13:99:0,0,4,9 chr2 136393658 . A G 1353.29 PASS AC=2;AF=0.63;AN=2;DP=2611;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant32-variant33-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,96:96:99:3095,288,0:0,0,39,57 chr2 136396300 . T C 280.28 PASS AC=2;AF=0.63;AN=2;DP=1204;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant32-variant33-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2026,201,0:0,0,37,30 chr2 136407445 . A G 1428.78 PASS AC=2;AF=0.63;AN=2;DP=2410;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant32-variant33-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 1/1:0,93:93:99:2884,278,0:0,0,60,33 chr2 136407479 . A G 1801.47 PASS AC=2;AF=0.758;AN=2;DP=4546;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant30-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:3582,357,0:0,0,74,46 chr2 136467119 . C T 832.84 PASS AC=2;AF=0.625;AN=2;DP=1492;MQ=60;set=variant-variant2-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant32-variant33-variant34-variant37-variant38-variant39 GT:AD:DP:GQ:PL:SB 1/1:1,76:77:99:2153,206,0:0,1,31,45 chr2 136467164 . C A 931.48 PASS AC=2;AF=1;AN=2;DP=1378;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,32:32:95:984,95,0:0,0,10,22 chr2 136499188 . T C 3175.02 PASS AC=2;AF=1;AN=2;DP=5853;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,147:147:99:4198,439,0:0,0,88,59 chr2 136511817 . A G 893.22 PASS AC=2;AF=0.62;AN=2;DP=1876;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant32-variant33-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:1856,189,0:0,0,27,36 chr2 136542427 . T TA 9007.2 PASS AC=2;AF=1;AN=2;DP=10718;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,201:201:99:6498,609,0:0,0,115,86 chr2 136542559 . G A 4708.86 PASS AC=2;AF=0.63;AN=2;DP=5522;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant32-variant33-variant34-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,181:181:99:7937,545,0:0,0,70,111 chr2 136542560 . A G 4708.86 PASS AC=2;AF=0.63;AN=2;DP=5453;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant32-variant33-variant34-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,177:177:99:7937,545,0:0,0,67,110 chr2 136545448 . AAC A 165.7 PASS AC=2;AF=0.615;AN=2;DP=679;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant32-variant33-variant34-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:1017,69,0:0,0,10,13 chr2 136548169 . A G 379.22 PASS AC=2;AF=1;AN=2;DP=430;FS=0;MQ=60;MQRankSum=0;ReadPosRankSum=-0.869;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,11:11:33:411,33,0:0,0,9,2 chr2 136548192 . G A 484.91 PASS AC=2;AF=1;AN=2;DP=635;FS=0;FractionInformativeReads=1;MQ=60;MQRankSum=-0.639;ReadPosRankSum=1.369;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,14:14:42:450,42,0:0,0,11,3 chr2 136552188 . G A 614.74 PASS AC=2;AF=0.615;AN=2;DP=1538;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant32-variant33-variant34-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,63:63:99:1943,189,0:0,0,41,22 chr2 136552371 . A G 1069.11 PASS AC=1;AF=0.5;AN=2;DP=473;MQ=60;set=variant5-variant11-variant13-variant23-variant33-variant37 GT:AD:DP:GQ:PL:SB 0/1:43,47:90:99:1344,0,1056:17,26,14,33 chr2 136555525 . T G 1159.46 PASS AC=2;AF=0.62;AN=2;DP=2010;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant32-variant33-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,72:72:99:2239,216,0:0,0,45,27 chr2 136555659 . T C 2715.98 PASS AC=1;AF=0.714;AN=2;DP=7364;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant15-variant16-variant17-variant18-variant19-variant20-variant21-variant22-variant23-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant39-variant40-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:114,67:181:99:1416,0,2750:60,54,26,41 chr2 136561735 . G A 