Interpreting Allele frequency equal to 1.0

Question

[ambi1999]

Hi,

In the following vcf file, the AF allele frequency of ALT allele is 1.0. Does it mean that it is not a true SNP of interest? Does it also mean that ALT allele always occurs and REF allele never occurs in the population?

Also not sure how allele count AC=37 is being calculated.

Chr1 pos=565286, REF=C, ALT=T, Info AC=37; AF=1.0 Format GT:AC:AF:NC Child=1:11:1.0:+T=4,- T=7 mother=1:26:1.0:+T=8,-T=18,

Cheers, Ambi.

Answer 1

[Ram]

The AF is not a measure of the population - it is a measure of the observed frequency in your samples. It just means that all your samples have an ALT allele at that particular location. AC=37 means that the allele was observed in 37 (11 "child" and 26 "mother" in your case) chromosomes.

[bioinforesearchquestions]

Hello Ram, If we annotate the above VCF with 1000G, dbSNP databases, there will be some fields with population allele frequency of AF_ASN=0.3, AF_EUR=0.4, AF_AMR=0.2..etc. What do these allele frequencies from asian, american and european population refer to?

Also, can you help with this post? What is the threshold vaue for mapping quality

[Ram]

Take a look at the 1000genomes population (http://www.1000genomes.org/category/population/). Population based frequency is calculated across all individuals of that ethnicity/population. If you search around, you'll find the dataset mapping each individual to their population.