--Dummydata1.var-- #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT IFS003-W Chr Start End Ref Alt Func.refGene Gene.refGene GeneDetail.refGene ExonicFunc.refGene AAChange.refGene Func.knownGene Gene.knownGene GeneDetail.knownGene ExonicFunc.knownGene AAChange.knownGene avsnp144 1000g2015aug_all 1000g2015aug_afr 1000g2015aug_amr 1000g2015aug_sas 1000g2015aug_eur 1000g2015aug_eas esp6500siv2_all esp6500siv2_ea esp6500siv2_aa ExAC_ALL ExAC_AFR ExAC_AMR ExAC_EAS ExAC_FIN ExAC_NFE ExAC_OTH ExAC_SAS cosmic70 SIFT_score SIFT_pred Polyphen2_HDIV_score Polyphen2_HDIV_pred Polyphen2_HVAR_score Polyphen2_HVAR_pred LRT_score LRT_pred MutationTaster_score MutationTaster_pred MutationAssessor_score MutationAssessor_pred FATHMM_score FATHMM_pred PROVEAN_score PROVEAN_pred VEST3_score CADD_raw CADD_phred DANN_score fathmm-MKL_coding_score fathmm-MKL_coding_pred MetaSVM_score MetaSVM_pred MetaLR_score MetaLR_pred integrated_fitCons_score integrated_confidence_value GERP++_RS phyloP7way_vertebrate phyloP20way_mammalian phastCons7way_vertebrate phastCons20way_mammalian SiPhy_29way_logOdds Interpro_domain dbscSNV_ADA_SCORE dbscSNV_RF_SCORE CLINSIG CLNDBN CLNACC CLNDSDB CLNDSDBID HRC_AF HRC_AC HRC_AN HRC_non1000G_AF HRC_non1000G_AC HRC_non1000G_AN Kaviar_AF Kaviar_AC Kaviar_AN nci60 KEY3 INFO_AC INFO_AF INFO_BaseQRankSum INFO_ClippingRankSum INFO_DP INFO_DS INFO_END INFO_ExcessHet INFO_FS INFO_HaplotypeScore INFO_InbreedingCoeff INFO_MLEAC INFO_MLEAF INFO_MQ INFO_MQRankSum INFO_QD INFO_RAW_MQ INFO_ReadPosRankSum INFO_SOR seq seq_flag AAchange Grantham Mutability FuentesFalsePositive ACMG chr1 14653 . C T 191.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.23;ClippingRankSum=0.00;DP=26;ExcessHet=3.0103;FS=6.641;MLEAC=1;MLEAF=0.500;MQ=32.19;MQRankSum=0.580;QD=7.38;ReadPosRankSum=-1.830e-01;SOR=2.280 GT:AD:DP:GQ:PL 0/1:15,11:26:99:220,0,292 chr1 14653 14653 C T ncRNA_exonic WASH7P intergenic NONE,MIR6859-3 dist=NONE;dist=2716 rs62635297 0.0011526 30 26028 chr1:14653:14653:C:T 1 0.5 1.23 0 26 no_DS no_END 3.0103 6.641 no_HaplotypeScore no_InbreedingCoeff 1 0.5 32.19 0.58 7.38 no_RAW_MQ -1.83E-01 2.28 AAGGAAGTAGGTCTGAGCAGCTTGTCCTGGCTGTGTCCATGTCAGAGCAA[C]GGCCCAAGTCTGGGTCTGGGGGGGAAGGTGTCATGGAGCCCCCTACGATT pass XX . 0 1 0 chr1 16949 . A C 240.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.57;ClippingRankSum=0.00;DP=39;ExcessHet=3.0103;FS=1.264;MLEAC=1;MLEAF=0.500;MQ=21.03;MQRankSum=-7.380e-01;QD=6.17;ReadPosRankSum=1.62;SOR=0.693 GT:AD:DP:GQ:PL 0/1:24,15:39:99:269,0,502 chr1 16949 16949 A C ncRNA_exonic WASH7P downstream MIR6859-3 rs199745162 0.0139776 0.0227 0.0144 0.0143 0.0159 0.0159444 415 26028 chr1:16949:16949:A:C 1 0.5 1.57 0 39 no_DS no_END 3.0103 1.264 no_HaplotypeScore no_InbreedingCoeff 1 0.5 21.03 -7.38E-01 6.17 no_RAW_MQ 1.62 0.693 CTGGAATGGTGCCAGGGGCAGAGGGGGCAATGCCGGGGCCCAGGTCGGCA[A]TGTACATGAGGTCGTTGGCAATGCCGGGCAGGTCAGGCAGGTAGGATGGA pass XX . 