##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\6343_S27.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\Sample639 -i D:\Illumina\MiSeqAnalysis\181130_M05705_0031_000000000-C5R45\Alignment_3\20181203_130703\Temp_03-VariantCalling\interval\6343_S27.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 6343_S27.bam chr1 11172778 rs538377160 A G 100 PASS DP=41;cosmic=1|COSN8317914;GMAF=G|0.0007987;AA=A;AF1000G=0.000799;phyloP=0.408;CSQT=1|MTOR|NM_004958.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:13:30,11:41:0.268:20:-100.0000:0.0889 chr1 11181327 rs11121691 C T 100 PASS DP=24;cosmic=1|COSM3996743;EVS=0.302091|72|6503;GMAF=T|0.2206;AA=C;AF1000G=0.220647;phyloP=0.56;CSQT=1|MTOR|NM_004958.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:39:11,13:24:0.542:20:-100.0000:0.0000 chr1 11190646 rs2275527 G A 100 PASS DP=37;cosmic=1|COSM3996746;EVS=0.305936|95|6503;GMAF=A|0.2286;AA=G;AF1000G=0.228634;phyloP=-0.401;CSQT=1|MTOR|NM_004958.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:59:21,16:37:0.432:20:-100.0000:0.0000 chr1 11205058 rs1057079 C T 100 PASS DP=19;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 0/1:12:7,12:19:0.632:20:-91.6535:0.0000 chr1 11288758 rs1064261 G A 100 PASS DP=45;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 0/1:53:28,17:45:0.378:20:-99.5096:0.0000 chr1 11294267 . C T 100 PASS DP=37;cosmic=1|COSM462630;phyloP=5.764;CSQT=1|MTOR|NM_004958.3|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:43:23,14:37:0.378:20:-89.8384:0.0000 chr1 11297762 rs7524202 T C 100 PASS DP=23;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 0/1:37:13,10:23:0.435:20:-100.0000:0.0000 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 0/1:57:16,19:35:0.543:20:-100.0000:0.0000 chr1 36563158 rs3738360 C A 100 PASS DP=46;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 0/1:97:23,23:46:0.500:20:-100.0000:0.0000 chr1 36563797 rs35495320 C T 100 PASS DP=19;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 0/1:28:11,8:19:0.421:20:-55.9446:0.0000 chr1 36565584 rs274753 C G 100 PASS DP=55;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 1/1:100:0,55:55:1.000:20:-100.0000:0.0000 chr1 36565617 rs274754 G A 100 PASS DP=55;EVS=0.652929|44|6503;GMAF=A|0.4826;AA=G;AF1000G=0.482628;phyloP=-1.5;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 0/1:100:28,27:55:0.491:20:-100.0000:0.0000 chr1 36565739 rs57985157 C T 100 PASS DP=34;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 0/1:72:17,17:34:0.500:20:-100.0000:0.0000 chr1 47881974 rs181190356 G A 100 PASS DP=21;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 0/1:25:13,8:21:0.381:20:-100.0000:0.0455 chr1 47882497 rs34082359 C T 100 PASS DP=22;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 0/1:31:13,9:22:0.409:20:-100.0000:0.0000 chr1 47883019 rs6666370 T C 100 PASS DP=47;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 1/1:100:0,47:47:1.000:20:-100.0000:0.0000 chr1 47883024 rs2820969 A G 100 PASS DP=44;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 1/1:100:0,44:44:1.000:20:-100.0000:0.0638 chr1 94471075 rs1762114 A G 100 PASS DP=33;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 1/1:100:0,33:33:1.000:20:-100.0000:0.0000 chr1 94476555 rs537831 G A 100 PASS DP=76;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 1/1:100:0,76:76:1.000:20:-100.0000:0.0000 chr1 94480037 rs2275033 C T 100 PASS