##fileformat=VCFv4.1 ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##annotator=MARS ##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[D:\Illumina\MiSeqAnalysis\200417_M04358_0133_000000000-CV8CW\Data\Intensities\BaseCalls\Alignment\20163-01-01_S18.bam] read_buffer_size=null phone_home=NO_ET gatk_key=null read_filter=[] intervals=[D:\Illumina\MiSeqAnalysis\200417_M04358_0133_000000000-CV8CW\Data\Intensities\BaseCalls\Alignment\Segment_intervals_M2.0.picard] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=C:\Illumina\MiSeq Reporter\Genomes\Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA\genome.fa nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=5000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=-1 defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=OFF log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_SITES standard_min_confidence_threshold_for_calling=1.0 standard_min_confidence_threshold_for_emitting=30.0 noSLOD=false annotateNDA=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 max_alternate_alleles=3 min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 noBandedIndel=false indelDebug=false ignoreSNPAlleles=false includeGVCFData=true dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false" ##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://C:\Illumina\MiSeq Reporter\Genomes\Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA\genome.fa ##gvcftools_version="0.12.1" ##gvcftools_cmdline="C:\Illumina\MiSeq Reporter\Workflows\EnrichmentWorker\gatk_to_gvcf.exe --no-default-filters --min-qd 0.0000 --min-gqx 10.0000 --min-mq 0.0000" ##source=GATK 1.6 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 20163-01-01 chr1 1853615 . T TCTGA 55892.64 PASS DP=847;FS=0.000;HRun=0;HaplotypeScore=595.5573;MQ=60;MQ0=0;QD=65.99;SB=-26683.61 GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:44,775:847:99:55893,2447,0:60:99:0.946 chr1 1854109 rs2803348 A G 7847.86 PASS BaseQRankSum=2.410;DP=776;Dels=0.00;FS=1.789;HRun=1;HaplotypeScore=30.1552;MQ=60;MQ0=0;MQRankSum=-0.770;QD=10.11;ReadPosRankSum=1.357;SB=-5021.74 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:439,337:776:99:7848,0,10539:60:99:0.434 chr1 1859131 rs4648734 C T 7648.41 PASS BaseQRankSum=3.902;DP=765;Dels=0.00;FS=1.818;HRun=0;HaplotypeScore=31.9408;MQ=60;MQ0=0;MQRankSum=-0.897;QD=10.00;ReadPosRankSum=0.726;SB=-4733.63 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:425,340:765:99:7648,0,9939:60:99:0.444 chr1 1861582 rs2803295 C T 13214.57 PASS BaseQRankSum=0.861;DP=1156;Dels=0.00;FS=0.211;HRun=0;HaplotypeScore=51.9261;MQ=60;MQ0=0;MQRankSum=1.099;QD=11.43;ReadPosRankSum=3.010;SB=-8687.06 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:600,555:1155:99:13215,0,14128:60:99:0.481 chr1 1873453 rs2748981 G A 4943.68 PASS BaseQRankSum=1.936;DP=495;Dels=0.00;FS=4.723;HRun=0;HaplotypeScore=14.6156;MQ=60;MQ0=0;MQRankSum=0.281;QD=9.99;ReadPosRankSum=-2.926;SB=-2150.60 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:289,206:495:99:4944,0,7230:60:99:0.416 chr1 1873514 rs2803326 A G 8618.00 PASS BaseQRankSum=2.936;DP=886;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=20.0605;MQ=60;MQ0=0;MQRankSum=0.668;QD=9.73;ReadPosRankSum=0.816;SB=-5892.20 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:502,383:886:99:8618,0,11963:60:99:0.433 chr1 1873525 rs2803327 T C 9053.34 PASS BaseQRankSum=1.804;DP=890;Dels=0.00;FS=0.495;HRun=0;HaplotypeScore=27.9579;MQ=60;MQ0=0;MQRankSum=0.418;QD=10.17;ReadPosRankSum=-0.242;SB=-6207.36 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:486,403:890:99:9053,0,11724:60:99:0.453 chr1 1875858 rs2803336 C G 6841.85 PASS BaseQRankSum=4.174;DP=871;Dels=0.00;FS=3.609;HRun=0;HaplotypeScore=34.3484;MQ=60;MQ0=0;MQRankSum=3.173;QD=7.86;ReadPosRankSum=1.288;SB=-4352.02 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:552,319:871:99:6842,0,12985:60:99:0.366 chr1 1875859 rs2803337 A G 6681.11 PASS BaseQRankSum=3.525;DP=862;Dels=0.00;FS=5.007;HRun=0;HaplotypeScore=35.2150;MQ=60;MQ0=0;MQRankSum=1.503;QD=7.75;ReadPosRankSum=1.239;SB=-4190.42 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:546,316:862:99:6681,0,12750:60:99:0.367 chr1 1884735 . CT C 675.49 R8 BaseQRankSum=-0.948;DP=302;FS=0.443;HRun=16;HaplotypeScore=1079.2338;MQ=60;MQ0=0;MQRankSum=-1.882;QD=2.24;ReadPosRankSum=2.983;SB=-330.16 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:191,56:302:99:715,0,2979:60:99:0.227 chr1 1885055 rs2474455 C T 15790.95 PASS DP=581;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=12.6141;MQ=60;MQ0=0;QD=27.18;SB=-10902.51;TI=NM_001080484;GI=KIAA1751;FC=Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,580:581:99:15791,1114,0:60:99:1.000 