Interpreting Allele frequency equal to 1.0
1
0
Entering edit mode
5.1 years ago
ambi1999 ▴ 50

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.

SNP vcf allele frequency allele count • 2.0k views
ADD COMMENT
0
Entering edit mode
5.1 years ago
Ram 34k

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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 1778 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6