##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\12067_S13.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\Sample625 -i D:\Illumina\MiSeqAnalysis\181130_M05705_0031_000000000-C5R45\Alignment_3\20181203_130703\Temp_03-VariantCalling\interval\12067_S13.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 12067_S13.bam chr1 11169676 rs2275525 C T 100 PASS DP=34;cosmic=1|COSN17135501,1|COSN17136377,1|COSN17147630;EVS=0.083654|85|6503;GMAF=T|0.1591;AA=T;AF1000G=0.159145;phyloP=-2.615;CSQT=1|MTOR|NM_004958.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:72:17,17:34:0.500:20:-100.0000:0.0000 chr1 11174331 rs17235654 T C 100 PASS DP=50;cosmic=1|COSN17135936,1|COSN17136783,1|COSN17148061;EVS=0.059203|58|6503;GMAF=C|0.1046;AA=C;AF1000G=0.104633;phyloP=-1.368;CSQT=1|MTOR|NM_004958.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:95:24,26:50:0.520:20:-100.0000:0.0000 chr1 11181457 rs17235633 G T 100 PASS DP=126;cosmic=1|COSN17135873,1|COSN17136719,1|COSN17148003;EVS=0.050976|80|6503;GMAF=T|0.09704;AA=G;AF1000G=0.097045;phyloP=-0.036;CSQT=1|MTOR|NM_004958.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:50,76:126:0.603:20:-100.0000:0.0000 chr1 11184489 rs868080 C T 100 PASS DP=50;GMAF=T|0.1587;AA=T;AF1000G=0.158746;phyloP=0.397;CSQT=1|MTOR|NM_004958.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:75:29,21:50:0.420:20:-100.0000:0.0000 chr1 11186897 rs3737611 A G 100 PASS DP=29;cosmic=1|COSN17135268,1|COSN17136134,1|COSN17147376;EVS=0.094879|48|6503;GMAF=G|0.1727;AA=G;AF1000G=0.172724;phyloP=0.958;CSQT=1|MTOR|NM_004958.3|intron_variant;CSQR=1|ENSR00001577753|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:10:10,19:29:0.655:20:-100.0000:0.0000 chr1 11194591 rs3730381 G A 100 PASS DP=64;GMAF=A|0.09724;AA=G;AF1000G=0.097244;phyloP=-1.872;CSQT=1|MTOR|NM_004958.3|intron_variant;CSQR=1|ENSR00001577755|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:81:39,25:64:0.391:20:-100.0000:0.0000 chr1 11205058 rs1057079 C T 100 PASS DP=18;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 0/1:38:9,9:18:0.500:20:-55.9446:0.0000 chr1 11206690 rs2275942 A T 100 PASS DP=60;cosmic=1|COSN162944,1|COSN17135394,1|COSN17147496,1|COSN17136251;EVS=0.050900|80|6503;GMAF=T|0.09704;AA=A;AF1000G=0.097045;phyloP=-0.412;CSQT=1|MTOR|NM_004958.3|intron_variant,1|MTOR-AS1|NR_046600.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:73:37,23:60:0.383:20:-100.0000:0.0323 chr1 11255008 rs2076658 T C 100 PASS DP=36;cosmic=1|COSM146401;EVS=0.051053|102|6503;GMAF=C|0.09844;AA=C;AF1000G=0.098442;phyloP=-1.066;CSQT=1|MTOR|NM_004958.3|intron_variant,1|ANGPTL7|NM_021146.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:76:18,18:36:0.500:20:-100.0000:0.0000 chr1 11259830 rs11121697 A C 100 PASS DP=62;cosmic=1|COSN19615715;GMAF=C|0.09704;AA=A;AF1000G=0.097045;phyloP=-0.669;CSQT=1|MTOR|NM_004958.3|intron_variant,1|ANGPTL7|NM_021146.3|downstream_gene_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:32,30:62:0.484:20:-100.0000:0.0000 chr1 11273418 rs12116957 T G 100 PASS DP=14;cosmic=1|COSN162946,1|COSN17136046,1|COSN17148183,1|COSN17136916;EVS=0.064586|59|6503;GMAF=G|0.1108;AA=G;AF1000G=0.110823;phyloP=-1.11;CSQT=1|MTOR|NM_004958.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:1:4,10:14:0.714:20:-78.7900:0.0000 chr1 11288758 rs1064261 G A 100 PASS DP=57;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 1/1:100:0,57:57:1.000:20:-100.0000:0.0000 chr1 11297762 rs7524202 T C 100 PASS DP=32;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 1/1:100:0,32:32:1.000:20:-100.0000:0.0000 chr1 11298739 rs12132215 T C 100 PASS DP=117;cosmic=1|COSN19670500;GMAF=C|0.08706;AA=T;AF1000G=0.087061;phyloP=0.344;CSQT=1|MTOR|NM_004958.