chr1 1886204 . A AGAGT 19302.23 PASS BaseQRankSum=16.703;DP=609;FS=2.095;HRun=0;HaplotypeScore=3382.1224;MQ=60;MQ0=0;MQRankSum=-0.549;QD=31.69;ReadPosRankSum=1.949;SB=-7756.56;TI=NM_001080484;GI=KIAA1751;FC=Noncoding;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:328,280:609:99:19302,0,18168:60:99:0.461 chr1 1886220 rs4648738 C T 8805.24 PASS BaseQRankSum=1.580;DP=706;Dels=0.00;FS=3.072;HRun=0;HaplotypeScore=16.3268;MQ=60;MQ0=0;MQRankSum=-0.747;QD=12.47;ReadPosRankSum=2.160;SB=-5299.44;TI=NM_001080484;GI=KIAA1751;FC=Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:340,366:706:99:8805,0,7943:60:99:0.518 chr1 1886222 rs2803287 T G 19541.55 PASS DP=707;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=15.5333;MQ=60;MQ0=0;QD=27.64;SB=-12245.05;TI=NM_001080484;GI=KIAA1751;FC=Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,707:707:99:19542,1385,0:60:99:1.000 chr1 1886344 . A ACAG 18134.48 PASS BaseQRankSum=19.923;DP=901;FS=1.691;HRun=0;HaplotypeScore=5144.2111;MQ=60;MQ0=0;MQRankSum=-0.035;QD=20.13;ReadPosRankSum=2.040;SB=-8656.36;TI=NM_001080484;GI=KIAA1751;FC=Noncoding;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:551,348:901:99:18134,0,26563:60:99:0.387 chr1 1886346 rs78279192 G C 9167.32 PASS BaseQRankSum=5.841;DP=820;Dels=0.00;FS=0.520;HRun=1;HaplotypeScore=371.4446;MQ=60;MQ0=0;MQRankSum=1.472;QD=11.18;ReadPosRankSum=2.436;SB=-5589.85;TI=NM_001080484;GI=KIAA1751;FC=Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:471,349:820:99:9167,0,11672:60:99:0.426 chr1 1886385 rs2803286 T C 26544.60 PASS DP=979;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=33.6873;MQ=60;MQ0=0;QD=27.11;SB=-18082.42;TI=NM_001080484;GI=KIAA1751;FC=Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,974:979:99:26545,1884,0:60:99:1.000 chr1 1886501 rs2748976 C A 5852.73 PASS BaseQRankSum=1.653;DP=1014;Dels=0.00;FS=2.918;HRun=0;HaplotypeScore=55.7465;MQ=59;MQ0=5;MQRankSum=1.841;QD=5.77;ReadPosRankSum=-2.295;SB=-5409.15;TI=NM_001080484;GI=KIAA1751;FC=Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:645,369:1014:99:5853,0,13600:59:99:0.364 chr1 1886519 rs2748975 C A 17367.58 PASS BaseQRankSum=1.373;DP=897;Dels=0.00;FS=16.281;HRun=0;HaplotypeScore=32.7987;MQ=59;MQ0=5;MQRankSum=1.386;QD=19.36;ReadPosRankSum=19.462;SB=-11496.12;TI=NM_001080484;GI=KIAA1751;FC=Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:199,696:897:99:17368,0,2424:59:99:0.778 chr1 1886859 rs3795290 C T 10577.20 PASS BaseQRankSum=3.467;DP=825;Dels=0.00;FS=5.309;HRun=0;HaplotypeScore=12.5246;MQ=60;MQ0=0;MQRankSum=0.863;QD=12.82;ReadPosRankSum=-1.416;SB=-6774.24;TI=NM_001080484;GI=KIAA1751;FC=Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:411,414:825:99:10577,0,10129:60:99:0.502 chr1 1887019 rs28548017 A G 22029.39 PASS DP=744;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=18.4389;MQ=60;MQ0=0;QD=29.61;SB=-13182.11;TI=NM_001080484;GI=KIAA1751;FC=Missense_X763Q;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,742:743:99:22029,1583,0:60:99:1.000 chr1 1887091 rs3838976 CG C 14998.10 PASS BaseQRankSum=21.193;DP=834;FS=1.076;HRun=1;HaplotypeScore=3171.8784;MQ=60;MQ0=0;MQRankSum=-1.320;QD=17.98;ReadPosRankSum=0.368;SB=-7276.22;TI=NM_001080484;GI=KIAA1751;FC=Frameshift;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:448,374:834:99:14998,0,16649:60:99:0.455 chr1 1887111 rs3838975 GC G 14675.83 PASS BaseQRankSum=20.109;DP=857;FS=1.999;HRun=2;HaplotypeScore=2989.4698;MQ=60;MQ0=0;MQRankSum=0.171;QD=17.12;ReadPosRankSum=0.199;SB=-7108.91;TI=NM_001080484;GI=KIAA1751;FC=Frameshift;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:446,404:857:99:14676,0,15920:60:99:0.475 chr1 1887245 rs28575980 G A 9998.59 PASS BaseQRankSum=3.183;DP=857;Dels=0.00;FS=6.149;HRun=0;HaplotypeScore=27.1447;MQ=60;MQ0=0;MQRankSum=-1.639;QD=11.67;ReadPosRankSum=-0.254;SB=-6385.58;TI=NM_001080484;GI=KIAA1751;FC=Synonymous_A687A;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:444,413:857:99:9999,0,10523:60:99:0.482 chr1 1888193 rs3820011 C A 6259.63 PASS BaseQRankSum=2.572;DP=655;Dels=0.00;FS=5.281;HRun=0;HaplotypeScore=18.8664;MQ=60;MQ0=0;MQRankSum=0.297;QD=9.56;ReadPosRankSum=0.633;SB=-3649.55;TI=NM_001080484;GI=KIAA1751;FC=Missense_G628C;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:386,267:655:99:6260,0,9492:60:99:0.409 chr1 1895177 rs7523728 C T 7502.73 PASS BaseQRankSum=4.361;DP=585;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=25.4051;MQ=60;MQ0=0;MQRankSum=0.211;QD=12.83;ReadPosRankSum=-0.034;SB=-3722.70;TI=NM_001080484;GI=KIAA1751;FC=Silent GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:278,307:585:99:7503,0,6854:60:99:0.525 chr1 1896440 rs16824585 G A 12063.23 PASS BaseQRankSum=1.972;DP=991;Dels=0.00;FS=0.984;HRun=1;HaplotypeScore=31.1120;MQ=60;MQ0=0;MQRankSum=-0.675;QD=12.17;ReadPosRankSum=-0.125;SB=-8118.50;TI=NM_001080484;GI=KIAA1751;FC=Synonymous_L488L;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:497,492:991:99:12063,0,12261:60:99:0.497 chr1 1900106 . T TCTC 6563.72 PASS BaseQRankSum=7.583;DP=394;FS=1.312;HRun=0;HaplotypeScore=420.7419;MQ=60;MQ0=0;MQRankSum=0.088;QD=16.66;ReadPosRankSum=-1.636;SB=-2340.40;TI=NM_001080484;GI=KIAA1751;FC=1AA_Insertion;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:267,125:394:99:6564,0,14834:60:99:0.319 chr1 1900232 rs16824588 T C 3590.44 PASS BaseQRankSum=2.289;DP=417;Dels=0.00;FS=2.664;HRun=0;HaplotypeScore=10.9883;MQ=60;MQ0=0;MQRankSum=-0.244;QD=8.61;ReadPosRankSum=-0.309;SB=-2379.12;TI=NM_001080484;GI=KIAA1751;FC=Missense_I363V;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:248,168:417:99:3590,0,6270:60:99:0.404 chr1 1916890 rs3795280 C T 9747.73 PASS BaseQRankSum=0.769;DP=848;Dels=0.00;FS=1.069;HRun=0;HaplotypeScore=26.2028;MQ=60;MQ0=0;MQRankSum=-0.158;QD=11.49;ReadPosRankSum=-0.065;SB=-6831.76;TI=NM_001080484;GI=KIAA1751;FC=Synonymous_L145L;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:424,424:848:99:9748,0,9953:60:99:0.500 chr1 1918358 . CT C 12346.32 PASS BaseQRankSum=4.490;DP=667;FS=0.575;HRun=1;HaplotypeScore=591.3601;MQ=60;MQ0=0;MQRankSum=1.902;QD=18.51;ReadPosRankSum=-0.022;SB=-5396.40;TI=NM_001080484;GI=KIAA1751;FC=Noncoding GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:338,329:667:99:12346,0,13114:60:99:0.493 chr1 1918488 rs4350140 A G 7833.96 PASS BaseQRankSum=1.804;DP=702;Dels=0.00;FS=3.547;HRun=0;HaplotypeScore=26.4672;MQ=60;MQ0=0;MQRankSum=-1.190;QD=11.16;ReadPosRankSum=-1.170;SB=-4591.58;TI=NM_001080484;GI=KIAA1751;FC=Silent GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:363,338:702:99:7834,0,8503:60:99:0.482 chr1 38023316 rs11749 C T 4510.48 PASS BaseQRankSum=1.164;DP=534;Dels=0.00;FS=6.313;HRun=0;HaplotypeScore=20.0848;MQ=60;MQ0=0;MQRankSum=-1.837;QD=8.45;ReadPosRankSum=-2.630;SB=-2358.78;TI=NM_003462;GI=DNALI1;FC=Missense_A87V;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:340,193:534:99:4510,0,8951:60:99:0.362 chr1 38027352 . C A 8219.88 PASS BaseQRankSum=4.719;DP=622;Dels=0.00;FS=0.304;HRun=0;HaplotypeScore=27.6791;MQ=60;MQ0=0;MQRankSum=-0.786;QD=13.22;ReadPosRankSum=-0.825;SB=-3827.85;TI=NM_003462;GI=DNALI1;FC=Silent GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:296,325:622:99:8220,0,7131:60:99:0.523 chr1 44457305 rs12403036 G A 11430.63 PASS BaseQRankSum=4.150;DP=1012;Dels=0.00;FS=5.068;HRun=0;HaplotypeScore=56.5401;MQ=60;MQ0=0;MQRankSum=0.353;QD=11.30;ReadPosRankSum=-1.374;SB=-8290.09;TI=NM_152499;GI=CCDC24;FC=Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:506,505:1012:99:11431,0,11873:60:99:0.500 chr1 118565953 rs10923472 G A 8058.95 PASS DP=263;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=5.5670;MQ=60;MQ0=0;QD=30.64;SB=-3375.63;TI=NM_206996;GI=SPAG17;FC=Missense_P1348L;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,263:263:99:8059,581,0:60:99:1.000 chr1 118583408 rs10923477 G A 5263.58 PASS DP=185;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.8100;MQ=60;MQ0=0;QD=28.45;SB=-3415.92;TI=NM_206996;GI=SPAG17;FC=Synonymous_Y1037Y;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,185:185:99:5264,376,0:60:99:1.000 chr1 118644430 rs10754367 A G 13906.81 PASS DP=494;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=10.0373;MQ=60;MQ0=0;QD=28.15;SB=-9710.55;TI=NM_206996;GI=SPAG17;FC=Synonymous_N189N;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,494:494:99:13907,990,0:60:99:1.000 chr1 156496188 rs6427315 A G 24539.48 PASS BaseQRankSum=1.683;DP=846;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=26.7396;MQ=60;MQ0=0;MQRankSum=-1.462;QD=29.01;ReadPosRankSum=1.552;SB=-16058.74;TI=NM_178229;GI=IQGAP3;FC=Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:1,845:846:99:24539,1764,0:60:99:0.999 chr1 156526387 rs11264498 C G 26959.29 PASS DP=997;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=25.0474;MQ=60;MQ0=0;QD=27.04;SB=-19120.19;TI=NM_178229;GI=IQGAP3;FC=Missense_V410L;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,997:997:99:26959,1911,0:60:99:1.000 chr1 156526444 rs2488269 T C 22901.45 PASS BaseQRankSum=1.670;DP=845;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=29.4962;MQ=60;MQ0=0;MQRankSum=-1.675;QD=27.10;ReadPosRankSum=1.350;SB=-13936.33;TI=NM_178229;GI=IQGAP3;FC=Missense_R391G;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:1,842:845:99:22901,1622,0:60:99:0.999 