287.87 PASS AC=2;AF=0.625;AN=2;DP=494;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant29-variant32-variant33-variant34-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,10:10:30:450,30,0:0,0,1,9 chr2 136565028 . C G 1073.53 PASS AC=2;AF=1;AN=2;DP=1614;FS=0;MQ=60;MQRankSum=-0.289;ReadPosRankSum=0.289;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,25:25:75:907,75,0:0,0,4,21 chr2 136575534 . T C 2746.76 PASS AC=2;AF=1;AN=2;DP=6825;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,144:144:99:4242,431,0:0,0,64,80 chr2 136581354 . T G 107.99 PASS AC=2;AF=1;AN=2;DP=248;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-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 chr2 136590746 . C T 1098.96 PASS AC=2;AF=0.611;AN=2;DP=2542;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant32-variant33-variant34-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,111:111:99:3297,332,0:0,0,55,56 chr2 136597806 . AAAC A 59.02 PASS AC=1;AF=0.5;AN=2;DP=51;MQ=60;set=variant23-variant39 GT:AD:DP:GQ:PL:SB 0/1:4,5:9:70:96,0,70:4,0,3,2 chr2 136597807 . AAC A 418.93 PASS AC=1;AF=0.595;AN=2;DP=560;set=variant2-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant16-filterInvariant17-filterInvariant20-variant22-filterInvariant23-variant24-filterInvariant25-filterInvariant32-variant33-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:5,4:9:70:70,0,96:3,2,4,0 chr2 136622543 . T G 241.85 PASS AC=2;AF=0.62;AN=2;DP=354;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant32-variant33-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,5:5:15:217,15,0:0,0,5,0 chr2 136622825 . A G 1396.47 PASS AC=2;AF=1;AN=2;DP=1368;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,26:26:78:900,78,0:0,0,7,19 chr2 136633771 . T C 596.74 PASS AC=2;AF=0.694;AN=2;DP=1547;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1428,134,0:0,0,32,13 chr2 136633962 . G A 1785.59 PASS AC=2;AF=0.615;AN=2;DP=3739;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant32-variant33-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,140:140:99:3944,418,0:0,0,64,76 chr2 136664812 . C T 822.42 PASS AC=1;AF=0.5;AN=2;DP=199;set=variant2-variant17-variant23 GT:AD:DP:GQ:PL:SB 0/1:29,29:58:99:653,0,464:11,18,14,15 chr2 136669264 . C T 68.9 PASS AC=1;AF=0.6;AN=2;DP=145;FractionInformativeReads=1;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant10-variant12-variant13-variant14-variant16-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant37-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:2,7:9:22:193,0,22:1,1,2,5 chr2 136680534 . A G 405.28 PASS AC=2;AF=0.625;AN=2;DP=308;FractionInformativeReads=1;MQ=60;set=variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant20-variant22-variant23-variant24-variant25-variant26-variant32-variant33-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,18:18:54:606,54,0:0,0,4,14 chr2 136690414 . TA T 686.85 PASS AC=2;AF=0.661;AN=2;DP=1075;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant33-filterInvariant34-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:739,51,0:0,0,7,10 chr2 136690425 . A G 695.58 PASS AC=2;AF=0.615;AN=2;DP=626;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant32-variant33-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,17:17:51:738,51,0:0,0,7,10 chr2 136719173 . A G 538.3 PASS AC=2;AF=0.615;AN=2;DP=961;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant32-variant33-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,39:39:99:1428,117,0:0,0,8,31 chr2 136740900 . T C 1123.26 PASS AC=2;AF=0.694;AN=2;DP=1636;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant17-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant28-variant29-variant32-variant33-variant34-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 1/1:0,54:54:99:1621,162,0:0,0,32,22 