DP=48;GMAF=T|0.3271;AA=T;AF1000G=0.327077;phyloP=-0.648;CSQT=1|ABCA4|NM_000350.2|intron_variant;CSQR=1|ENSR00000541012|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:79:22,26:48:0.542:20:-100.0000:0.0000 chr1 94487354 rs472908 G A 100 PASS DP=36;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 0/1:54:16,20:36:0.556:20:-100.0000:0.0270 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 94528363 rs4147833 C T 100 PASS DP=37;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 0/1:27:14,23:37:0.622:20:-100.0000:0.0000 chr1 94544276 rs4147830 G A 53 PASS DP=11;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 0/1:11:7,4:11:0.364:20:-100.0000:0.0000 chr1 94576893 rs2297635 G A 100 PASS DP=19;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 0/1:28:11,8:19:0.421:20:-55.9446:0.0000 chr1 94576968 rs2297634 T C 100 PASS DP=19;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 0/1:28:11,8:19:0.421:20:-100.0000:0.0000 chr1 94578548 rs4847281 T C 100 LowDP DP=8;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 ./.:0:0,8:8:1.000:20:-69.8586:0.0000 chr1 154943024 rs115587781 G A 100 PASS DP=16;EVS=0.007251|21|5103;GMAF=A|0.008586;AA=G;AF1000G=0.008586;phyloP=2.879;CSQT=1|SHC1|NM_001130040.1|5_prime_UTR_variant,1|CKS1B|NM_001826.2|upstream_gene_variant;CSQR=1|ENSR00000545467|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:34:8,8:16:0.500:20:-57.9561:0.0000 chr1 206944233 rs1554286 A G 100 PASS DP=20;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 0/1:8:7,13:20:0.650:20:-73.4051:0.0000 chr1 206944645 rs1518111 T C 100 PASS DP=32;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 0/1:60:17,15:32:0.469:20:-100.0000:0.0000 chr2 1642537 rs386642327 TGC CGT 100 PASS DP=45;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 1/1:100:0,45:45:1.000:20:-100.0000:0.0000 chr2 1642545 rs6742039 C G 100 PASS DP=45;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 1/1:100:0,45:45:1.000:20:-100.0000:0.0000 chr2 1647171 rs6730800 T C 100 PASS DP=50;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 1/1:100:0,50:50:1.000:20:-100.0000:0.0000 chr2 1651842 rs11685976 C A 100 PASS DP=22;cosmic=1|COSN15304688,1|COSN15323800,1|COSN8867748,1|COSN19673469;GMAF=A|0.2448;AA=C;AF1000G=0.244808;phyloP=-0.312;CSQT=1|PXDN|NM_012293.1|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:35:10,12:22:0.545:20:-100.0000:0.0435 chr2 1652660 rs3811613 G A 100 PASS DP=37;clinvar=1|benign;cosmic=1|COSM3757715;EVS=0.250239|16|6278;GMAF=A|0.2448;AA=G;AF1000G=0.244808;phyloP=0.047;CSQT=1|PXDN|NM_012293.1|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:61:17,20:37:0.541:20:-100.0000:0.0513 chr2 1652822 rs1863135 T G 100 PASS DP=58;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 1/1:100:0,58:58:1.000:20:-100.0000:0.0000 chr2 1657358 . T TA 100 PASS DP=28;CSQT=1|PXDN|NM_012293.1|intron_variant;CSQR=1|ENSR00000675456|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:59:14,14:28:0.500:20:-95.2673:0.0000 chr2 1664654 rs17841813 A G 100 PASS DP=16;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 1/1:58:0,16:16:1.000:20:-100.0000:0.0000 chr2 113532885 rs3783550 G T 100 PASS DP=26;EVS=0.725896|55|6503;GMAF=G|0.3796;AA=T;AF1000G=0.620407;phyloP=-1.505;CSQT=1|IL1A|NM_000575.