chr1 156532908 rs16837492 C A 12102.13 PASS DP=420;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=10.1312;MQ=60;MQ0=0;QD=28.81;SB=-5765.19;TI=NM_178229;GI=IQGAP3;FC=Silent GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,420:420:99:12102,870,0:60:99:1.000 chr1 156532977 rs1171547 T C 22858.25 PASS BaseQRankSum=1.720;DP=867;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=20.6201;MQ=60;MQ0=0;MQRankSum=-0.496;QD=26.36;ReadPosRankSum=-0.640;SB=-15046.52;TI=NM_178229;GI=IQGAP3;FC=Synonymous_Q249Q;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:1,865:867:99:22858,1610,0:60:99:0.999 chr1 156536221 rs2066377 G C 14378.05 PASS DP=516;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=28.8967;MQ=60;MQ0=0;QD=27.86;SB=-8583.77;TI=NM_178229;GI=IQGAP3;FC=Synonymous_P81P;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,516:516:99:14378,1020,0:60:99:1.000 chr1 156536251 rs947662 T C 18324.76 PASS DP=693;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=36.1967;MQ=60;MQ0=0;QD=26.44;SB=-12341.12;TI=NM_178229;GI=IQGAP3;FC=Synonymous_L71L;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,692:693:99:18325,1291,0:60:99:1.000 chr1 156536353 rs947663 A G 14552.20 PASS DP=517;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=13.4331;MQ=60;MQ0=0;QD=28.15;SB=-8087.18;TI=NM_178229;GI=IQGAP3;FC=Silent GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,517:517:99:14552,1044,0:60:99:1.000 chr1 156539154 rs6427319 T C 17243.06 PASS BaseQRankSum=0.382;DP=643;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=19.4809;MQ=60;MQ0=0;MQRankSum=1.978;QD=26.82;ReadPosRankSum=1.548;SB=-12289.14;TI=NM_178229;GI=IQGAP3;FC=Silent GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:4,639:643:99:17243,1141,0:60:99:0.994 chr1 159860259 rs2501320 G A 15908.25 PASS DP=543;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=9.0902;MQ=60;MQ0=0;QD=29.30;SB=-7857.00;TI=NM_012337;GI=CCDC19;FC=Silent GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,543:543:99:15908,1141,0:60:99:1.000 chr1 245133489 rs7545078 T G 10325.85 PASS BaseQRankSum=1.687;DP=387;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=32.3233;MQ=60;MQ0=0;MQRankSum=-0.219;QD=26.68;ReadPosRankSum=-0.103;SB=-5945.92;TI=NM_032328,NR_026586;GI=EFCAB2,EFCAB2;FC=Silent,Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:1,386:387:99:10326,734,0:60:99:0.997 chr1 245133539 rs7542813 A G 7027.89 PASS DP=271;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=12.2906;MQ=60;MQ0=0;QD=25.93;SB=-4133.56;TI=NM_032328,NR_026586;GI=EFCAB2,EFCAB2;FC=Silent,Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,270:271:99:7028,497,0:60:99:1.000 chr1 245133549 rs10536649 GGC G 9747.57 PASS DP=239;FS=0.000;HRun=0;HaplotypeScore=2161.3113;MQ=60;MQ0=0;QD=40.78;SB=-3818.50;TI=NM_032328,NR_026586;GI=EFCAB2,EFCAB2;FC=Noncoding,Noncoding;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:36,203:239:99:9748,635,0:60:99:0.849 chr1 245133623 . T TCCTCC 29444.68 PASS DP=398;FS=0.000;HRun=0;HaplotypeScore=2045.1488;MQ=60;MQ0=0;QD=73.98;SB=-12999.95;TI=NM_032328,NR_026586;GI=EFCAB2,EFCAB2;FC=Noncoding,Noncoding;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:45,343:398:99:29445,1165,0:60:99:0.884 chr1 245133662 rs61844237 G C 5828.90 PASS BaseQRankSum=1.588;DP=617;Dels=0.00;FS=0.607;HRun=2;HaplotypeScore=59.7546;MQ=60;MQ0=0;MQRankSum=1.058;QD=9.45;ReadPosRankSum=-0.674;SB=-4355.31;TI=NM_032328,NR_026586,NR_026588,NM_001143943,NR_026587;GI=EFCAB2,EFCAB2,EFCAB2,EFCAB2,EFCAB2;FC=Silent,Silent,Silent,Silent,Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:330,286:617:99:5829,0,7022:60:99:0.464 chr1 245222673 . C CT 3675.11 R8 BaseQRankSum=1.881;DP=418;FS=0.744;HRun=10;HaplotypeScore=1165.6394;MQ=60;MQ0=0;MQRankSum=-0.067;QD=8.79;ReadPosRankSum=0.794;SB=-1613.63;TI=NM_032328,NR_026586,NR_026588,NM_001143943,NR_026587;GI=EFCAB2,EFCAB2,EFCAB2,EFCAB2,EFCAB2;FC=Noncoding,Noncoding,Noncoding,Noncoding,Noncoding GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:233,165:418:99:3675,0,5251:60:99:0.415 chr1 245245378 rs10927386 T C 1600.42 PASS BaseQRankSum=-0.725;DP=245;Dels=0.00;FS=8.104;HRun=0;HaplotypeScore=7.3434;MQ=60;MQ0=0;MQRankSum=0.062;QD=6.53;ReadPosRankSum=-2.245;SB=-659.78;TI=NM_032328,NR_026586,NR_026588,NM_001143943,NR_026587;GI=EFCAB2,EFCAB2,EFCAB2,EFCAB2,EFCAB2;FC=Silent,Silent,Silent,Silent,Silent GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:170,75:245:99:1630,0,4103:60:99:0.306 chr1 