chr2 136743143 . G C 1466.89 PASS AC=1;AF=0.625;AN=2;DP=5014;MQ=60;set=variant-variant5-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant16-variant18-variant20-variant22-variant23-variant24-variant25-variant26-variant32-variant33-variant37-variant38-variant39-variant42 GT:AD:DP:GQ:PL:SB 0/1:92,91:183:99:2214,0,2277:38,54,39,52 chr2 136873077 . C T 2507.96 PASS AC=1;AF=0.5;AN=2;DP=202;FS=3.175;FractionInformativeReads=1;MQ=60;MQRankSum=-1.718;QD=12.42;ReadPosRankSum=0.902;SOR=0.874;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:100,102:202:99:2536,0,2412:49,51,56,46 chr2 136873549 . A T 1695.97 PASS AC=1;AF=0.613;AN=2;DP=3111;MQ=60;set=variant3-variant4-variant7-variant8-variant9-variant10-variant11-variant12-variant15-variant17-variant18-variant21-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 0/1:44,31:75:99:654,0,1206:21,23,21,10 chr2 137639616 . C T 377.42 PASS AC=2;AF=1;AN=2;DP=588;FS=0;MQ=60;MQRankSum=1.239;ReadPosRankSum=-0.743;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,8:8:24:345,24,0:0,0,8,0 chr2 137640006 . CTTT CTT,C 358.97 PASS AC=1,0;AF=0.833,0.026;AN=2;DP=599;FS=0;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-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-variant39-variant40-variant41-variant43-variant44 GT:DP:GQ:SB 0/1:9:3:0,1,1,7 chr2 137814477 . C G 4457.54 PASS AC=1;AF=0.625;AN=2;DP=3945;MQ=60;set=variant-variant6-variant7-variant9-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant24-variant25-variant26-variant29-variant30-variant31-variant32-variant34-variant35-variant36-variant37-variant38-variant39-variant41-variant43 GT:AD:DP:GQ:PL:SB 0/1:83,56:139:99:1394,0,2321:41,42,28,28 chr2 137999979 . G C 691.43 PASS AC=1;AF=0.545;AN=2;DP=1009;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant6-variant7-variant8-variant10-variant11-variant14-variant15-variant16-variant18-variant20-variant23-variant25-variant29-variant33-variant35-variant37-variant39-variant40-variant43 GT:AD:DP:GQ:PL:SB 0/1:18,17:35:99:441,0,507:14,4,12,5 chr2 138000226 . T C 2282.63 PASS AC=2;AF=0.966;AN=2;DP=2195;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,45:45:99:1623,135,0:0,0,14,31 chr2 138030271 . G A 860.27 PASS AC=1;AF=0.742;AN=2;DP=1154;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant9-variant10-variant11-variant12-variant13-variant14-variant15-variant16-variant18-variant19-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant33-variant34-variant35-variant37-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:17,18:35:99:531,0,463:5,12,4,14 chr2 138033349 . A T 302.39 PASS AC=1;AF=0.5;AN=2;DP=46;FS=0;MQ=60;set=variant12-variant23-variant31 GT:AD:DP:GQ:PL:SB 0/1:6,6:12:99:211,0,192:5,1,6,0 chr2 138163391 . T C 442.25 PASS AC=2;AF=0.92;AN=2;DP=1742;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,40:40:99:1473,120,0:0,0,10,30 chr2 138169158 . T C 1215.66 PASS AC=2;AF=1;AN=2;DP=1634;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,36:36:99:1162,108,0:0,0,24,12 chr2 138208631 . G T 630.95 PASS AC=2;AF=0.7;AN=2;DP=2155;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-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,53:53:99:1986,159,0:0,0,9,44 chr2 138237038 . C T 687.04 PASS AC=1;AF=0.814;AN=2;DP=1890;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-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 0/1:18,27:45:99:635,0,433:12,6,13,14 chr2 138375815 . T C 1409.06 PASS AC=1;AF=0.556;AN=2;DP=683;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant20-variant23-variant28-variant33-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:41,25:66:99:623,0,1252:31,10,18,7 chr2 138375896 . G A 3782.84 PASS