0 1 0 chr1 17020 . G A 58.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-4.670e-01;ClippingRankSum=0.00;DP=43;ExcessHet=3.0103;FS=23.602;MLEAC=1;MLEAF=0.500;MQ=21.00;MQRankSum=0.00;QD=1.37;ReadPosRankSum=-1.126e+00;SOR=1.132 GT:AD:DP:GQ:PL 0/1:34,9:43:87:87,0,789 chr1 17020 17020 G A ncRNA_exonic WASH7P downstream MIR6859-3 rs199740902 0.0141002 367 26028 chr1:17020:17020:G:A 1 0.5 -4.67E-01 0 43 no_DS no_END 3.0103 23.602 no_HaplotypeScore no_InbreedingCoeff 1 0.5 21 0 1.37 no_RAW_MQ -1.13E+00 1.132 ATGCCGGGCAGGTCAGGCAGGTAGGATGGAACATCAATCTCAGGCACCTG[G]CCCAGGTCTGGCACATAGAAGTAGTTCTCTGGGACCTGCAAGATTAGGCA pass XX . 0 1 0 chr1 17385 . G A 81.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.653;ClippingRankSum=0.00;DP=71;ExcessHet=3.0103;FS=3.091;MLEAC=1;MLEAF=0.500;MQ=48.65;MQRankSum=0.417;QD=1.15;ReadPosRankSum=1.02;SOR=0.311 GT:AD:DP:GQ:PL 0/1:60,11:71:99:110,0,1715 chr1 17385 17385 G A ncRNA_exonic;splicing MIR6859-1,MIR6859-2,MIR6859-3,MIR6859-4;WASH7P NR_024540:exon6:c.588-17C>T ncRNA_exonic MIR6859-3 rs201535981 0.2454 0.2331 0.2857 0.0423 0.2817 0.2743 0.2321 0.2092 0.0015912 246 154602 chr1:17385:17385:G:A 1 0.5 0.653 0 71 no_DS no_END 3.0103 3.091 no_HaplotypeScore no_InbreedingCoeff 1 0.5 48.65 0.417 1.15 no_RAW_MQ 1.02 0.311 AGCCAGGGGGTCCAGGAAGACATACTTCTTCTACCTACAGAGGCGACATG[G]GGGTCAGGCAAGCTGACACCCGCTGTCCTGAGCCCATGTTCCTCTCCCAC pass XX . 0 0 0 chr1 17408 . C G 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-9.480e-01;ClippingRankSum=0.00;DP=94;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=52.27;MQRankSum=-8.570e-01;QD=1.45;ReadPosRankSum=0.359;SOR=0.527 GT:AD:DP:GQ:PL 0/1:79,14:93:99:163,0,2339 chr1 17408 17408 C G ncRNA_exonic MIR6859-1,MIR6859-2,MIR6859-3,MIR6859-4 ncRNA_exonic MIR6859-3 rs747093451 0.0352 0.0339 0.049 0 0.0273 0.0438 0 0.0074 0.0013842 214 154602 chr1:17408:17408:C:G 1 0.5 -9.48E-01 0 94 no_DS no_END 3.0103 0 no_HaplotypeScore no_InbreedingCoeff 1 0.5 52.27 -8.57E-01 1.45 no_RAW_MQ 0.359 0.527 ACTTCTTCTACCTACAGAGGCGACATGGGGGTCAGGCAAGCTGACACCCG[C]TGTCCTGAGCCCATGTTCCTCTCCCACATCATCAGGGGCACAGCGTGCAC pass XX . 0 0 0 chr1 17697 . G C 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.529e+00;ClippingRankSum=0.00;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=39.25;MQRankSum=-8.310e-01;QD=4.49;ReadPosRankSum=1.07;SOR=0.124 GT:AD:DP:GQ:PL 0/1:21,7:28:99:154,0,714 chr1 17697 17697 G C ncRNA_exonic WASH7P upstream MIR6859-3 rs374995955 0.0155602 405 26028 chr1:17697:17697:G:C 1 0.5 -2.53E+00 0 28 no_DS no_END 3.0103 0 no_HaplotypeScore no_InbreedingCoeff 1 0.5 39.25 -8.31E-01 4.49 no_RAW_MQ 1.07 0.124 GCTGATGTTGCTGGGAAGACCCCCAAGTCCCTCTTCTGCATCGTCCTCGG[G]CTCCGGCTTGGTGCTCACGCACACAGGAAAGTCCTTCAGCTTCTCCTGAG pass XX . 0 1 0