245245402 rs10927387 C T 2173.59 PASS BaseQRankSum=2.776;DP=284;Dels=0.00;FS=15.735;HRun=0;HaplotypeScore=6.3022;MQ=60;MQ0=0;MQRankSum=-2.351;QD=7.65;ReadPosRankSum=0.873;SB=-749.90;TI=NM_032328,NR_026586,NR_026588,NM_001143943,NR_026587;GI=EFCAB2,EFCAB2,EFCAB2,EFCAB2,EFCAB2;FC=Synonymous_P67P,Silent,Silent,Synonymous_P67P,Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:191,93:284:99:2204,0,4694:60:99:0.327 chr1 245251020 rs1047707 G T 5089.18 PASS BaseQRankSum=4.921;DP=376;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=13.8866;MQ=60;MQ0=0;MQRankSum=0.753;QD=13.54;ReadPosRankSum=-0.343;SB=-3304.74;TI=NM_032328,NR_026586,NR_026588,NM_001143943,NR_026587;GI=EFCAB2,EFCAB2,EFCAB2,EFCAB2,EFCAB2;FC=Silent,Silent,Silent,Silent,Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:181,195:376:99:5089,0,4460:60:99:0.519 chr1 245251140 rs4658695 T G 5295.81 PASS DP=211;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=5.5427;MQ=60;MQ0=0;QD=25.10;SB=-3649.94;TI=NM_032328,NR_026586,NR_026588,NM_001143943,NR_026587;GI=EFCAB2,EFCAB2,EFCAB2,EFCAB2,EFCAB2;FC=Silent,Silent,Silent,Silent,Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,211:211:99:5296,370,0:60:99:1.000 chr1 245286313 rs4658701 G A 6737.57 PASS BaseQRankSum=0.726;DP=519;Dels=0.00;FS=1.023;HRun=0;HaplotypeScore=20.3222;MQ=60;MQ0=0;MQRankSum=0.442;QD=12.98;ReadPosRankSum=-0.102;SB=-3878.39;TI=NR_026586,NM_001143943,NR_026587;GI=EFCAB2,EFCAB2,EFCAB2;FC=Silent,Silent,Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:264,253:519:99:6738,0,6666:60:99:0.489 chr2 26647277 rs7423300 T G 16594.66 PASS BaseQRankSum=1.714;DP=564;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=9.0732;MQ=60;MQ0=0;MQRankSum=-1.400;QD=29.42;ReadPosRankSum=-1.333;SB=-8181.34;TI=NM_145038;GI=C2orf39;FC=Synonymous_A165A;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:1,563:564:99:16595,1204,0:60:99:0.998 chr2 26667615 rs61509377 T C 20575.32 PASS DP=761;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=22.3579;MQ=60;MQ0=0;QD=27.04;SB=-14201.34;TI=NM_145038;GI=C2orf39;FC=Missense_W399R;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,761:761:99:20575,1454,0:60:99:1.000 chr2 26671544 rs4072407 A G 18177.76 PASS BaseQRankSum=2.397;DP=651;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=29.1048;MQ=60;MQ0=0;MQRankSum=0.967;QD=27.92;ReadPosRankSum=1.397;SB=-9188.66;TI=NM_145038;GI=C2orf39;FC=Silent GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:2,648:650:99:18178,1297,0:60:99:0.997 chr2 26676322 rs1402962 A G 22254.40 PASS DP=788;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=29.3585;MQ=60;MQ0=0;QD=28.24;SB=-13841.53;TI=NM_145038;GI=C2orf39;FC=Synonymous_E608E;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,788:788:99:22254,1595,0:60:99:1.000 chr2 68357264 . T A 114.80 SB BaseQRankSum=-2.345;DP=23;Dels=0.00;FS=12.879;HRun=0;HaplotypeScore=4.9655;MQ=58;MQ0=0;MQRankSum=1.225;QD=4.99;ReadPosRankSum=-3.396;SB=-1.53 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:17,6:23:99:145,0,448:58:99:0.261 chr2 68358046 . CTT C 569.43 LowVariantFreq;R8 BaseQRankSum=-0.783;DP=286;FS=1.242;HRun=21;HaplotypeScore=1107.5620;MQ=60;MQ0=0;MQRankSum=-1.142;QD=1.99;ReadPosRankSum=1.140;SB=-180.85;TI=NM_138458;GI=WDR92;FC=Noncoding;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:162,18:286:99:608,0,3119:60:99:0.100 chr2 68358341 rs62145930 T C 6966.13 PASS BaseQRankSum=2.036;DP=622;Dels=0.00;FS=2.044;HRun=0;HaplotypeScore=26.2256;MQ=60;MQ0=0;MQRankSum=-1.186;QD=11.20;ReadPosRankSum=-1.749;SB=-3950.11;TI=NM_138458;GI=WDR92;FC=Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:332,289:622:99:6966,0,8325:60:99:0.465 chr2 68364478 rs13009282 T C 810.37 PASS BaseQRankSum=1.313;DP=104;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=3.7818;MQ=60;MQ0=0;MQRankSum=-0.395;QD=7.79;ReadPosRankSum=-0.422;SB=-583.86;TI=NM_138458;GI=WDR92;FC=Missense_M241V;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:66,38:104:99:840,0,1504:60:99:0.365 chr2 120303820 rs2579624 A T 3505.67 PASS BaseQRankSum=0.460;DP=439;Dels=0.00;FS=6.498;HRun=0;HaplotypeScore=17.6078;MQ=60;MQ0=0;MQRankSum=0.416;QD=7.99;ReadPosRankSum=-0.141;SB=-1832.24;TI=NM_001029996;GI=PCDP1;FC=Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:281,157:439:99:3506,0,6667:60:99:0.358 chr2 120317621 . CTT C 899.72 LowVariantFreq;R8 BaseQRankSum=0.279;DP=243;FS=5.566;HRun=20;HaplotypeScore=841.4342;MQ=60;MQ0=0;MQRankSum=-0.085;QD=3.70;ReadPosRankSum=0.267;SB=-340.82;TI=NM_001029996;GI=PCDP1;FC=Noncoding GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:129,18:243:99:939,0,2419:60:99:0.122 