AC=1;AF=0.615;AN=2;DP=2431;MQ=60;set=variant-variant4-variant5-variant13-variant18-variant19-variant20-variant23-variant26-variant28-variant33-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:90,64:154:99:2418,0,3531:54,36,38,26 chr2 138375898 . C A 2486.94 PASS AC=1;AF=0.556;AN=2;DP=1563;MQ=60;set=variant-variant4-variant5-variant20-variant23-variant28-variant33-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:90,65:155:99:2418,0,3531:54,36,39,26 chr2 138375972 . A T 2729.45 PASS AC=1;AF=0.556;AN=2;DP=1789;MQ=60;set=variant-variant4-variant5-variant20-variant23-variant28-variant33-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:88,83:171:99:1979,0,2314:37,51,45,38 chr2 138376209 . C T 776.55 PASS AC=1;AF=0.556;AN=2;DP=600;FractionInformativeReads=1;MQ=60;set=variant-variant4-variant5-variant20-variant23-variant28-variant33-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:32,32:64:99:799,0,742:11,21,11,21 chr2 138399937 . A G 675.89 PASS AC=1;AF=0.563;AN=2;DP=321;MQ=60;set=variant-variant20-variant23-variant28-variant32-variant33-variant38-variant42 GT:AD:DP:GQ:PL:SB 0/1:27,29:56:99:818,0,714:19,8,21,8 chr2 138420996 . A G 1327.45 PASS AC=1;AF=0.671;AN=2;DP=3307;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant13-variant14-variant15-variant17-variant18-variant19-variant20-variant21-variant23-variant24-variant26-variant27-variant28-variant31-variant32-variant33-variant34-variant35-variant38-variant39-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:49,32:81:99:660,0,1158:27,22,19,13 chr2 138434663 . T C 11499.1 PASS AC=2;AF=0.909;AN=2;DP=13566;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,307:307:99:9316,921,0:0,0,158,149 chr2 138435014 . T G 1724.62 PASS AC=2;AF=0.78;AN=2;DP=4640;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-variant27-variant28-variant29-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant37-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,97:97:99:3524,291,0:0,0,32,65 chr2 138721597 . C T 593.6 PASS AC=1;AF=0.629;AN=2;DP=1746;FractionInformativeReads=1;MQ=60;set=variant2-variant3-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant15-variant16-variant17-variant18-variant20-variant21-variant23-variant24-variant25-variant26-variant27-variant28-variant29-variant30-variant31-variant33-variant35-variant36-variant38-variant39-variant40-variant41-variant42-variant43-variant44 GT:AD:DP:GQ:PL:SB 0/1:27,26:53:99:591,0,680:13,14,12,14 chr2 138721942 . ATTT A,AT,ATTTT,ATT 1807.38 PASS AC=0,1,0,0;AF=0.093,0.384,0.012,0.151;AN=2;DP=4428;set=variant-variant2-variant3-variant4-variant5-variant6-variant7-variant8-variant9-variant10-variant11-variant12-variant13-variant14-variant15-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:DP:GQ:SB 0/2:72:99:17,13,33,9 chr2 138725002 . C T 156.22 PASS AC=2;AF=1;AN=2;DP=564;FS=0;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,9:9:27:252,27,0:0,0,4,5 chr2 138759649 . C T 3395.91 PASS AC=1;AF=0.6;AN=2;DP=1014;MQ=60;set=variant4-variant9-variant14-variant20-variant23-variant27-variant32-variant34-variant38-variant39 GT:AD:DP:GQ:PL:SB 0/1:54,35:89:99:689,0,1288:25,29,17,18 chr2 138762873 . C CTT 648.74 PASS AC=1;AF=0.545;AN=2;DP=557;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant14-variant20-variant23-variant24-variant27-variant28-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:11,7:18:99:254,0,406:3,8,0,7 chr2 138771219 . G A 530.16 PASS AC=1;AF=0.545;AN=2;DP=675;FractionInformativeReads=1;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant14-variant20-variant23-variant24-variant27-variant28-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:25,21:46:99:616,0,685:18,7,17,4 chr2 138771760 . A G 1180.6 PASS AC=1;AF=0.545;AN=2;DP=1782;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant14-variant20-variant23-variant24-variant27-variant28-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:33,39:72:99:1064,0,849:20,13,23,16 