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##fileformat=VCFv4.0
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=SnpCluster,Description="Filters clusters of 'INT1' or more SNPs within a run of 'INT2' bases [win=3,count=2]">
##FILTER=<ID=StrandBias,Description="Min P-value for strand bias (INFO/PV4) [0.0001]">
##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]">
##FILTER=<ID=MaxDP,Description="Maximum read depth (INFO/DP or INFO/DP4) [34]">
##FILTER=<ID=BaseQualBias,Description="Min P-value for baseQ bias (INFO/PV4) [0]">
##FILTER=<ID=MinMQ,Description="Minimum RMS mapping quality for SNPs (INFO/MQ) [10]">
##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]">
##FILTER=<ID=Qual,Description="Minimum value of the QUAL field [10]">
##FILTER=<ID=VDB,Description="Minimum Variant Distance Bias (INFO/VDB) [0]">
##FILTER=<ID=GapWin,Description="Window size for filtering adjacent gaps [3]">
##FILTER=<ID=MapQualBias,Description="Min P-value for mapQ bias (INFO/PV4) [0]">
##FILTER=<ID=SnpGap,Description="SNP within INT bp around a gap to be filtered [10]">
##FILTER=<ID=RefN,Description="Reference base is N []">
##FILTER=<ID=MinDP,Description="Minimum read depth (INFO/DP or INFO/DP4) [2]">
#CHROM POS ID REF ALT QUAL FILTER INFO
1 100 . GTTT G 1806 q10;MaxDP DP=35
1 104 . C . 1792 PASS DP=32
1 105 . C T 246 SnpGap;SnpCluster DP=10
1 106 . C A 246 SnpGap;SnpCluster DP=10
2 107 . C . 1806 q10;MaxDP DP=35
2 108 . C . 1792 PASS DP=32
2 109 . C . 628 q10 DP=21
2 110 . C G 1016 SnpGap;SnpCluster DP=22
2 111 . C G 727 SnpGap;SnpCluster DP=30
2 112 . C G 246 SnpGap;SnpCluster DP=10
2 113 . C . 246 PASS DP=10
2 114 . T . 246 PASS DP=10
2 115 . T . 246 PASS DP=10
2 116 . T . 246 PASS DP=10
2 117 . T A 246 SnpGap;SnpCluster DP=10
2 118 . T C 246 SnpGap;SnpCluster DP=10
2 119 . TAAA T 246 SnpCluster DP=10
2 124 . TA T 246 GapWin DP=10
2 128 . T TA 246 SnpCluster DP=10
2 130 . C A 246 SnpGap;SnpCluster DP=10
2 131 . T A 246 SnpGap;SnpCluster DP=10
2 132 . T A 246 SnpGap;SnpCluster DP=10
2 133 . T A 246 SnpGap;SnpCluster DP=10
2 134 . T A 246 SnpGap;SnpCluster DP=10
2 135 . T C 246 SnpGap;SnpCluster DP=10
2 136 . TT T 246 GapWin;SnpCluster DP=10;AF=0.1
2 138 . TT T 246 SnpCluster DP=10;AF=0.2
2 140 . TT T 246 GapWin;SnpCluster DP=10;AF=0.1
17 12412 . CAGAGAGAGA CAGAGAGAGAGA 74.8 MaxDP INDEL;DP=5388;AF1=0.006576;CI95=0.005525,0.01105;DP4=2077,2367,21,22;MQ=47;FQ=74.8;PV4=0.88,1,0.34,0.021
17 12427 . G A 999 MaxDP;SnpGap DP=5557;AF1=0.06028;CI95=0.04972,0.07182;DP4=2461,2689,106,74;MQ=47;FQ=999;PV4=0.0038,1,2.6e-12,1
17 69284 . G A 14.6 MaxDP;SnpGap DP=3946;AF1=0.003468;CI95=0.002762,0.008287;DP4=1529,2177,7,9;MQ=44;FQ=14.6;PV4=1,0.035,0.098,1
17 69293 . GTTTCATTTC GTTTCTTTTCATTTC 999 MaxDP INDEL;DP=3568;AF1=0.1295;CI95=0.1077,0.1547;DP4=1014,1238,118,121;MQ=44;FQ=999;PV4=0.22,1,9.4e-54,1
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