##fileformat=VCFv4.1 ##fileDate=20181203 ##source=Pisces 5.2.3.6 ##Pisces_cmdline="-BamPaths D:\Illumina\MiSeqAnalysis\181130_M05705_0031_000000000-C5R45\Alignment_3\20181203_130703\Temp_03-VariantCalling\stitchedBams\16420_S8.bam -GenomePaths C:\Illumina\Genomes\Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFasta -gVCF True -OutFolder D:\Illumina\MiSeqAnalysis\181130_M05705_0031_000000000-C5R45\Alignment_3\20181203_130703\Temp_03.04-VariantCalling.VariantCalling\Sample620 -i D:\Illumina\MiSeqAnalysis\181130_M05705_0031_000000000-C5R45\Alignment_3\20181203_130703\Temp_03-VariantCalling\interval\16420_S8.intervals.picard -CallMNVs True -MaxMNVLength 3 -MaxGapBetweenMNV 1 -MinimumFrequency 0.01 -MinBaseCallQuality 20 -MaxVariantQScore 100 -MinVariantQScore 20 -CrushVcf True -MinDP 10 -ReportNoCalls True -Ploidy diploid -EnableSingleStrandFilter False -MinDPFilter 10 -MaxAcceptableStrandBiasFilter 0.5 -VariantQualityFilter 30 -MinVariantFrequencyFilter 0.2 -RMxNFilter 5,9,0.35 -MaxNumThreads 2" ##reference=C:\Illumina\Genomes\Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFasta ##ALT=,Description="There is an overlapping other allele that has been called in a separate VCF record"> ##INFO= ##annotator=Illumina Annotation Engine 1.6.2.0 ##annotatorDataVersion=84.24.38 ##annotatorTranscriptSource=RefSeq ##dataSource=ClinVar,version:20170227,release date:2017-02-27 ##dataSource=COSMIC,version:80,release date:2017-02-13 ##dataSource=dbSNP,version:149,release date:2016-11-21 ##dataSource=ExAC,version:0.3.1,release date:2016-03-16 ##dataSource=EVS,version:2,release date:2013-11-13 ##dataSource=1000 Genomes Project,version:Phase 3 v5a,release date:2013-05-27 ##dataSource=phyloP,version:hg19,release date:2009-11-10 ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 16420_S8.bam chr1 11187477 rs138733485 G A 100 PASS DP=21;GMAF=A|0.002995;AA=G;AF1000G=0.002995;phyloP=-0.948;CSQT=1|MTOR|NM_004958.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:40:11,10:21:0.476:20:-100.0000:0.0000 chr1 11205058 rs1057079 C T 100 PASS DP=22;cosmic=1|COSM4142146;EVS=0.545902|115|6503;GMAF=C|0.4525;AA=C;AF1000G=0.547524;phyloP=0.078;CSQT=1|MTOR|NM_004958.3|synonymous_variant,1|MTOR-AS1|NR_046600.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:80:0,22:22:1.000:20:-100.0000:0.0000 chr1 11288758 rs1064261 G A 100 PASS DP=105;cosmic=1|COSM4142152;EVS=0.617561|95|6503;GMAF=G|0.2995;AA=A;AF1000G=0.700479;phyloP=-0.406;CSQT=1|MTOR|NM_004958.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,105:105:1.000:20:-100.0000:0.0000 chr1 11297762 rs7524202 T C 100 PASS DP=30;GMAF=T|0.2991;AA=C;AF1000G=0.700879;phyloP=-0.016;CSQT=1|MTOR|NM_004958.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,30:30:1.000:20:-100.0000:0.0323 chr1 11301714 rs1135172 A G 100 PASS DP=35;cosmic=1|COSM4142157;EVS=0.585345|98|6503;GMAF=A|0.3604;AA=G;AF1000G=0.639577;phyloP=0.008;CSQT=1|MTOR|NM_004958.3|synonymous_variant;CSQR=1|ENSR00001577764|regulatory_region_variant,1|ENSR00001577765|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,35:35:1.000:20:-100.0000:0.0000 chr1 36563158 rs3738360 C A 100 PASS DP=65;EVS=0.783869|40|6503;GMAF=C|0.3437;AA=C;AF1000G=0.65635;phyloP=0.367;CSQT=1|ADPRHL2|NM_017825.2|downstream_gene_variant,1|COL8A2|NM_005202.2|3_prime_UTR_variant;CSQR=1|ENSR00001581936|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:53:25,40:65:0.615:20:-100.0000:0.0152 chr1 36563574 . A G 100 PASS DP=85;phyloP=2.718;CSQT=1|ADPRHL2|NM_017825.2|downstream_gene_variant,1|COL8A2|NM_005202.2|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:42,43:85:0.506:20:-100.0000:0.0230 chr1 36563797 rs35495320 C T 100 PASS DP=14;cosmic=1|COSM5452443;EVS=0.022429|2|4882;GMAF=T|0.1815;AA=C;AF1000G=0.18151;phyloP=-0.349;CSQT=1|ADPRHL2|NM_017825.2|downstream_gene_variant,1|COL8A2|NM_005202.2|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:1:4,10:14:0.714:20:-62.8843:0.0000 chr1 36565175 rs66899567 G A 100 PASS