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:60,57:117:0.487:20:-100.0000:0.0000 chr1 11301714 rs1135172 A G 100 PASS DP=39;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 1/1:100:0,39:39:1.000:20:-100.0000:0.0488 chr1 11303153 rs12141961 C A 100 PASS DP=43;cosmic=1|COSN162947,1|COSN17135429,1|COSN17147539,1|COSN17136304;EVS=0.051207|50|6503;GMAF=A|0.09704;AA=C;AF1000G=0.097045;phyloP=-0.538;CSQT=1|MTOR|NM_004958.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:87:22,21:43:0.488:20:-100.0000:0.0000 chr1 36563158 rs3738360 C A 100 PASS DP=47;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 1/1:100:1,46:47:0.979:20:-100.0000:0.0408 chr1 36565175 rs66899567 G A 100 PASS DP=44;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 1/1:100:0,44:44:1.000:20:-100.0000:0.0000 chr1 36565584 rs274753 C G 100 PASS DP=65;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 1/1:100:0,65:65:1.000:20:-100.0000:0.0000 chr1 47881974 rs181190356 G A 100 PASS DP=25;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 0/1:24:10,15:25:0.600:20:-100.0000:0.0000 chr1 47883019 rs6666370 T C 100 PASS DP=73;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 1/1:100:0,73:73:1.000:20:-100.0000:0.0000 chr1 47883024 rs2820969 A G 100 PASS DP=72;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 1/1:100:0,72:72:1.000:20:-100.0000:0.0137 chr1 59042181 rs14008 G T 100 PASS DP=93;clinvar=1|likely_benign;EVS=0.149207|16|6491;GMAF=T|0.1571;AA=G;AF1000G=0.157149;phyloP=-0.115;CSQT=1|TACSTD2|NM_002353.2|missense_variant;CSQR=1|ENSR00000537412|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:44,49:93:0.527:20:-100.0000:0.0000 chr1 59042882 rs232835 T G 100 PASS DP=11;clinvar=1|likely_benign;GMAF=G|0.1569;AA=G;AF1000G=0.156949;phyloP=-0.489;CSQT=1|TACSTD2|NM_002353.2|5_prime_UTR_variant;CSQR=1|ENSR00000537412|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:6:4,7:11:0.636:20:-100.0000:0.0833 chr1 94471075 rs1762114 A G 100 PASS DP=27;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 1/1:98:0,27:27:1.000:20:-100.0000:0.0000 chr1 94476555 rs537831 G A 100 PASS DP=89;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 1/1:100:0,89:89:1.000:20:-100.0000:0.0000 chr1 94487354 rs472908 G A 100 PASS DP=53;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 1/1:8:15,38:53:0.717:20:-100.0000:0.0185 chr1 94495930 rs547806 T C 100 PASS DP=17;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 1/1:62:0,17:17:1.000:20:-100.0000:0.0000 chr1 94497662 . AT A 100 R5x9 DP=44;cosmic=1|COSN1110290;CSQT=1|ABCA4|NM_000350.2|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:0:34,10:44:0.227:20:-54.4648:0.0000 chr1 94528363 rs4147833 C T 100 PASS DP=67;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 1/1:100:0,67:67:1.000:20:-100.0000:0.0000 chr1 94544125 rs754218262 C T 20 LowDP;q30 DP=1;phyloP=0.106;CSQT=1|ABCA4|NM_000350.2|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC ./.:0:0,1:1:1.000:20:-100.0000:0.9167 chr1 94544135 rs564661476;rs397762117 A AC 100 PASS DP=11;clinvar=1|benign,1|benign,1|benign,1|benign,1|benign;EVS=0.724121|131|6260;CSQT=1|ABCA4|NM_000350.2|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:6:4,7:11:0.636:20:-100.0000:0.0000 