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:55:13,13:26:0.500:20:-100.0000:0.0000 chr2 113875509 rs2234677 G A 100 PASS DP=33;clinvar=1|benign;cosmic=1|COSN6674370;EVS=0.205869|70|2283;GMAF=A|0.1865;AA=G;AF1000G=0.186502;phyloP=-1.239;CSQT=1|IL1RN|NM_173841.2|5_prime_UTR_variant;CSQR=1|ENSR00001045708|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,33:33:1.000:20:-100.0000:0.0294 chr2 113875565 rs2234678 A G 100 PASS DP=35;clinvar=1|benign;EVS=0.198062|142|6503;GMAF=G|0.1859;AA=a;AF1000G=0.185903;phyloP=-0.975;CSQT=1|IL1RN|NM_173841.2|5_prime_UTR_variant;CSQR=1|ENSR00001045708|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,35:35:1.000:20:-100.0000:0.0278 chr2 113875584 rs2234679 G C 100 PASS DP=35;clinvar=1|benign;EVS=0.198216|150|6503;GMAF=C|0.1859;AA=C;AF1000G=0.185903;phyloP=-0.13;CSQT=1|IL1RN|NM_173841.2|5_prime_UTR_variant;CSQR=1|ENSR00001045708|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,35:35:1.000:20:-100.0000:0.0278 chr2 113875631 rs16065 T C 100 PASS DP=35;cosmic=1|COSN6674371;EVS=0.193987|118|6503;GMAF=C|0.1857;AA=C;AF1000G=0.185703;phyloP=-0.305;CSQT=1|IL1RN|NM_173841.2|intron_variant;CSQR=1|ENSR00001045708|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,35:35:1.000:20:-100.0000:0.0278 chr2 113877495 rs928940 G T 100 PASS DP=49;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 1/1:100:0,49:49:1.000:20:-100.0000:0.0000 chr2 113877538 rs4251986 G C 100 PASS DP=50;cosmic=1|COSN19673851;GMAF=C|0.1875;AA=G;AF1000G=0.1875;phyloP=-0.009;CSQT=1|IL1RN|NM_173841.2|intron_variant;CSQR=1|ENSR00001706991|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,50:50:1.000:20:-100.0000:0.0000 chr2 113877713 rs878972 A C 100 PASS DP=40;clinvar=1|benign;EVS=0.198985|82|6503;GMAF=C|0.1897;AA=C;AF1000G=0.189696;phyloP=-0.013;CSQT=1|IL1RN|NM_173841.2|splice_region_variant&intron_variant;CSQR=1|ENSR00001706991|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,40:40:1.000:20:-100.0000:0.0000 chr2 113887207 rs419598 T C 100 PASS DP=69;clinvar=1|benign;cosmic=1|COSM3766493,1|COSM3766494,1|COSM3766495;EVS=0.206136|159|6503;GMAF=C|0.1917;AA=T;AF1000G=0.191693;phyloP=-0.225;CSQT=1|IL1RN|NM_173841.2|synonymous_variant;CSQR=1|ENSR00000677374|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,69:69:1.000:20:-100.0000:0.0000 chr2 113887262 rs423904 C T 100 PASS DP=41;cosmic=1|COSN6674388;EVS=0.206059|92|6503;GMAF=T|0.1917;AA=C;AF1000G=0.191693;phyloP=-0.501;CSQT=1|IL1RN|NM_173841.2|intron_variant;CSQR=1|ENSR00000677374|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,41:41:1.000:20:-100.0000:0.0000 chr2 113887273 rs446433 G A 100 PASS DP=41;cosmic=1|COSN6674389;EVS=0.205828|80|6503;GMAF=A|0.1917;AA=G;AF1000G=0.191693;phyloP=0.225;CSQT=1|IL1RN|NM_173841.2|intron_variant;CSQR=1|ENSR00000677374|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,41:41:1.000:20:-100.0000:0.0000 chr2 113887294 rs495282 G C 100 PASS DP=41;cosmic=1|COSN6674390;EVS=0.213973|50|2283;GMAF=C|0.1917;AA=C;AF1000G=0.191693;phyloP=-0.283;CSQT=1|IL1RN|NM_173841.2|intron_variant;CSQR=1|ENSR00000677374|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,41:41:1.000:20:-100.0000:0.0000 chr2 113887338 rs495410 A C 100 PASS DP=39;cosmic=1|COSN6674391;GMAF=C|0.1917;AA=A;AF1000G=0.191693;phyloP=-1.097;CSQT=1|IL1RN|NM_173841.2|intron_variant;CSQR=1|ENSR00000677374|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,39:39:1.000:20:-100.0000:0.0000 chr2 113887399 rs442710 G A 100 PASS DP=39;cosmic=1|COSN6674392;GMAF=A|0.1917;AA=A;AF1000G=0.191693;phyloP=-0.449;CSQT=1|IL1RN|NM_173841.2|intron_variant;CSQR=1|ENSR00000677374|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,39:39:1.000:20:-100.0000:0.0000 