chr2 120366057 rs11398750 G GT,GTT 2981.76 R8 BaseQRankSum=-2.265;DP=169;FS=8.690;HaplotypeScore=417.3227;MQ=60;MQ0=0;MQRankSum=1.378;QD=17.64;ReadPosRankSum=-0.809;SB=-1063.99;TI=NM_001029996;GI=PCDP1;FC=Noncoding GT:AD:DP:GQ:PL:MQ:GQX:VF 1/2:20,108,33:169:99:3060,397,358,1997,0,2442:60:99:0.876 chr2 120369300 rs10864986 T C 8140.36 PASS DP=292;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=7.2734;MQ=60;MQ0=0;QD=27.88;SB=-4665.12;TI=NM_001029996;GI=PCDP1;FC=Synonymous_V145V;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,291:292:99:8140,581,0:60:99:1.000 chr2 120388412 rs2272058 G A 18152.17 PASS DP=665;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=29.0969;MQ=60;MQ0=0;QD=27.30;SB=-11108.68;TI=NM_001029996;GI=PCDP1;FC=Missense_V351I;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,663:665:99:18152,1288,0:60:99:1.000 chr2 120404629 . ATT A,AT 5673.37 R8 BaseQRankSum=-1.323;DP=344;FS=1.591;HaplotypeScore=497.2104;MQ=60;MQ0=0;MQRankSum=0.624;QD=16.49;ReadPosRankSum=-0.017;SB=-2124.82;TI=NM_001029996;GI=PCDP1;FC=Noncoding GT:AD:DP:GQ:PL:MQ:GQX:VF 1/2:70,56,1:344:99:5673,3680,4471,900,0,741:60:99:0.449 chr2 120414083 rs6761357 C T 18411.53 PASS BaseQRankSum=2.442;DP=637;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=23.4723;MQ=60;MQ0=0;MQRankSum=0.384;QD=28.90;ReadPosRankSum=-0.345;SB=-12252.23;TI=NM_001029996;GI=PCDP1;FC=Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:2,634:637:99:18412,1315,0:60:99:0.997 chr2 219545309 rs2303565 T C 7905.23 PASS BaseQRankSum=3.815;DP=719;Dels=0.00;FS=5.355;HRun=4;HaplotypeScore=23.4416;MQ=60;MQ0=0;MQRankSum=0.369;QD=10.99;ReadPosRankSum=0.109;SB=-4882.55;TI=NM_015690;GI=STK36;FC=Silent GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:374,345:719:99:7905,0,8263:60:99:0.480 chr2 219555262 rs1344642 G A 5339.55 PASS BaseQRankSum=1.991;DP=537;Dels=0.00;FS=3.776;HRun=0;HaplotypeScore=41.3203;MQ=60;MQ0=0;MQRankSum=1.487;QD=9.94;ReadPosRankSum=0.266;SB=-2722.35;TI=NM_015690;GI=STK36;FC=Missense_R583Q;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:314,223:537:99:5340,0,7646:60:99:0.415 chr2 219562675 rs1863704 G A 7227.62 PASS BaseQRankSum=2.155;DP=678;Dels=0.00;FS=0.278;HRun=0;HaplotypeScore=19.3662;MQ=60;MQ0=0;MQRankSum=-1.381;QD=10.66;ReadPosRankSum=1.668;SB=-4983.19;TI=NM_015690;GI=STK36;FC=Missense_G1003D;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:367,309:677:99:7228,0,8755:60:99:0.457 chr2 237247036 . G GA 3085.14 R8 BaseQRankSum=2.497;DP=366;FS=0.000;HRun=9;HaplotypeScore=299.7474;MQ=60;MQ0=0;MQRankSum=0.029;QD=8.43;ReadPosRankSum=-1.340;SB=-1246.84;TI=NM_024726;GI=IQCA1;FC=Noncoding GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:216,139:366:99:3124,0,5161:60:99:0.392 chr2 237374309 rs35432941 C T 7841.22 PASS BaseQRankSum=3.979;DP=568;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=15.6064;MQ=60;MQ0=0;MQRankSum=0.292;QD=13.80;ReadPosRankSum=-0.759;SB=-4683.26;TI=NM_024726;GI=IQCA1;FC=Synonymous_Q255Q;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:254,313:568:99:7841,0,6199:60:99:0.552 chr3 60898434 rs11130795 T C 670.18 LowVariantFreq BaseQRankSum=0.971;DP=277;Dels=0.00;FS=2.835;HRun=0;HaplotypeScore=14.4726;MQ=60;MQ0=0;MQRankSum=-0.756;QD=2.42;ReadPosRankSum=-1.374;SB=-384.46;TI=NM_002012,NM_001166243;GI=FHIT,FHIT;FC=Silent,Silent GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:229,47:277:99:700,0,5208:60:99:0.170 chr3 126142496 rs13064828 T C 6274.64 PASS BaseQRankSum=3.732;DP=562;Dels=0.00;FS=2.764;HRun=1;HaplotypeScore=26.9677;MQ=60;MQ0=0;MQRankSum=-1.405;QD=11.16;ReadPosRankSum=0.115;SB=-2608.09;TI=NM_182628;GI=CCDC37;FC=Silent GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:315,247:562:99:6275,0,7910:60:99:0.440 chr3 127872175 rs11920225 C G 9632.07 PASS BaseQRankSum=4.410;DP=845;Dels=0.00;FS=4.406;HRun=0;HaplotypeScore=21.9302;MQ=60;MQ0=0;MQRankSum=0.245;QD=11.40;ReadPosRankSum=-0.040;SB=-6596.34 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:413,432:845:99:9632,0,9661:60:99:0.511 chr3 166960278 rs11923256 G T 3323.91 PASS BaseQRankSum=0.595;DP=324;Dels=0.00;FS=0.867;HRun=1;HaplotypeScore=14.6809;MQ=60;MQ0=0;MQRankSum=-0.159;QD=10.26;ReadPosRankSum=-0.221;SB=-1883.57;TI=NM_001199202,NM_001199201,NM_024687;GI=ZBBX,ZBBX,ZBBX;FC=Silent,Silent,Silent GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:181,142:324:99:3324,0,4254:60:99:0.440 chr3 167000256 rs12638625 G C 3881.06 PASS BaseQRankSum=1.601;DP=481;Dels=0.00;FS=7.550;HRun=1;HaplotypeScore=17.5127;MQ=60;MQ0=0;MQRankSum=-0.930;QD=8.07;ReadPosRankSum=0.385;SB=-2016.51;TI=NM_001199202,NM_001199201,NM_024687;GI=ZBBX,ZBBX,ZBBX;FC=Missense_A607G,Missense_A675G,Missense_A636G;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:308,173:481:99:3881,0,7239:60:99:0.360 