DP=32;GMAF=A|0.156;AA=G;AF1000G=0.15595;phyloP=0.042;CSQT=1|COL8A2|NM_005202.2|intron_variant;CSQR=1|ENSR00001581937|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:21:22,10:32:0.313:20:-100.0000:0.0000 chr1 36565584 rs274753 C G 100 PASS DP=77;GMAF=C|0.07827;AA=G;AF1000G=0.921725;phyloP=-0.461;CSQT=1|COL8A2|NM_005202.2|intron_variant;CSQR=1|ENSR00001581937|regulatory_region_variant,1|ENSR00000076318|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,77:77:1.000:20:-100.0000:0.0000 chr1 36565739 rs57985157 C T 100 PASS DP=51;EVS=0.011533|30|6503;GMAF=T|0.09665;AA=T;AF1000G=0.096645;phyloP=-0.138;CSQT=1|COL8A2|NM_005202.2|synonymous_variant;CSQR=1|ENSR00001581937|regulatory_region_variant,1|ENSR00000076318|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:25,26:51:0.510:20:-100.0000:0.0000 chr1 47881974 rs181190356 G A 100 PASS DP=29;clinvar=1|benign;GMAF=A|0.08866;AA=G;AF1000G=0.088658;phyloP=1.618;CSQT=1|FOXE3|NM_012186.2|5_prime_UTR_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:44:13,16:29:0.552:20:-100.0000:0.0333 chr1 47882497 rs34082359 C T 100 PASS DP=30;clinvar=1|benign;cosmic=1|COSM3751263;EVS=0.313176|9|6383;GMAF=T|0.2786;AA=c;AF1000G=0.278554;phyloP=-0.391;CSQT=1|FOXE3|NM_012186.2|synonymous_variant;CSQR=1|ENSR00001583800|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:0:9,21:30:0.700:20:-100.0000:0.0323 chr1 47883019 rs6666370 T C 100 PASS DP=81;GMAF=T|0.2031;AA=C;AF1000G=0.796925;phyloP=-0.792;CSQT=1|FOXE3|NM_012186.2|3_prime_UTR_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,81:81:1.000:20:-100.0000:0.0122 chr1 47883024 rs2820969 A G 100 PASS DP=82;GMAF=A|0.005192;AA=G;AF1000G=0.994808;phyloP=0.19;CSQT=1|FOXE3|NM_012186.2|3_prime_UTR_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,81:82:0.988:20:-100.0000:0.0000 chr1 94471075 rs1762114 A G 100 PASS DP=30;clinvar=1|benign,1|benign,1|benign,1|benign,1|benign;cosmic=1|COSM3997712;EVS=0.775719|112|6503;GMAF=A|0.23;AA=G;AF1000G=0.769968;phyloP=-3.057;CSQT=1|ABCA4|NM_000350.2|synonymous_variant;CSQR=1|ENSR00001522544|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,30:30:1.000:20:-100.0000:0.0000 chr1 94476555 rs537831 G A 100 PASS DP=111;clinvar=1|not_provided;cosmic=1|COSN8862524;GMAF=G|0.3085;AA=A;AF1000G=0.691494;phyloP=-4.216;CSQT=1|ABCA4|NM_000350.2|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,111:111:1.000:20:-100.0000:0.0000 chr1 94481239 . AC A 20 LowDP;q30 DP=1;CSQT=1|ABCA4|NM_000350.2|intron_variant;CSQR=1|ENSR00000541012|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC ./.:0:0,1:1:1.000:20:-100.0000:0.0000 chr1 94487354 rs472908 G A 100 PASS DP=96;clinvar=1|not_provided,1|benign;cosmic=1|COSN15324643,1|COSN8862525;EVS=0.630231|41|6500;GMAF=G|0.4111;AA=A;AF1000G=0.588858;phyloP=0.368;CSQT=1|ABCA4|NM_000350.2|intron_variant;CSQR=1|ENSR00001522546|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:39,57:96:0.594:20:-100.0000:0.0000 chr1 94495930 rs547806 T C 100 PASS DP=24;GMAF=T|0.01178;AA=C;AF1000G=0.988219;phyloP=-1.706;CSQT=1|ABCA4|NM_000350.2|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:87:0,24:24:1.000:20:-100.0000:0.0000 chr1 94497662 . AT A 79 R5x9 DP=40;cosmic=1|COSN1110290;CSQT=1|ABCA4|NM_000350.2|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:0:32,8:40:0.200:20:-42.4537:0.0000 chr1 94528363 rs4147833 C T 100 PASS DP=44;clinvar=1|not_provided;GMAF=T|0.3736;AA=C;AF1000G=0.373602;phyloP=-0.036;CSQT=1|ABCA4|NM_000350.2|intron_variant;CSQR=1|ENSR00001587959|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:71:20,24:44:0.545:20:-100.0000:0.0000 chr1 94544234 rs3112831 T C 100 PASS DP=24;clinvar=1|likely_benign,1|benign,1|likely_benign,1|likely_benign,1|likely_benign,1|likely_benign;cosmic=1|COSM3735986,1|COSM3735987;EVS=0.260649|188|6503;GMAF=C|0.2208;AA=C;AF1000G=0.220847;phyloP=4.076;CSQT=1|ABCA4|NM_000350.2|missense_variant;CSQR=1|ENSR00001522555|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:28:10,14:24:0.583:20:-100.0000:0.0000 