Take one VCF file for example,
##fileformat=VCFv4.1 ##samtoolsVersion=0.1.16 (r963:234) ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> ##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the site allele frequency of the first ALT allele"> .... #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SLVi33.16 SLVi33.25 SLVi33.26 chr1 85691 . C T 6.26 . DP=2;AF1=1;CI95=0.3333,1;DP4=0,0,2,0;MQ=40;FQ=-28.9 GT:PL:GQ 0/1:0,0,0:3 1/1:20,3,0:4 1/1:18,3,0:4 chr1 88338 . G A 6.95 . DP=3;AF1=1;CI95=0.1667,1;DP4=0,0,2,1;MQ=30;FQ=-28.1 GT:PL:GQ 0/1:0,0,0:3 0/1:0,0,0:3 1/1:38,9,0:8
The DP=2 at chr1:85691, however, there are three individuals in the file, why does every individual has genotype? As AF1 means allele frequency of ALT allele, it supposed to be AF1=5/6 at chr1:85691, why it's truely AF1=1? I'm so confused, anybody can help me? Thanks in advance.