chr2 138771918 . A T 1676.98 PASS AC=1;AF=0.545;AN=2;DP=2136;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant14-variant20-variant23-variant24-variant27-variant28-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:44,36:80:99:905,0,1241:19,25,15,21 chr2 138772694 . C T 1831.01 PASS AC=1;AF=0.545;AN=2;DP=4213;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant14-variant20-variant23-variant24-variant27-variant28-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:73,107:180:99:2440,0,1554:31,42,48,59 chr2 138773229 . G A 3110.74 PASS AC=1;AF=0.545;AN=2;DP=6085;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant14-variant20-variant23-variant24-variant27-variant28-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42 GT:AD:DP:GQ:PL:SB 0/1:133,114:247:99:3088,0,3617:57,76,60,54 chr2 138773638 . C T 5304.42 PASS AC=1;AF=0.542;AN=2;DP=8896;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant14-variant20-variant23-variant24-variant27-variant28-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:190,121:311:99:2920,0,4834:92,98,67,54 chr2 138773752 . T C 5404.98 PASS AC=1;AF=0.542;AN=2;DP=9284;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant10-variant11-variant14-variant20-variant23-variant24-variant27-variant28-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant41-variant42 GT:AD:DP:GQ:PL:SB 0/1:184,166:350:99:4084,0,4728:91,93,80,86 chr2 138773811 . C G,A 5274.74 PASS AC=1,0;AF=0.522,0.022;AN=2;DP=7946;MQ=60;set=variant-variant3-variant4-variant5-variant6-variant8-variant9-variant11-variant14-variant20-variant23-variant24-variant27-variant28-variant30-variant32-variant34-variant35-variant36-variant38-variant39-variant40-variant42 GT:DP:GQ:SB 0/1:314:99:72,80,76,86 chr2 139036688 . C G 445.34 PASS AC=2;AF=0.743;AN=2;DP=2228;set=variant-variant2-variant3-variant4-variant5-variant6-variant8-variant9-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-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:1,49:50:99:1452,104,0:1,0,20,29 chr2 139045855 . C T 1840.87 PASS AC=2;AF=0.563;AN=2;DP=1281;MQ=60;set=variant9-variant17-variant19-variant23-variant24-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,151:151:99:4563,450,0:0,0,73,78 chr2 139045972 . T C 1242.62 PASS AC=2;AF=0.708;AN=2;DP=5033;FractionInformativeReads=1;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-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-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:3891,377,0:0,0,58,68 chr2 139045987 . C T 1671.54 PASS AC=2;AF=0.563;AN=2;DP=1023;MQ=60;set=variant9-variant17-variant19-variant23-variant24-variant37-variant39-variant41 GT:AD:DP:GQ:PL:SB 1/1:0,120:120:99:3737,359,0:0,0,54,66 chr2 139046301 . A G 4933.16 PASS AC=2;AF=0.708;AN=2;DP=14979;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-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-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:2,403:405:99:11808,1163,0:1,1,202,201 chr2 139046385 . G A 3208.13 PASS AC=2;AF=0.708;AN=2;DP=10826;set=variant2-variant3-variant4-variant5-variant6-variant8-variant9-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-variant41-variant42-variant43 GT:AD:DP:GQ:PL:SB 1/1:0,265:265:99:8284,793,0:0,0,93,172 chr2 139308191 . C A 1249.93 PASS AC=1;AF=0.5;AN=2;DP=98;FS=0.777;FractionInformativeReads=1;MQ=60;MQRankSum=-0.283;QD=12.75;ReadPosRankSum=1.067;SOR=0.585;set=variant23 GT:AD:DP:GQ:PL:SB 0/1:39,59:98:99:1278,0,1031:16,23,26,33 chr2 139308397 . TTC TTCTCTCTC,T,TTCTCTCTCTC,TTCTC,TTCTCTC,TTCTCTCTCTCTC 2241.78 PASS AC=1,0,0,0,0,0;AF=0.558,0.07,0.047,0.058,0.012,0.012;AN=2;DP=1871;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 0/1:28:99:10,9,8,1 chr2 139326879 . G C 4487.42 PASS