chr1 94544276 rs4147830 G A 100 PASS DP=24;clinvar=1|not_provided,1|benign,1|benign,1|benign,1|benign,1|benign;EVS=0.465477|128|6503;GMAF=G|0.4852;AA=G;AF1000G=0.514776;phyloP=1.577;CSQT=1|ABCA4|NM_000350.2|intron_variant;CSQR=1|ENSR00001522555|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:35:14,10:24:0.417:20:-100.0000:0.0000 chr1 94549029 rs526016 A G 100 PASS DP=35;clinvar=1|not_provided,1|benign;cosmic=1|COSN19623402,1|COSN20281454;EVS=0.244881|57|6495;GMAF=G|0.1977;AA=A;AF1000G=0.197684;phyloP=-0.264;CSQT=1|ABCA4|NM_000350.2|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:47:21,14:35:0.400:20:-100.0000:0.0278 chr1 94576893 rs2297635 G A 100 PASS DP=33;GMAF=A|0.2212;AA=G;AF1000G=0.221246;phyloP=-0.75;CSQT=1|ABCA4|NM_000350.2|intron_variant;CSQR=1|ENSR00001587977|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:58:18,15:33:0.455:20:-93.3432:0.0000 chr1 94576968 rs2297634 T C 100 PASS DP=33;clinvar=1|not_provided,1|benign;cosmic=1|COSN15654490;EVS=0.473089|46|6503;GMAF=T|0.4531;AA=C;AF1000G=0.546925;phyloP=-3.871;CSQT=1|ABCA4|NM_000350.2|intron_variant;CSQR=1|ENSR00001587977|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:58:18,15:33:0.455:20:-100.0000:0.0000 chr1 94578548 rs4847281 T C 100 PASS DP=11;clinvar=1|benign;EVS=0.987698|111|6503;GMAF=T|0.01298;AA=C;AF1000G=0.987021;phyloP=-2.955;CSQT=1|ABCA4|NM_000350.2|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:40:0,11:11:1.000:20:-86.0242:0.0000 chr1 206944233 rs1554286 A G 100 PASS DP=19;EVS=0.750884|106|6503;GMAF=A|0.4081;AA=G;AF1000G=0.591853;phyloP=1.334;CSQT=1|IL10|NM_000572.2|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:69:0,19:19:1.000:20:-100.0000:0.0000 chr1 206944645 rs1518111 T C 100 PASS DP=25;cosmic=1|COSN19767692,1|COSN8861895;EVS=0.732589|75|2283;GMAF=T|0.4269;AA=C;AF1000G=0.573083;phyloP=-1.494;CSQT=1|IL10|NM_000572.2|intron_variant;CSQR=1|ENSR00000551734|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:91:0,25:25:1.000:20:-100.0000:0.0000 chr1 228113163 rs3795768 A G 100 PASS DP=77;cosmic=1|COSM425495;EVS=0.753507|7|6345;GMAF=A|0.3123;AA=G;AF1000G=0.6877;phyloP=-4.017;CSQT=1|WNT9A|NM_003395.2|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:39,38:77:0.494:20:-15.2938:0.0610 chr2 1642537 rs386642327 TGC CGT 100 PASS DP=82;GMAF=T|0.1218;CSQT=1|PXDN|NM_012293.1|intron_variant;CSQR=1|ENSR00001696178|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,82:82:1.000:20:-100.0000:0.0000 chr2 1642545 rs6742039 C G 100 PASS DP=81;cosmic=1|COSN6678655;GMAF=C|0.1218;AA=C;AF1000G=0.878195;phyloP=0.175;CSQT=1|PXDN|NM_012293.1|intron_variant;CSQR=1|ENSR00001696178|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,81:81:1.000:20:-100.0000:0.0122 chr2 1647171 rs6730800 T C 100 PASS DP=74;clinvar=1|benign;EVS=0.863442|70|6327;GMAF=T|0.09225;AA=C;AF1000G=0.907748;phyloP=-0.045;CSQT=1|PXDN|NM_012293.1|synonymous_variant;CSQR=1|ENSR00001696179|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,74:74:1.000:20:-100.0000:0.0133 chr2 1652822 rs1863135 T G 100 PASS DP=81;clinvar=1|benign;EVS=0.899146|32|6207;GMAF=T|0.0645;AA=G;AF1000G=0.935503;phyloP=-0.143;CSQT=1|PXDN|NM_012293.1|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,81:81:1.000:20:-100.0000:0.0122 chr2 1664654 rs17841813 A G 100 PASS DP=62;clinvar=1|benign;EVS=0.713489|87|6279;GMAF=A|0.1891;AA=G;AF1000G=0.810903;phyloP=-0.535;CSQT=1|PXDN|NM_012293.1|splice_region_variant&synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,62:62:1.000:20:-100.0000:0.0313 chr2 113877495 rs928940 G T 100 PASS DP=93;GMAF=G|0.2909;AA=T;AF1000G=0.709065;phyloP=-0.241;CSQT=1|IL1RN|NM_173841.2|intron_variant;CSQR=1|ENSR00001706991|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:54,39:93:0.419:20:-100.0000:0.0211 chr2 113890304 rs315952 T C 100 PASS DP=56;clinvar=1|benign;EVS=0.333154|94|6503;GMAF=C|0.35;AA=C;AF1000G=0.35004;phyloP=-2.655;CSQT=1|IL1RN|NM_173841.2|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,56:56:1.000:20:-100.0000:0.0000 chr2 113890586 rs315951 C G 100 PASS DP=34;clinvar=1|benign;GMAF=G|0.355;AA=c;AF1000G=0.355032;phyloP=0.648;CSQT=1|IL1RN|NM_173841.2|3_prime_UTR_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,34:34:1.000:20:-100.0000:0.0000 chr2 135741061 rs12623713 G A 100 PASS DP=16;GMAF=A|0.3626;AA=G;AF1000G=0.36262;phyloP=-0.454;CSQT=1|MAP3K19|NM_025052.