chr1 94544276 rs4147830 G A 100 PASS DP=26;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 1/1:94:0,26:26:1.000:20:-100.0000:0.0000 chr1 94568491 rs4847278 A G 100 PASS DP=69;GMAF=G|0.3405;AA=A;AF1000G=0.340455;phyloP=-0.522;CSQT=1|ABCA4|NM_000350.2|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:34,35:69:0.507:20:-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=22;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 0/1:46:11,11:22:0.500:20:-69.1198:0.0000 chr1 206944645 rs1518111 T C 100 PASS DP=42;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 0/1:78:20,22:42:0.524:20:-100.0000:0.0233 chr1 228112121 rs4653889 A G 100 PASS DP=55;EVS=0.570198|36|6503;GMAF=A|0.4838;AA=G;AF1000G=0.516174;phyloP=0.263;CSQT=1|WNT9A|NM_003395.2|intron_variant;CSQR=1|ENSR00001599361|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:1,54:55:0.982:20:-100.0000:0.0000 chr1 228113163 rs3795768 A G 100 PASS DP=55;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 1/1:100:0,55:55:1.000:20:-100.0000:0.0000 chr2 1642537 rs386642327 TGC CGT 100 PASS DP=76;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 1/1:100:0,76:76:1.000:20:-100.0000:0.0000 chr2 1642545 rs6742039 C G 100 PASS DP=76;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 1/1:100:0,76:76:1.000:20:-100.0000:0.0000 chr2 1643243 rs139025351 C T 100 PASS DP=40;EVS=0.000567|63|6176;GMAF=T|0.002995;AA=C;AF1000G=0.002995;phyloP=-1.266;CSQT=1|PXDN|NM_012293.1|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:17:14,26:40:0.650:20:-100.0000:0.0000 chr2 1647171 rs6730800 T C 100 PASS DP=52;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 1/1:100:0,52:52:1.000:20:-100.0000:0.0000 chr2 1652822 rs1863135 T G 100 PASS DP=61;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 1/1:100:0,61:61:1.000:20:-100.0000:0.0161 chr2 1664654 rs17841813 A G 100 PASS DP=68;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 1/1:100:0,68:68:1.000:20:-100.0000:0.0000 chr2 1683889 rs796323306;rs368301056 A AGATGGTGTGTGTGTG 100 PASS DP=72;CSQT=1|PXDN|NM_012293.1|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:91:44,28:72:0.389:20:-100.0000:0.0000 chr2 1683923 rs72763569 G T 100 PASS DP=70;cosmic=1|COSN19648512;EVS=0.112945|29|6180;GMAF=T|0.1012;AA=g;AF1000G=0.101238;phyloP=1.597;CSQT=1|PXDN|NM_012293.1|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:39,31:70:0.443:20:-100.0000:0.0541 chr2 113532885 rs3783550 G T 100 PASS DP=39;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 0/1:54:17,22:39:0.564:20:-100.0000:0.0000 chr2 113877495 rs928940 G T 100 PASS DP=90;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 1/1:100:0,90:90:1.000:20:-100.0000:0.0217 chr2 113890304 rs315952 T C 100 PASS DP=52;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 0/1:76:23,29:52:0.558:20:-100.0000:0.0370 chr2 113890586 rs315951 C G 100 PASS DP=23;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 0/1:37:13,10:23:0.435:20:-69.1198:0.0000 chr2 135741061 rs12623713 G A 100 PASS DP=22;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 1/1:80:0,22:22:1.000:20:-100.0000:0.0000 chr2 135741425 rs16831223 C A 100 PASS DP=34;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 0/1:64:18,16:34:0.471:20:-100.0000:0.0000 chr2 135744007 rs3905317 T C 100 PASS DP=34;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 0/1:64:18,16:34:0.471:20:-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 135744469 rs55999472 T C 100 PASS