chr3 167023493 rs35864545 C T 4787.15 PASS BaseQRankSum=1.070;DP=433;Dels=0.00;FS=0.722;HRun=2;HaplotypeScore=8.0468;MQ=60;MQ0=0;MQRankSum=1.265;QD=11.06;ReadPosRankSum=1.047;SB=-3452.58;TI=NM_001199202,NM_001199201,NM_024687;GI=ZBBX,ZBBX,ZBBX;FC=Missense_E526K,Missense_E555K,Missense_E555K;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:220,212:433:99:4787,0,5084:60:99:0.491 chr3 167023624 rs35190925 A G 3883.97 PASS BaseQRankSum=3.532;DP=398;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=23.7994;MQ=60;MQ0=0;MQRankSum=-0.280;QD=9.76;ReadPosRankSum=0.825;SB=-2826.68;TI=NM_001199202,NM_001199201,NM_024687;GI=ZBBX,ZBBX,ZBBX;FC=Missense_I482T,Missense_I511T,Missense_I511T;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:220,178:398:99:3884,0,5307:60:99:0.447 chr3 167023738 rs13096767 G C 3650.60 PASS BaseQRankSum=0.681;DP=285;Dels=0.00;FS=2.038;HRun=1;HaplotypeScore=3.7643;MQ=60;MQ0=0;MQRankSum=0.451;QD=12.81;ReadPosRankSum=-1.489;SB=-1910.42;TI=NM_001199202,NM_001199201,NM_024687;GI=ZBBX,ZBBX,ZBBX;FC=Unknown_444,Unknown_473,Unknown_473;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:135,149:285:99:3651,0,3138:60:99:0.525 chr3 167034814 rs13068132 T C 892.27 PASS BaseQRankSum=1.641;DP=97;Dels=0.00;FS=1.716;HRun=0;HaplotypeScore=0.0000;MQ=60;MQ0=0;MQRankSum=0.507;QD=9.20;ReadPosRankSum=0.793;SB=-500.36;TI=NM_001199202,NM_001199201,NM_024687;GI=ZBBX,ZBBX,ZBBX;FC=Synonymous_L362L,Synonymous_L391L,Synonymous_L391L;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:62,35:97:99:922,0,1541:60:99:0.361 chr3 167051726 rs10936530 A G 3011.92 PASS BaseQRankSum=0.866;DP=348;Dels=0.00;FS=5.196;HRun=0;HaplotypeScore=7.5600;MQ=60;MQ0=0;MQRankSum=-0.137;QD=8.65;ReadPosRankSum=-1.584;SB=-1366.49;TI=NM_001199202,NM_001199201,NM_024687;GI=ZBBX,ZBBX,ZBBX;FC=Synonymous_F163F,Synonymous_F192F,Synonymous_F192F;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:221,127:348:99:3042,0,5382:60:99:0.365 chr3 167051769 rs11923054 T C 2928.26 PASS BaseQRankSum=0.174;DP=154;Dels=0.00;FS=11.088;HRun=0;HaplotypeScore=3.7615;MQ=60;MQ0=0;MQRankSum=0.057;QD=19.01;ReadPosRankSum=-0.349;SB=-1172.30;TI=NM_001199202,NM_001199201,NM_024687;GI=ZBBX,ZBBX,ZBBX;FC=Missense_K149R,Missense_K178R,Missense_K178R;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:48,106:154:99:2958,0,1346:60:99:0.688 chr3 167068256 rs4619784 T A 4877.06 PASS BaseQRankSum=-0.155;DP=522;Dels=0.00;FS=1.024;HRun=0;HaplotypeScore=10.8752;MQ=60;MQ0=0;MQRankSum=-0.269;QD=9.34;ReadPosRankSum=0.285;SB=-3359.16;TI=NM_001199202,NM_001199201,NM_024687;GI=ZBBX,ZBBX,ZBBX;FC=Missense_K131N,Missense_K160N,Missense_K160N;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:307,215:522:99:4877,0,7470:60:99:0.412 chr3 167077691 rs4257551 T A 8932.60 PASS DP=307;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=20.1283;MQ=60;MQ0=0;QD=29.10;SB=-3924.37;TI=NM_001199202,NM_001199201,NM_024687;GI=ZBBX,ZBBX,ZBBX;FC=Synonymous_V104V,Synonymous_V133V,Synonymous_V133V;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,307:307:99:8933,644,0:60:99:1.000 chr3 169558025 rs3732451 C T 9184.71 PASS BaseQRankSum=5.073;DP=815;Dels=0.00;FS=0.251;HRun=0;HaplotypeScore=34.7658;MQ=60;MQ0=0;MQRankSum=-1.308;QD=11.27;ReadPosRankSum=1.672;SB=-6493.36;TI=NM_024727;GI=LRRC31;FC=Synonymous_A468A;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:415,399:815:99:9185,0,9992:60:99:0.490 chr3 169566090 rs9290375 A G 3847.36 PASS BaseQRankSum=2.477;DP=326;Dels=0.00;FS=2.637;HRun=0;HaplotypeScore=7.5353;MQ=60;MQ0=0;MQRankSum=-0.853;QD=11.80;ReadPosRankSum=-2.021;SB=-1704.97;TI=NM_024727;GI=LRRC31;FC=Silent GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:168,158:326:99:3847,0,4457:60:99:0.485 chr3 180334623 rs7612917 C T 2407.03 PASS BaseQRankSum=3.519;DP=392;Dels=0.00;FS=0.828;HRun=1;HaplotypeScore=12.7373;MQ=60;MQ0=0;MQRankSum=-0.049;QD=6.14;ReadPosRankSum=-1.358;SB=-1668.38;TI=NM_181426;GI=CCDC39;FC=Synonymous_V799V;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:269,122:392:99:2437,0,6221:60:99:0.312 chr3 180365043 . T TA 57.12 R8;SB BaseQRankSum=0.282;DP=25;FS=4.506;HRun=11;HaplotypeScore=96.2523;MQ=60;MQ0=0;MQRankSum=1.551;QD=2.28;ReadPosRankSum=1.198;SB=-8.38;TI=NM_181426;GI=CCDC39;FC=Noncoding GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:17,5:25:96.15:96,0,240:60:57:0.227 chr3 180365956 rs6769457 G A 6464.54 PASS