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:58:0,16:16:1.000:20:-100.0000:0.0000 chr2 135741425 rs16831223 C A 100 PASS DP=53;cosmic=1|COSN19623135,1|COSN20281157;EVS=0.007844|65|6502;GMAF=A|0.09105;AA=C;AF1000G=0.091054;phyloP=0.08;CSQT=1|MAP3K19|NM_025052.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:84:23,30:53:0.566:20:-100.0000:0.0364 chr2 135744007 rs3905317 T C 100 PASS DP=32;cosmic=1|COSM4001180,1|COSM4001181;EVS=0.008304|76|6503;GMAF=C|0.09225;AA=T;AF1000G=0.092252;phyloP=1.201;CSQT=1|MAP3K19|NM_025052.3|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:60:17,15:32:0.469:20:-100.0000:0.0000 chr2 135744416 rs1112542 C G 100 PASS DP=33;cosmic=1|COSM5021320,1|COSM5021321;EVS=0.050361|162|6503;GMAF=G|0.1252;AA=C;AF1000G=0.1252;phyloP=3.185;CSQT=1|MAP3K19|NM_025052.3|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:43:20,13:33:0.394:20:-100.0000:0.0000 chr2 135745392 rs11888766 G A 100 PASS DP=74;cosmic=1|COSM4415693;EVS=0.208596|60|6503;GMAF=A|0.2394;AA=G;AF1000G=0.239417;phyloP=-0.308;CSQT=1|MAP3K19|NM_025052.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:35,39:74:0.527:20:-100.0000:0.0133 chr2 135745545 rs11899779 C T 100 PASS DP=34;cosmic=1|COSM4415123;EVS=0.259111|95|6503;GMAF=T|0.3626;AA=T;AF1000G=0.36262;phyloP=0.493;CSQT=1|MAP3K19|NM_025052.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,34:34:1.000:20:-100.0000:0.0000 chr2 135745722 rs10928526 A G 100 PASS DP=54;cosmic=1|COSM4133139;EVS=0.259342|105|6503;GMAF=G|0.3628;AA=G;AF1000G=0.362819;phyloP=-0.29;CSQT=1|MAP3K19|NM_025052.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,54:54:1.000:20:-100.0000:0.0357 chr2 135762980 rs7606415 C T 100 PASS DP=32;EVS=0.235891|111|6503;GMAF=T|0.3405;AA=C;AF1000G=0.340455;phyloP=0.099;CSQT=1|MAP3K19|NM_025052.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,32:32:1.000:20:-100.0000:0.0000 chr2 189899541 rs4666770 T C 100 PASS DP=86;cosmic=1|COSN19619790;GMAF=T|0.1552;AA=C;AF1000G=0.844848;phyloP=-1.115;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,86:86:1.000:20:-100.0000:0.0000 chr2 189899572 rs7420715 T C 100 PASS DP=85;GMAF=T|0.1552;AA=C;AF1000G=0.844848;phyloP=0.056;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,85:85:1.000:20:-100.0000:0.0116 chr2 189901295 rs12693526 G A 100 PASS DP=90;clinvar=1|benign;cosmic=1|COSN19615392;EVS=0.712782|14|6462;GMAF=G|0.3566;AA=G;AF1000G=0.643371;phyloP=-0.332;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,90:90:1.000:20:-100.0000:0.0000 chr2 189907937 rs6434312 A G 100 PASS DP=105;cosmic=1|COSM4001449;EVS=0.971321|94|6503;GMAF=A|0.05911;AA=G;AF1000G=0.940895;phyloP=-0.085;CSQT=1|COL5A2|NM_000393.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,105:105:1.000:20:-100.0000:0.0000 chr2 189918787 rs6738371 C T 100 PASS DP=19;GMAF=C|0.3596;AA=C;AF1000G=0.640375;phyloP=0.41;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:69:0,19:19:1.000:20:-100.0000:0.0000 chr2 189923104 rs7556733 A G 100 PASS DP=86;EVS=0.962863|50|6503;GMAF=A|0.05691;AA=G;AF1000G=0.943091;phyloP=-1.181;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,86:86:1.000:20:-100.0000:0.0115 chr2 189923630 rs398090949;rs398080909;rs5837121;rs574915386 AT A 100 PASS DP=41;clinvar=1|benign;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:61:7,34:41:0.829:20:-100.0000:0.0000 chr2 189925548 rs6414122 T A 100 PASS DP=90;clinvar=1|benign;EVS=0.962325|31|6503;GMAF=T|0.05751;AA=A;AF1000G=0.942492;phyloP=-0.376;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,90:90:1.000:20:-100.0000:0.0000 chr2 189926219 rs111688859 CT C 100 PASS