chr2 113888465 rs448341 A G 100 PASS DP=21;cosmic=1|COSN6674396;GMAF=G|0.1929;AA=G;AF1000G=0.192891;phyloP=-0.518;CSQT=1|IL1RN|NM_173841.2|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:76:0,21:21:1.000:20:-100.0000:0.0000 chr2 113888470 rs434792 C G 100 PASS DP=21;cosmic=1|COSN6674397;GMAF=G|0.1929;AA=G;AF1000G=0.192891;phyloP=-0.425;CSQT=1|IL1RN|NM_173841.2|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:76:0,21:21:1.000:20:-100.0000:0.0000 chr2 113888557 rs451578 G A 100 PASS DP=21;cosmic=1|COSN6674398;GMAF=A|0.1947;AA=A;AF1000G=0.194688;phyloP=-0.956;CSQT=1|IL1RN|NM_173841.2|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:76:0,21:21:1.000:20:-100.0000:0.0000 chr2 113888579 rs432014 T C 100 PASS DP=21;cosmic=1|COSN17437787,1|COSN6674399;EVS=0.236583|54|6503;GMAF=C|0.221;AA=C;AF1000G=0.221046;phyloP=0.999;CSQT=1|IL1RN|NM_173841.2|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:76:0,21:21:1.000:20:-100.0000:0.0000 chr2 113888793 rs454078 A T 100 PASS DP=56;cosmic=1|COSN6674400;GMAF=T|0.1909;AA=A;AF1000G=0.190895;phyloP=-0.867;CSQT=1|IL1RN|NM_173841.2|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,56:56:1.000:20:-100.0000:0.0000 chr2 135756265 rs58663889 G T 100 PASS DP=61;EVS=0.083231|35|6494;GMAF=T|0.147;AA=G;AF1000G=0.146965;phyloP=-0.534;CSQT=1|MAP3K19|NM_025052.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:90:27,34:61:0.557:20:-100.0000:0.0000 chr2 189899541 rs4666770 T C 100 PASS DP=35;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 0/1:57:16,19:35:0.543:20:-100.0000:0.0278 chr2 189899572 rs7420715 T C 100 PASS DP=34;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 0/1:61:16,18:34:0.529:20:-100.0000:0.0556 chr2 189901295 rs12693526 G A 100 PASS DP=60;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 0/1:82:25,34:60:0.567:20:-100.0000:0.0000 chr2 189907937 rs6434312 A G 100 PASS DP=81;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 1/1:100:0,81:81:1.000:20:-100.0000:0.0000 chr2 189916845 rs138326711 G A 100 PASS DP=48;EVS=0.004380|106|2283;GMAF=A|0.002596;AA=G;AF1000G=0.002596;phyloP=-1;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:23:17,31:48:0.646:20:-100.0000:0.0000 chr2 189918787 rs6738371 C T 100 PASS DP=22;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 0/1:35:10,12:22:0.545:20:-100.0000:0.0000 chr2 189923104 rs7556733 A G 100 PASS DP=57;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 1/1:100:0,57:57:1.000:20:-100.0000:0.0000 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 0/1:70:19,22:41:0.537:20:-100.0000:0.0000 chr2 189925548 rs6414122 T A 100 PASS DP=45;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 1/1:100:0,45:45:1.000:20:-100.0000:0.0000 chr2 189926228 rs369656754 TA T 75 R5x9 DP=30;cosmic=1|COSN15667082;GMAF=T|0.138;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:1:23,7:30:0.233:20:-32.1788:0.0000 chr2 189927506 rs7424947 C G 100 PASS DP=21;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 0/1:40:11,10:21:0.476:20:-100.0000:0.0000 chr2 189932831 rs2229495 T C 100 PASS DP=22;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 1/1:80:0,22:22:1.000:20:-100.0000:0.0000 chr2 189953285 rs5837124;rs397758641;rs746250131 A AAATG 100 PASS DP=50;cosmic=1|COSN19656478;AF1000G=0.798323;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:72:22,28:50:0.560:20:-100.0000:0.0000 