BaseQRankSum=5.584;DP=510;Dels=0.00;FS=1.066;HRun=0;HaplotypeScore=14.1337;MQ=60;MQ0=0;MQRankSum=0.438;QD=12.68;ReadPosRankSum=-1.339;SB=-3383.10;TI=NM_181426;GI=CCDC39;FC=Synonymous_S453S;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:241,268:510:99:6465,0,5623:60:99:0.527 chr3 180565309 rs6443724 T A 10811.77 PASS BaseQRankSum=1.689;DP=399;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=10.6742;MQ=60;MQ0=0;MQRankSum=-0.551;QD=27.10;ReadPosRankSum=1.202;SB=-7505.47 GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:1,398:399:99:10812,765,0:60:99:0.997 chr3 197659160 rs67877771 C G 2027.06 PASS BaseQRankSum=1.743;DP=274;Dels=0.00;FS=6.173;HRun=1;HaplotypeScore=17.0821;MQ=60;MQ0=0;MQRankSum=0.887;QD=7.40;ReadPosRankSum=-0.354;SB=-1034.02;TI=NM_032263,NM_001134435;GI=IQCG,IQCG;FC=Missense_D177H,Missense_D177H;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:181,91:274:99:2057,0,4469:60:99:0.335 chr3 197665599 rs9880989 G T 6805.67 PASS BaseQRankSum=3.217;DP=573;Dels=0.00;FS=11.989;HRun=0;HaplotypeScore=21.9949;MQ=60;MQ0=0;MQRankSum=0.183;QD=11.88;ReadPosRankSum=0.245;SB=-4155.48;TI=NM_032263,NM_001134435;GI=IQCG,IQCG;FC=Missense_A112D,Missense_A112D;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:292,281:573:99:6806,0,7144:60:99:0.490 chr4 185999543 rs6841061 G A 2628.15 PASS BaseQRankSum=2.225;DP=363;Dels=0.00;FS=6.662;HRun=3;HaplotypeScore=11.8291;MQ=60;MQ0=0;MQRankSum=-1.360;QD=7.24;ReadPosRankSum=-0.337;SB=-1385.52 GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:242,121:363:99:2658,0,6241:60:99:0.333 chr5 10442068 rs1047426 C T 12513.43 PASS BaseQRankSum=1.724;DP=454;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=26.1857;MQ=60;MQ0=0;MQRankSum=-0.572;QD=27.56;ReadPosRankSum=-0.794;SB=-6189.37;TI=NM_031916;GI=ROPN1L;FC=Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:1,453:454:99:12513,885,0:60:99:0.998 chr5 13691045 rs2896111 T C 8671.77 PASS DP=319;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=9.0362;MQ=60;MQ0=0;QD=27.18;SB=-5480.73;TI=NM_001369;GI=DNAH5;FC=Silent;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,319:319:99:8672,614,0:60:99:1.000 chr5 13701525 rs3734111 T C 4172.04 PASS DP=141;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.8667;MQ=60;MQ0=0;QD=29.59;SB=-1676.63;TI=NM_001369;GI=DNAH5;FC=Synonymous_T4453T;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,141:141:99:4172,301,0:60:99:1.000 chr5 13701536 rs3734110 T C 3515.48 PASS DP=108;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=1.7882;MQ=60;MQ0=0;QD=32.55;SB=-877.49;TI=NM_001369;GI=DNAH5;FC=Missense_I4450V;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,108:108:99:3515,259,0:60:99:1.000 chr5 13714740 rs30175 G A 16176.90 PASS DP=591;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=11.9941;MQ=60;MQ0=0;QD=27.37;SB=-9780.23;TI=NM_001369;GI=DNAH5;FC=Silent GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,591:591:99:16177,1147,0:60:99:1.000 chr5 13719022 rs30169 T G 19404.00 PASS BaseQRankSum=1.717;DP=705;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=23.5911;MQ=60;MQ0=0;MQRankSum=-1.624;QD=27.52;ReadPosRankSum=0.379;SB=-13034.27;TI=NM_001369;GI=DNAH5;FC=Synonymous_G4156G;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:1,703:705:99:19404,1376,0:60:99:0.999 chr5 13719089 rs30168 G A 19522.98 PASS DP=731;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=28.5010;MQ=60;MQ0=0;QD=26.71;SB=-14252.44;TI=NM_001369;GI=DNAH5;FC=Missense_A4134V;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 1/1:0,728:731:99:19523,1379,0:60:99:1.000 chr5 13754394 rs2401809 C T 9640.47 PASS BaseQRankSum=3.758;DP=856;Dels=0.00;FS=0.245;HRun=0;HaplotypeScore=27.9701;MQ=60;MQ0=0;MQRankSum=0.552;QD=11.26;ReadPosRankSum=-0.514;SB=-6656.13;TI=NM_001369;GI=DNAH5;FC=Synonymous_T3491T;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:455,400:856:99:9640,0,10731:60:99:0.468 chr5 13762972 rs6554812 T C 4763.24 PASS BaseQRankSum=2.968;DP=466;Dels=0.00;FS=1.548;HRun=0;HaplotypeScore=14.5004;MQ=60;MQ0=0;MQRankSum=1.236;QD=10.22;ReadPosRankSum=-1.106;SB=-2523.41;TI=NM_001369;GI=DNAH5;FC=Synonymous_E3380E;EXON GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:262,204:466:99:4763,0,6514:60:99:0.438 chr5 13842027 rs35805633 CA C 390.46 R8 BaseQRankSum=-0.313;DP=139;FS=4.234;HRun=19;HaplotypeScore=647.8226;MQ=60;MQ0=0;MQRankSum=1.191;QD=2.81;ReadPosRankSum=0.228;SB=-203.39;TI=NM_001369;GI=DNAH5;FC=Noncoding GT:AD:DP:GQ:PL:MQ:GQX:VF 0/1:74,25:139:99:429,0,560:60:99:0.253 chr5 13850750 rs6554820 A G 6055.64 PASS BaseQRankSum=2.002;DP=532;Dels=0.00;FS=1.817;HRun=1;HaplotypeScore=21.1512;MQ=60;MQ0=0;MQRankSum=0.532;QD=11.38;ReadPosRankSum=-0.425;SB=-3502.46;TI=NM_