DP=36;AF1000G=0.008986;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:76:18,18:36:0.500:20:-100.0000:0.0000 chr2 189926228 . T TA 100 PASS DP=36;GMAF=T|0.138;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:53:21,15:36:0.417:20:-89.8384:0.0000 chr2 189927506 rs7424947 C G 100 PASS DP=26;GMAF=C|0.1705;AA=G;AF1000G=0.829473;phyloP=-0.215;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:94:0,26:26:1.000:20:-100.0000:0.0000 chr2 189929414 . A G 23 q30 DP=10;phyloP=0.477;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:0:8,2:10:0.200:20:-100.0000:0.0000 chr2 189932831 rs2229495 T C 100 PASS DP=36;EVS=0.962633|77|6503;GMAF=T|0.05711;AA=C;AF1000G=0.942891;phyloP=-2.844;CSQT=1|COL5A2|NM_000393.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,36:36:1.000:20:-100.0000:0.0000 chr2 189953285 rs5837124;rs397758641;rs746250131 A AAATG 100 PASS DP=81;cosmic=1|COSN19656478;AF1000G=0.798323;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,81:81:1.000:20:-100.0000:0.0000 chr2 189974958 rs4128539 G T 100 PASS DP=79;EVS=0.939951|72|6503;GMAF=G|0.1114;AA=T;AF1000G=0.888578;phyloP=-0.223;CSQT=1|COL5A2|NM_000393.3|synonymous_variant;CSQR=1|ENSR00001712810|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,79:79:1.000:20:-100.0000:0.0000 chr2 209168853 rs893256 C T 100 PASS DP=35;EVS=0.921113|48|6503;GMAF=C|0.08926;AA=C;AF1000G=0.910743;phyloP=0.565;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,35:35:1.000:20:-100.0000:0.0000 chr2 209184980 rs10932258 G A 100 PASS DP=50;clinvar=1|benign;cosmic=1|COSM4133415;EVS=0.992151|90|6498;GMAF=G|0.008187;AA=A;AF1000G=0.991813;phyloP=3.604;CSQT=1|PIKFYVE|NM_015040.3|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,50:50:1.000:20:-100.0000:0.0000 chr2 209184999 rs10932259 C T 100 PASS DP=50;clinvar=1|benign;cosmic=1|COSM4133416;EVS=0.922135|100|6492;GMAF=C|0.08846;AA=C;AF1000G=0.911542;phyloP=1.019;CSQT=1|PIKFYVE|NM_015040.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,50:50:1.000:20:-100.0000:0.0000 chr2 209190330 rs2363468 T C 100 PASS DP=62;clinvar=1|benign;EVS=0.922420|63|6503;GMAF=T|0.08826;AA=C;AF1000G=0.911741;phyloP=0.579;CSQT=1|PIKFYVE|NM_015040.3|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,62:62:1.000:20:-100.0000:0.0000 chr2 209190519 rs893254 A T 100 PASS DP=36;clinvar=1|benign;EVS=0.922344|65|6503;GMAF=A|0.08846;AA=A;AF1000G=0.911542;phyloP=1.35;CSQT=1|PIKFYVE|NM_015040.3|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,36:36:1.000:20:-100.0000:0.0000 chr2 209190528 rs893253 C G 100 PASS DP=36;clinvar=1|benign;EVS=0.923112|68|6503;GMAF=C|0.08786;AA=G;AF1000G=0.912141;phyloP=-0.255;CSQT=1|PIKFYVE|NM_015040.3|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,36:36:1.000:20:-100.0000:0.0000 chr2 209191082 rs1529979 C A 100 PASS DP=68;clinvar=1|benign;EVS=0.922344|98|6503;GMAF=C|0.08846;AA=A;AF1000G=0.911542;phyloP=2.372;CSQT=1|PIKFYVE|NM_015040.3|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,68:68:1.000:20:-100.0000:0.0000 chr2 209191099 rs1529978 T C 100 PASS DP=68;clinvar=1|benign;EVS=0.994618|103|6503;GMAF=T|0.003994;AA=C;AF1000G=0.996006;phyloP=-0.071;CSQT=1|PIKFYVE|NM_015040.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,68:68:1.000:20:-100.0000:0.0000 chr2 209194696 rs1437414 G C 100 PASS DP=66;EVS=0.928477|72|2279;GMAF=G|0.08786;AA=C;AF1000G=0.912141;phyloP=-0.68;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,66:66:1.000:20:-100.0000:0.0000 chr2 209195133 rs12694109 T C 37 LowDP DP=2;GMAF=T|0.1643;AA=T;AF1000G=0.835663;phyloP=-0.618;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC ./.:0:0,2:2:1.000:20:-100.0000:0.0000 chr2 209200394 rs6718402 A C 100 PASS DP=60;GMAF=A|0.08826;AA=A;AF1000G=0.911741;phyloP=0.18;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,60:60:1.000:20:-100.0000:0.0000 chr2 209201739 rs7596571 T C 100 PASS DP=31;GMAF=T|0.01697;AA=C;AF1000G=0.983027;phyloP=-1.077;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,31:31:1.000:20:-100.0000:0.0000 