Question: Interpreting Allele frequency equal to 1.0
0
gravatar for ambi1999
2.5 years ago by
ambi199930
United Kingdom/Cardiff/Cardiff Metropolitan University
ambi199930 wrote:

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.

ADD COMMENTlink modified 2.5 years ago by RamRS20k • written 2.5 years ago by ambi199930
0
gravatar for RamRS
2.5 years ago by
RamRS20k
Houston, TX
RamRS20k wrote:

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 COMMENTlink written 2.5 years ago by RamRS20k

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 REPLYlink modified 2.5 years ago • written 2.5 years ago by bioinforesearchquestions200

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 REPLYlink written 2.5 years ago by RamRS20k
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