Fq Column In Mpileup Vcf Output.

Question

[Tiffani]

Hello the line that I have is :

22 22716000 . T A,X 76 . DP=23;AF1=1;AC1=2;DP4=0,0,8,3;MQ=57;FQ=-60 GT:PL:GQ 1/1:109,33,0,109,33,109:63

I'm wondering what FQ means as well as AF1 and DP4

thanks

Answer 1

[Tiffani]

Consensus quality. If positive, FQ equals the phred-scaled probability of there being two or more different alleles. If negative, FQ equals the minus phred-scaled probability of all chromosomes being identical. Notably, given one sample, FQ is positive at hets and negative at homs.