1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
|
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##reference=file://hwe.fa
##contig=<ID=15,length=301>
##ALT=<ID=*,Description="Represents allele(s) other than observed.">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of raw reads supporting an indel">
##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of raw reads supporting an indel">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths (high-quality bases)">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA07000 NA07056 NA12046 NA12144 NA12156 NA12234 NA12249 NA12282 NA12283 NA12286 NA12340 NA12341 NA12342 NA12399 NA12414 NA12546 NA12717 NA12718 NA12748 NA12749 NA12750 NA12776 NA12828 NA12843 NA18502 NA18867 NA18908 NA18933 NA18934 NA19108 NA19117 NA19119 NA19129 NA19131 NA19138 NA19147 NA19149 NA19159 NA19185 NA19189 NA19197 NA19198 NA19206 NA19213 NA19214 NA19223 NA19235 NA19236 NA19238 NA19239 NA19248 NA19256
15 201 . A G 1211.32 . DP=80;VDB=0.895839;SGB=-4.94122;RPB=0.999937;MQB=0.979662;MQSB=0.974642;BQB=0.739382;MQ0F=0;AC=55;AN=104;DP4=19,17,21,15;MQ=59 GT:PL:AD 0/0:0,3,36:1,0 0/0:0,6,93:2,0 0/0:0,3,33:1,0 0/0:0,3,32:1,0 0/0:0,3,36:1,0 0/0:0,3,32:1,0 0/0:0,3,40:1,0 0/0:0,6,79:2,0 0/0:0,3,42:1,0 0/0:0,6,64:2,0 0/0:0,6,67:2,0 0/0:0,6,66:2,0 0/0:0,9,96:3,0 0/0:0,3,32:1,0 0/0:0,3,36:1,0 0/0:0,3,31:1,0 0/0:0,3,44:1,0 0/0:0,3,44:1,0 0/0:0,6,61:2,0 0/0:0,3,60:1,0 0/0:0,6,60:2,0 0/0:0,6,57:2,0 0/0:0,3,31:1,0 0/0:0,6,68:2,0 0/1:0,3,60:1,0 1/1:39,3,0:0,1 1/1:31,3,0:0,1 1/1:37,3,0:0,1 1/1:60,3,0:0,1 1/1:38,3,0:0,1 1/1:36,3,0:0,1 1/1:37,3,0:0,1 1/1:85,9,0:0,3 1/1:39,3,0:0,1 1/1:31,3,0:0,1 1/1:63,6,0:0,2 1/1:29,3,0:0,1 1/1:32,3,0:0,1 1/1:43,3,0:0,1 1/1:27,3,0:0,1 1/1:43,3,0:0,1 1/1:34,3,0:0,1 1/1:46,3,0:0,1 1/1:144,12,0:0,4 1/1:59,3,0:0,1 1/1:16,3,0:0,1 1/1:37,3,0:0,1 1/1:57,6,0:0,2 1/1:91,6,0:0,2 1/1:21,3,0:0,1 1/1:52,6,0:0,2 1/1:26,3,0:0,1
|