DP=33;GMAF=C|0.003195;AA=T;AF1000G=0.003195;phyloP=2.81;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:-76.9209:0.0000 chr2 135745392 rs11888766 G A 100 PASS DP=63;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 0/1:94:28,35:63:0.556:20:-100.0000:0.0000 chr2 135745545 rs11899779 C T 100 PASS DP=46;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 1/1:100:0,46:46:1.000:20:-100.0000:0.0000 chr2 135745722 rs10928526 A G 100 PASS DP=47;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 1/1:100:0,47:47:1.000:20:-100.0000:0.0000 chr2 189899541 rs4666770 T C 100 PASS DP=65;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 1/1:100:0,65:65:1.000:20:-100.0000:0.0000 chr2 189899572 rs7420715 T C 100 PASS DP=65;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 1/1:100:0,65:65:1.000:20:-100.0000:0.0000 chr2 189901295 rs12693526 G A 100 PASS DP=100;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 1/1:100:0,100:100:1.000:20:-100.0000:0.0000 chr2 189907937 rs6434312 A G 100 PASS DP=102;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 1/1:100:0,102:102:1.000:20:-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 189922016 rs796104895 GAA G 45 LowDP DP=6;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC ./.:0:3,3:6:0.500:20:-100.0000:0.0000 chr2 189923104 rs7556733 A G 100 PASS DP=55;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 1/1:100:0,55:55:1.000:20:-100.0000:0.0000 chr2 189923630 rs398090949;rs398080909;rs5837121;rs574915386 AT A 100 PASS DP=44;clinvar=1|benign;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:35:10,34:44:0.773:20:-100.0000:0.0000 chr2 189925548 rs6414122 T A 100 PASS DP=81;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 1/1:100:0,81:81:1.000:20:-100.0000:0.0000 chr2 189927506 rs7424947 C G 100 PASS DP=29;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 1/1:100:0,29:29:1.000:20:-100.0000:0.0000 chr2 189932831 rs2229495 T C 100 PASS DP=32;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 1/1:100:0,32:32:1.000:20:-100.0000:0.0000 chr2 189953285 rs5837124;rs397758641;rs746250131 A AAATG 100 PASS DP=70;cosmic=1|COSN19656478;AF1000G=0.798323;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,70:70:1.000:20:-100.0000:0.0000 chr2 189974958 rs4128539 G T 100 PASS DP=50;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 1/1:100:0,50:50:1.000:20:-100.0000:0.0000 chr2 209168853 rs893256 C T 100 PASS DP=25;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 1/1:91:0,25:25:1.000:20:-100.0000:0.0000 chr2 209184980 rs10932258 G A 100 PASS DP=22;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 1/1:80:0,22:22:1.000:20:-100.0000:0.0000 chr2 209184999 rs10932259 C T 100 PASS DP=22;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 1/1:80:0,22:22:1.000:20:-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=26;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 1/1:94:0,26:26:1.000:20:-100.0000:0.0000 chr2 209190528 rs893253 C G 100 PASS DP=26;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 1/1:94:0,26:26:1.000:20:-100.0000:0.0000 chr2 209191082 rs1529979 C A 100 PASS DP=39;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 1/1:100:0,39:39:1.000:20:-100.0000:0.0000 chr2 209191099 rs1529978 T C 100 PASS DP=39;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 1/1:100:0,39:39:1.000:20:-100.0000:0.0000 chr2 209194696 rs1437414 G C 100 PASS DP=42;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 