AC=2;AF=1;AN=2;DP=5873;FS=0;MQ=60;MQRankSum=1.347;ReadPosRankSum=0.93;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,128:128:99:3570,383,0:0,0,66,62 chr2 139327055 . A G 2369.13 PASS AC=1;AF=0.5;AN=2;DP=1023;set=variant3-variant9-variant14-variant18-variant19-variant22-variant23-variant30-variant32-variant41 GT:AD:DP:GQ:PL:SB 0/1:41,49:90:99:1421,0,939:22,19,30,19 chr2 139329256 . C T 7590.6 PASS AC=2;AF=0.989;AN=2;DP=9907;FS=0;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,188:188:99:5832,563,0:0,0,113,75 chr2 139429068 . G A 4008.67 PASS AC=2;AF=0.813;AN=2;DP=6763;MQ=60;set=variant-variant2-variant3-variant4-variant5-variant7-variant8-variant9-variant10-variant11-variant12-variant13-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 1/1:1,144:145:99:4612,425,0:0,1,73,71 chr2 140989774 . GT G 12689.9 PASS AC=2;AF=0.737;AN=2;DP=14835;MQ=60;set=variant-variant2-variant4-variant5-variant6-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-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,329:329:99:10454,989,0:0,0,170,159 chr2 140989843 . A G 11431 PASS AC=2;AF=0.711;AN=2;DP=12883;set=variant-variant2-variant4-variant5-variant6-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-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,272:272:99:8511,815,0:0,0,117,155 chr2 140990351 . T A 8350.61 PASS AC=2;AF=1;AN=2;DP=10038;FS=0;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,215:215:99:6342,643,0:0,0,107,108 chr2 140992337 . C A 4029.18 PASS AC=2;AF=0.684;AN=2;DP=5146;MQ=60;set=variant-variant2-variant4-variant5-variant6-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-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,126:126:99:3688,378,0:0,0,68,58 chr2 141004513 . C T 740.04 PASS AC=2;AF=0.75;AN=2;DP=699;MQ=60;set=variant-variant2-variant4-variant5-variant6-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-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,12:12:36:503,36,0:0,0,12,0 chr2 141004529 . A G 989.69 PASS AC=2;AF=0.966;AN=2;DP=1258;FractionInformativeReads=1;MQ=60;set=Intersection GT:AD:DP:GQ:PL:SB 1/1:0,23:23:69:915,69,0:0,0,21,2 chr2 141032088 . C T 4661.96 PASS AC=2;AF=0.75;AN=2;DP=6034;MQ=60;set=variant-variant2-variant4-variant5-variant6-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-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,159:159:99:4752,475,0:0,0,82,77 chr2 141113798 . G A 667.51 PASS AC=2;AF=0.688;AN=2;DP=574;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant6-variant8-variant9-variant13-variant14-variant15-variant16-variant17-variant19-variant20-variant22-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant36-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:1,24:25:64:704,64,0:1,0,16,8 chr2 141128977 . C T 46.28 PASS AC=2;AF=0.738;AN=2;DP=124;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant4-variant8-variant9-variant13-variant14-variant15-variant16-variant17-variant20-variant22-variant23-variant27-variant28-variant30-variant32-variant33-variant34-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,3:3:9:135,9,0:0,0,0,3 chr2 141202412 . C T 39.5 PASS AC=2;AF=0.563;AN=2;DP=49;FS=0;FractionInformativeReads=1;MQ=60;set=variant-variant2-variant9-variant13-variant17-variant22-variant23-variant30 GT:AD:DP:GQ:PL:SB 1/1:0,4:4:12:180,12,0:0,0,0,4 chr2 141260668 . A G 1094.68 PASS AC=2;AF=0.688;AN=2;DP=2896;MQ=60;set=variant-variant2-variant4-variant6-variant7-variant8-variant9-variant12-variant13-variant14-variant16-variant17-variant19-variant20-variant22-variant23-variant25-variant26-variant27-variant28-variant30-variant31-variant32-variant33-variant34-variant35-variant36-variant39-variant40-variant41-variant43-variant44 GT:AD:DP:GQ:PL:SB 1/1:0,67:67:99:2117,201,0:0,0,24,43 chr2 141267744 . T C 278.95 PASS AC=2;AF=1;AN=2;DP=864;FS=0;FractionInforma