chr2 209204714 rs2289171 G A 74 PASS DP=18;cosmic=1|COSN166391,1|COSN18890388,1|COSN20282112,1|COSN19624383;EVS=0.307136|44|6502;GMAF=A|0.3123;AA=G;AF1000G=0.3123;phyloP=-0.322;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:14:12,6:18:0.333:20:-100.0000:0.0000 chr2 209209827 rs2304544 G A 100 PASS DP=69;clinvar=1|benign;EVS=0.921652|54|6503;GMAF=G|0.08906;AA=A;AF1000G=0.910942;phyloP=-1.449;CSQT=1|PIKFYVE|NM_015040.3|splice_region_variant&intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,69:69:1.000:20:-100.0000:0.0548 chr2 209209997 rs2043718 C T 100 PASS DP=43;GMAF=C|0.008187;AA=T;AF1000G=0.991813;phyloP=0.163;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,43:43:1.000:20:-100.0000:0.0000 chr2 209212707 rs2304545 G A 100 PASS DP=30;clinvar=1|benign;EVS=0.683069|111|6503;GMAF=G|0.2839;AA=G;AF1000G=0.716054;phyloP=0.162;CSQT=1|PIKFYVE|NM_015040.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,30:30:1.000:20:-100.0000:0.0000 chr2 209214770 rs2118297 A G 100 PASS DP=64;clinvar=1|benign;EVS=0.921793|116|6502;GMAF=A|0.08886;AA=A;AF1000G=0.911142;phyloP=0.473;CSQT=1|PIKFYVE|NM_015040.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,64:64:1.000:20:-100.0000:0.0000 chr2 209215448 rs994696 A G 100 PASS DP=38;EVS=0.922178|44|6502;GMAF=A|0.08886;AA=A;AF1000G=0.911142;phyloP=-0.562;CSQT=1|PIKFYVE|NM_015040.3|intron_variant;CSQR=1|ENSR00001714460|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,38:38:1.000:20:-100.0000:0.0000 chr2 209215586 rs994697 A G 100 PASS DP=101;clinvar=1|benign;EVS=0.921882|129|6503;GMAF=A|0.08886;AA=G;AF1000G=0.911142;phyloP=-0.301;CSQT=1|PIKFYVE|NM_015040.3|synonymous_variant;CSQR=1|ENSR00001714460|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,101:101:1.000:20:-100.0000:0.0000 chr2 209219049 rs6435452 T A 54 LowDP DP=3;GMAF=T|0.08886;AA=T;AF1000G=0.911142;phyloP=0.257;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC ./.:0:0,3:3:1.000:20:-100.0000:0.0000 chr2 209219190 rs6435453 A G 100 PASS DP=70;GMAF=A|0.08826;AA=A;AF1000G=0.911741;phyloP=-0.43;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,70:70:1.000:20:-100.0000:0.0000 chr2 227872182 rs2228557 G A 100 PASS DP=79;clinvar=1|benign,1|benign;cosmic=1|COSM3757991;EVS=0.460410|193|6100;GMAF=G|0.4856;AA=A;AF1000G=0.514377;phyloP=0.537;CSQT=1|COL4A4|NM_000092.4|synonymous_variant;CSQR=1|ENSR00001716056|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:36,43:79:0.544:20:-100.0000:0.0125 chr2 227872995 rs2228555 T C 100 PASS DP=82;clinvar=1|benign,1|benign;cosmic=1|COSM3757992;EVS=0.585705|55|6324;GMAF=T|0.3594;AA=C;AF1000G=0.640575;phyloP=-0.16;CSQT=1|COL4A4|NM_000092.4|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:40,42:82:0.512:20:-100.0000:0.0120 chr2 227873028 rs13419076 A G 100 PASS DP=81;clinvar=1|benign,1|benign;EVS=0.454801|42|6228;GMAF=A|0.4844;AA=G;AF1000G=0.515575;phyloP=-1.917;CSQT=1|COL4A4|NM_000092.4|splice_region_variant&intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:39,42:81:0.519:20:-100.0000:0.0122 chr2 227874957 rs4423583 C T 100 PASS DP=29;GMAF=C|0.4834;AA=T;AF1000G=0.516573;phyloP=-0.859;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:67:14,15:29:0.517:20:-97.3268:0.0000 chr2 227877037 rs10188770 G A 100 PASS DP=32;cosmic=1|COSN8867960;EVS=0.471249|43|6191;GMAF=G|0.4794;AA=G;AF1000G=0.520567;phyloP=0.723;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:60:17,15:32:0.469:20:-100.0000:0.0000 chr2 227886773 rs3752895 A G 100 PASS DP=85;clinvar=1|benign,1|benign;cosmic=1|COSM3757993;EVS=0.478246|113|5976;GMAF=A|0.4738;AA=G;AF1000G=0.526158;phyloP=1.999;CSQT=1|COL4A4|NM_000092.4|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:45,38:85:0.447:20:-100.0000:0.0000 chr2 227886925 rs3752896 C T 100 PASS DP=32;cosmic=1|COSN8867961,1|COSN8867962;EVS=0.411268|92|6035;GMAF=T|0.4485;AA=C;AF1000G=0.448482;phyloP=-0.599;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:44:19,13:32:0.406:20:-76.9209:0.0000 