1/1:100:0,42:42:1.000:20:-100.0000:0.0000 chr2 209200394 rs6718402 A C 100 PASS DP=53;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 1/1:100:0,53:53:1.000:20:-100.0000:0.0000 chr2 209201739 rs7596571 T C 100 PASS DP=37;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 1/1:100:0,37:37:1.000:20:-100.0000:0.0000 chr2 209204714 rs2289171 G A 100 PASS DP=19;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 0/1:0:6,13:19:0.684:20:-100.0000:0.0000 chr2 209209827 rs2304544 G A 100 PASS DP=41;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 1/1:100:0,41:41:1.000:20:-100.0000:0.0682 chr2 209209997 rs2043718 C T 100 PASS DP=49;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 1/1:100:0,49:49:1.000:20:-100.0000:0.0200 chr2 209212707 rs2304545 G A 100 PASS DP=25;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 1/1:91:0,25:25:1.000:20:-100.0000:0.0385 chr2 209214770 rs2118297 A G 100 PASS DP=61;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 1/1:100:1,60:61:0.984:20:-100.0000:0.0000 chr2 209215448 rs994696 A G 100 PASS DP=33;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 1/1:100:0,33:33:1.000:20:-100.0000:0.0000 chr2 209215586 rs994697 A G 100 PASS DP=97;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 1/1:100:0,97:97:1.000:20:-100.0000:0.0000 chr2 209219049 rs6435452 T A 20 LowDP;q30 DP=1;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 ./.:0:0,1:1:1.000:20:-100.0000:0.0000 chr2 209219190 rs6435453 A G 100 PASS DP=56;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 1/1:100:0,56:56:1.000:20:-100.0000:0.0000 chr2 227872182 rs2228557 G A 100 PASS DP=63;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 0/1:94:28,35:63:0.556:20:-100.0000:0.0000 chr2 227872995 rs2228555 T C 100 PASS DP=69;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 0/1:100:38,31:69:0.449:20:-100.0000:0.0000 chr2 227873028 rs13419076 A G 100 PASS DP=69;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 0/1:100:38,31:69:0.449:20:-100.0000:0.0000 chr2 227874957 rs4423583 C T 100 PASS DP=36;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 0/1:68:19,17:36:0.472:20:-100.0000:0.0000 chr2 227877037 rs10188770 G A 100 PASS DP=34;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 0/1:33:22,12:34:0.353:20:-100.0000:0.0000 chr2 227886773 rs3752895 A G 100 PASS DP=53;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 0/1:93:29,24:53:0.453:20:-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 0/1:40:12,15:27:0.556:20:-99.5418:0.0000 chr2 227892619 rs2228556 C T 100 PASS DP=124;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 0/1:100:67,57:124:0.460:20:-57.9561:0.0159 chr2 227892720 rs2229813 C T 100 PASS DP=109;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 0/1:100:61,48:109:0.440:20:-100.0000:0.0000 chr2 227895125 rs1917127 A G 100 PASS DP=28;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 0/1:59:14,14:28:0.500:20:-100.0000:0.0345 chr2 227896652 rs13423714 C G 100 PASS DP=67;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 0/1:100:38,29:67:0.433:20:-100.0000:0.0000 chr2 227896886 rs2229812 C T 100 PASS DP=27;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 1/1:0:8,19:27:0.704:20:-100.0000:0.0000 chr2 227896976 rs10203363 C T 100 PASS DP=27;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 1/1:0:8,19:27:0.704:20:-100.0000:0.0000 chr2 227915601 rs2272204 G T 100 PASS DP=35;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 0/1:47:21,14:35:0.400:20:-91.5381:0.0000 