chr2 189962098 rs73051214 T C 100 PASS DP=48;EVS=0.042442|55|6503;GMAF=C|0.0655;AA=T;AF1000G=0.065495;phyloP=-0.065;CSQT=1|COL5A2|NM_000393.3|intron_variant;CSQR=1|ENSR00001549874|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:24,24:48:0.500:20:-100.0000:0.0204 chr2 189974958 rs4128539 G T 100 PASS DP=37;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 1/1:100:0,37:37:1.000:20:-100.0000:0.0000 chr2 209168853 rs893256 C T 100 PASS DP=28;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 1/1:100:0,28:28:1.000:20:-100.0000:0.0000 chr2 209184980 rs10932258 G A 100 PASS DP=28;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 1/1:100:0,28:28:1.000:20:-100.0000:0.0000 chr2 209184999 rs10932259 C T 100 PASS DP=28;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 1/1:100:0,28:28:1.000:20:-100.0000:0.0000 chr2 209190330 rs2363468 T C 100 PASS DP=52;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 1/1:100:0,52:52:1.000:20:-100.0000:0.0000 chr2 209190519 rs893254 A T 100 PASS DP=35;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 1/1:100:0,35:35:1.000:20:-100.0000:0.0000 chr2 209190528 rs893253 C G 100 PASS DP=35;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 1/1:100:0,35:35:1.000:20:-100.0000:0.0000 chr2 209191082 rs1529979 C A 100 PASS DP=45;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 1/1:100:0,45:45:1.000:20:-100.0000:0.0000 chr2 209191099 rs1529978 T C 100 PASS DP=45;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 1/1:100:0,45:45:1.000:20:-100.0000:0.0000 chr2 209194696 rs1437414 G C 100 PASS DP=34;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 1/1:100:0,34:34:1.000:20:-100.0000:0.0000 chr2 209200394 rs6718402 A C 100 PASS DP=30;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 1/1:100:0,30:30:1.000:20:-100.0000:0.0000 chr2 209201739 rs7596571 T C 100 PASS DP=47;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 1/1:100:0,47:47:1.000:20:-100.0000:0.0208 chr2 209209827 rs2304544 G A 100 PASS DP=40;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 1/1:100:0,40:40:1.000:20:-100.0000:0.0244 chr2 209209997 rs2043718 C T 100 PASS DP=36;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 1/1:100:0,36:36:1.000:20:-100.0000:0.0000 chr2 209212707 rs2304545 G A 100 PASS DP=15;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 1/1:54:0,15:15:1.000:20:-100.0000:0.0000 chr2 209214770 rs2118297 A G 100 PASS DP=41;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 1/1:100:0,41:41:1.000:20:-100.0000:0.0000 chr2 209215448 rs994696 A G 100 PASS DP=25;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 1/1:91:0,25:25:1.000:20:-100.0000:0.0000 chr2 209215586 rs994697 A G 100 PASS DP=66;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 1/1:100:0,66:66:1.000:20:-100.0000:0.0000 chr2 209219049 rs6435452 T A 70 LowDP DP=4;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 ./.:0:0,4:4:1.000:20:-100.0000:0.0000 chr2 209219190 rs6435453 A G 100 PASS DP=35;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 1/1:100:0,35:35:1.000:20:-100.0000:0.0000 chr2 209219289 rs779817448 C G 100 PASS DP=35;phyloP=0.112;CSQT=1|PIKFYVE|NM_015040.3|splice_region_variant&intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:57:16,19:35:0.543:20:-100.0000:0.0000 chr2 227872182 rs2228557 G A 100 PASS DP=67;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 