chr2 227892619 rs2228556 C T 100 PASS DP=111;clinvar=1|benign,1|benign;cosmic=1|COSM1752390;EVS=0.454637|56|5952;GMAF=T|0.4918;AA=T;AF1000G=0.491813;phyloP=0.477;CSQT=1|COL4A4|NM_000092.4|splice_region_variant&synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:51,60:111:0.541:20:-31.0847:0.0177 chr2 227892720 rs2229813 C T 100 PASS DP=104;clinvar=1|likely_pathogenic,1|benign,1|benign;cosmic=1|COSM1752392;EVS=0.454830|27|5911;GMAF=T|0.493;AA=T;AF1000G=0.493011;phyloP=0.077;CSQT=1|COL4A4|NM_000092.4|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:48,56:104:0.538:20:-100.0000:0.0000 chr2 227895125 rs1917127 A G 88 PASS DP=19;cosmic=1|COSN8867963,1|COSN8867964;EVS=0.454085|101|6022;GMAF=G|0.4966;AA=G;AF1000G=0.496605;phyloP=-0.061;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:21:12,7:19:0.368:20:-100.0000:0.0000 chr2 227896652 rs13423714 C G 100 PASS DP=70;clinvar=1|benign,1|benign;EVS=0.451309|34|6110;GMAF=G|0.496;AA=C;AF1000G=0.496006;phyloP=-0.301;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:31,39:70:0.557:20:-100.0000:0.0141 chr2 227896886 rs2229812 C T 100 PASS DP=30;clinvar=1|benign,1|benign;cosmic=1|COSM3757994;EVS=0.452558|76|5923;GMAF=T|0.4956;AA=T;AF1000G=0.495607;phyloP=-0.79;CSQT=1|COL4A4|NM_000092.4|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:63:14,15:30:0.500:20:-100.0000:0.0000 chr2 227896976 rs10203363 C T 100 PASS DP=31;clinvar=1|benign,1|benign;cosmic=1|COSM3757995;EVS=0.451201|36|5953;GMAF=T|0.495;AA=C;AF1000G=0.495008;phyloP=-0.718;CSQT=1|COL4A4|NM_000092.4|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:60:15,16:31:0.516:20:-100.0000:0.0000 chr2 227915601 rs2272204 G T 100 PASS DP=28;GMAF=G|0.4527;AA=G;AF1000G=0.547324;phyloP=-0.534;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:51:15,13:28:0.464:20:-80.3261:0.0000 chr2 227915832 rs1800517 G A 100 PASS DP=101;clinvar=1|benign,1|benign;cosmic=1|COSM4001525;EVS=0.518593|111|5997;GMAF=G|0.4527;AA=G;AF1000G=0.547324;phyloP=2.772;CSQT=1|COL4A4|NM_000092.4|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:46,55:101:0.545:20:-100.0000:0.0000 chr2 227920474 rs1320406 G A 100 PASS DP=21;GMAF=A|0.4922;AA=G;AF1000G=0.492212;phyloP=-0.61;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:33:12,9:21:0.429:20:-100.0000:0.0000 chr2 227921977 rs4536647 A G 100 PASS DP=23;GMAF=A|0.3333;AA=G;AF1000G=0.666733;phyloP=-0.246;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:29:14,9:23:0.391:20:-100.0000:0.0000 chr2 227922015 rs4566357 A G 100 PASS DP=23;GMAF=A|0.3335;AA=a;AF1000G=0.666534;phyloP=0.103;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:29:14,9:23:0.391:20:-100.0000:0.0000 chr2 227922104 rs7567789 T C 100 PASS DP=23;cosmic=1|COSN19692653;EVS=0.657633|10|5922;GMAF=T|0.3335;AA=T;AF1000G=0.666534;phyloP=-0.149;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:29:14,9:23:0.391:20:-52.5279:0.0000 chr2 227922109 rs7567796 T A 100 PASS DP=23;cosmic=1|COSN19692654;EVS=0.624452|11|5926;GMAF=T|0.3662;AA=T;AF1000G=0.633786;phyloP=0.119;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:29:14,9:23:0.391:20:-52.5279:0.0000 chr2 227924817 . G GAAA 29 LowDP;q30 DP=5;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC ./.:0:3,2:5:0.400:20:-100.0000:0.0000 chr2 227927189 rs35717623;rs398081120;rs796278870 GT G 100 PASS DP=27;AF1000G=0.558307;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:53:14,13:27:0.481:20:-100.0000:0.0000 chr2 227954599 rs2229814 G A 100 PASS DP=90;clinvar=1|benign,1|benign;cosmic=1|COSM3757996;EVS=0.509039|111|5974;GMAF=G|0.4515;AA=A;AF1000G=0.548522;phyloP=-0.088;CSQT=1|COL4A4|NM_000092.4|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:51,39:90:0.433:20:-100.0000:0.0000 chr2 227966148 rs16823202 C T 100 PASS DP=59;cosmic=1|COSN18720449,1|COSN19634668;EVS=0.656236|18|2269;GMAF=C|0.4163;AA=T;AF1000G=0.583666;phyloP=-0.103;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,59:59:1.000:20:-100.0000:0.0000 chr2 227966298 