chr2 227915832 rs1800517 G A 100 PASS DP=62;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 0/1:98:28,34:62:0.548:20:-100.0000:0.0000 chr2 227920474 rs1320406 G A 100 PASS DP=28;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 0/1:59:14,14:28:0.500:20:-100.0000:0.0000 chr2 227921977 rs4536647 A G 100 PASS DP=19;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 0/1:23:8,11:19:0.579:20:-100.0000:0.0500 chr2 227922015 rs4566357 A G 100 PASS DP=20;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 0/1:31:9,11:20:0.550:20:-100.0000:0.0000 chr2 227922104 rs7567789 T C 100 PASS DP=22;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 0/1:35:9,13:22:0.591:20:-71.1533:0.0000 chr2 227922109 rs7567796 T A 100 PASS DP=22;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 0/1:35:9,13:22:0.591:20:-73.4051:0.0000 chr2 227924817 . G GA 34 LowDP DP=3;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC ./.:0:1,2:3:0.667:20:-100.0000:0.0000 chr2 227927189 rs35717623;rs398081120;rs796278870 GT G 68 R5x9 DP=23;AF1000G=0.558307;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:6:17,6:23:0.261:20:-100.0000:0.0000 chr2 227954599 rs2229814 G A 100 PASS DP=56;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 1/1:100:0,56:56:1.000:20:-100.0000:0.0000 chr2 227967830 rs398081123;rs573969560;rs796369993;rs10707643 GA G 100 PASS DP=34;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:49:20,14:34:0.412:20:-91.5381:0.0000 chr2 227973193 rs10174459 G A 100 PASS DP=15;cosmic=1|COSN8867965;GMAF=A|0.1851;AA=G;AF1000G=0.185104;phyloP=2.93;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:16:3,12:15:0.800:20:-100.0000:0.0625 chr2 227973623 rs12475686 A G 100 PASS DP=64;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 0/1:100:36,28:64:0.438:20:-100.0000:0.0154 chr2 227973873 rs58363082 T C 100 PASS DP=29;cosmic=1|COSN8867966;EVS=0.195243|149|5150;GMAF=C|0.2867;AA=C;AF1000G=0.286741;phyloP=-0.556;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:34:18,11:29:0.379:20:-100.0000:0.0000 chr2 227973878 rs59938187 C T 100 PASS DP=29;cosmic=1|COSN8867967;EVS=0.191942|151|5150;GMAF=T|0.2845;AA=C;AF1000G=0.284545;phyloP=0.048;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:34:18,11:29:0.379:20:-100.0000:0.0000 chr2 227973892 rs73082223 T C 100 PASS DP=29;cosmic=1|COSN8867968;EVS=0.262746|137|6002;GMAF=C|0.3522;AA=T;AF1000G=0.352236;phyloP=-1.218;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:34:18,11:29:0.379:20:-100.0000:0.0000 chr2 227979533 rs12465531 A C 100 PASS DP=54;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 1/1:100:0,54:54:1.000:20:-100.0000:0.0000 chr2 228102752 rs1882435 C A 100 PASS DP=28;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 0/1:14:10,18:28:0.643:20:-100.0000:0.0345 chr2 228109626 rs113428834 T TG 100 PASS DP=47;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 1/1:100:5,42:47:0.894:20:-100.0000:0.0000 chr2 228109784 rs6750210 C T 100 PASS DP=46;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 1/1:100:0,46:46:1.000:20:-100.0000:0.0213 chr2 228111435 rs10178458 T C 100 PASS DP=54;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 1/1:100:0,54:54:1.000:20:-100.0000:0.0000 chr2 228113175 rs6436669 A G 100 PASS DP=109;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 1/1:100:0,109:109:1.000:20:-100.0000:0.0268 chr2 228118403 rs12621551 T G 100 PASS DP=15;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 G