0/1:100:37,30:67:0.448:20:-100.0000:0.0147 chr2 227872783 rs190148408 G C 100 PASS DP=28;cosmic=1|COSM329268;EVS=0.002466|31|6083;GMAF=C|0.001198;AA=G;AF1000G=0.001198;phyloP=1.921;CSQT=1|COL4A4|NM_000092.4|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:14:10,18:28:0.643:20:-100.0000:0.0000 chr2 227872995 rs2228555 T C 100 PASS DP=58;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 1/1:100:0,58:58:1.000:20:-100.0000:0.0000 chr2 227873028 rs13419076 A G 100 PASS DP=58;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 0/1:78:25,33:58:0.569:20:-100.0000:0.0000 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=30;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 0/1:56:16,14:30:0.467:20:-100.0000:0.0000 chr2 227886773 rs3752895 A G 100 PASS DP=44;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 0/1:93:22,22:44:0.500:20:-100.0000:0.0000 chr2 227886925 rs3752896 C T 100 PASS DP=27;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 0/1:51:13,14:27:0.519:20:-99.5418:0.0000 chr2 227892619 rs2228556 C T 100 PASS DP=81;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 0/1:100:37,44:81:0.543:20:-31.0847:0.0000 chr2 227892720 rs2229813 C T 100 PASS DP=73;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 0/1:100:32,41:73:0.562:20:-100.0000:0.0000 chr2 227895125 rs1917127 A G 100 PASS DP=24;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 0/1:39:11,13:24:0.542:20:-100.0000:0.0000 chr2 227896652 rs13423714 C G 100 PASS DP=43;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 0/1:56:26,17:43:0.395:20:-100.0000:0.0227 chr2 227896886 rs2229812 C T 100 PASS DP=20;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 0/1:19:8,12:20:0.600:20:-100.0000:0.0000 chr2 227896976 rs10203363 C T 100 PASS DP=20;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 0/1:19:8,12:20:0.600:20:-100.0000:0.0000 chr2 227915601 rs2272204 G T 100 PASS DP=33;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 0/1:30:13,20:33:0.606:20:-100.0000:0.0000 chr2 227915832 rs1800517 G A 100 PASS DP=49;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 0/1:53:20,29:49:0.592:20:-100.0000:0.0000 chr2 227915924 rs2272205 T C 100 PASS DP=48;EVS=0.079822|55|5957;GMAF=C|0.106;AA=T;AF1000G=0.10603;phyloP=-0.066;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:45:19,29:48:0.604:20:-100.0000:0.0204 chr2 227920474 rs1320406 G A 50 PASS DP=13;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 0/1:8:9,4:13:0.308:20:-100.0000:0.0000 chr2 227921977 rs4536647 A G 81 PASS DP=24;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 0/1:12:17,7:24:0.292:20:-100.0000:0.0000 chr2 227922015 rs4566357 A G 81 PASS DP=24;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 0/1:12:17,7:24:0.292:20:-100.0000:0.0000 chr2 227922104 rs7567789 T C 95 PASS DP=25;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 0/1:18:17,8:25:0.320:20:-35.7958:0.0000 chr2 227922109 rs7567796 T A 95 PASS DP=25;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 0/1:18:17,8:25:0.320:20:-36.8971:0.0000 chr2 227922321 rs3769641 A G 100 PASS DP=33;clinvar=1|benign,1|likely_benign;EVS=0.074102|56|6039;GMAF=G|0.103;AA=A;AF1000G=0.103035;phyloP=1.885;CSQT=1|COL4A4|NM_000092.4|splice_region_variant&intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:43:20,13:33:0.394:20:-100.0000:0.0000 chr2 227927189 rs35717623;rs398081120;rs796278870 GT G 95 PASS DP=15