rs59443812;rs397724904 T TA 100 PASS DP=56;AF1000G=0.535343;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:6:18,38:56:0.679:20:-100.0000:0.0000 chr2 227967601 rs11274738;rs150877371 ACAATATTTCAGCAATAGGGAAAG A 100 LowDP DP=8;EVS=0.560269|98|5575;AF1000G=0.604832;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC ./.:0:1,7:8:0.875:20:-100.0000:0.0000 chr2 227967830 rs398081123;rs573969560;rs796369993;rs10707643 GA G 100 PASS DP=38;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:14:10,28:38:0.737:20:-100.0000:0.0000 chr2 227973410 rs55741079 C A 100 PASS DP=24;GMAF=A|0.3391;AA=C;AF1000G=0.339058;phyloP=-0.34;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:35:14,10:24:0.417:20:-100.0000:0.0400 chr2 227973623 rs12475686 A G 100 PASS DP=69;EVS=0.622897|30|5944;GMAF=A|0.3996;AA=A;AF1000G=0.600439;phyloP=0.246;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:34,35:69:0.507:20:-100.0000:0.0282 chr2 227979261 rs76770753 A G 63 PASS DP=15;cosmic=1|COSN8867970;EVS=0.000523|27|2867;GMAF=G|0.02157;AA=A;AF1000G=0.021565;phyloP=0.359;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:12:10,5:15:0.333:20:-26.3206:0.0000 chr2 227979533 rs12465531 A C 100 PASS DP=82;GMAF=A|0.3578;AA=C;AF1000G=0.642173;phyloP=-2.486;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:40,42:82:0.512:20:-100.0000:0.0000 chr2 228102723 rs13424243 G C 100 PASS DP=31;clinvar=1|benign,1|benign;cosmic=1|COSM3757997,1|COSM3757998;EVS=0.351087|174|5933;GMAF=C|0.2302;AA=G;AF1000G=0.230232;phyloP=1.782;CSQT=1|COL4A3|NM_000091.4|missense_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:54:17,14:31:0.452:20:-95.2673:0.0000 chr2 228102752 rs1882435 C A 100 PASS DP=31;clinvar=1|benign,1|benign;cosmic=1|COSN166420,1|COSN19624384,1|COSN20282113,1|COSN19674657;EVS=0.284798|137|5927;GMAF=A|0.3051;AA=A;AF1000G=0.305112;phyloP=-1.334;CSQT=1|COL4A3|NM_000091.4|intron_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:49:14,17:31:0.548:20:-100.0000:0.0000 chr2 228109626 rs113428834 T TG 100 PASS DP=31;EVS=0.766122|68|5629;GMAF=G|0.009585;AF1000G=0.749201;CSQT=1|COL4A3|NM_000091.4|intron_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:25:7,24:31:0.774:20:-100.0000:0.0000 chr2 228109784 rs6750210 C T 100 PASS DP=32;EVS=0.738043|25|2279;GMAF=C|0.252;AA=C;AF1000G=0.748003;phyloP=0.006;CSQT=1|COL4A3|NM_000091.4|intron_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,32:32:1.000:20:-100.0000:0.0000 chr2 228111435 rs10178458 T C 100 PASS DP=62;clinvar=1|benign,1|benign;EVS=0.770425|65|5924;GMAF=T|0.2033;AA=t;AF1000G=0.796725;phyloP=1.132;CSQT=1|COL4A3|NM_000091.4|missense_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,62:62:1.000:20:-100.0000:0.0000 chr2 228113175 rs6436669 A G 100 PASS DP=132;clinvar=1|benign,1|benign;EVS=0.770131|57|5899;GMAF=A|0.2037;AA=G;AF1000G=0.796326;phyloP=-0.094;CSQT=1|COL4A3|NM_000091.4|missense_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,132:132:1.000:20:-100.0000:0.0075 chr2 228118403 rs12621551 T G 100 PASS DP=18;EVS=0.772528|168|6159;GMAF=T|0.2131;AA=T;AF1000G=0.786941;phyloP=-0.184;CSQT=1|COL4A3|NM_000091.4|intron_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:65:0,18:18:1.000:20:-100.0000:0.0000 chr2 228118815 rs77431913 G A 100 PASS DP=83;clinvar=1|benign,1|likely_benign;EVS=0.023215|90|6009;GMAF=A|0.06709;AA=G;AF1000G=0.067093;phyloP=0.999;CSQT=1|COL4A3|NM_000091.4|intron_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:44,39:83:0.470:20:-100.0000:0.0000 chr2 228118867 rs80109666 G A 100 PASS DP=83;clinvar=1|benign,1|likely_benign;EVS=0.022712|109|6010;GMAF=A|0.0607;AA=G;AF1000G=0.060703;phyloP=-1.344;CSQT=1|COL4A3|NM_000091.4|missense_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:44,39:83:0.470:20:-100.0000:0.0000 chr2 228118949 rs7559693 C G 100 PASS DP=82;EVS=0.316251|67|2283;GMAF=G|0.3315;AA=G;AF1000G=0.33147;phyloP=-0.438;CSQT=1|COL4A3|NM_000091.4|intron_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:43,39:82:0.476:20:-100.0