Question: Question about homozygous concept in a paper sentence
gravatar for mangfu100
6.2 years ago by
Korea, Republic Of
mangfu100730 wrote:


I am reading a paper that is about a software tools VarScan2.

In that context, There is a sentence that I don't understand. Below is the sentence.

By default, VarScan2 require minimum coverage of 3X, minimum phread base quality of 20, allele frequency of at least 8% and P-value of < 0.05. Variants with a variant allele frequency of >75% are called homozygous.


I don't understand that why allele frequency greater than 75% becomes homozygous?

and How can I decide the homo and het considering only the allele frequency?

Is there any feature of characteristic that decide the homo or het regarding the allele frequency?

(I already know the simple concept of allele frequency. I searched the wiki and got it what it means)

It's very confused concept for me to understand allele frequency connected to nucleotide base level.

I think it might be easy for you because i have not much backgrounds in genetics.

I hope you understand !

I am looking forward to your a reply.

Thank you!



sequence next-gen alignment gene • 1.9k views
ADD COMMENTlink modified 6.1 years ago by Biostar ♦♦ 20 • written 6.2 years ago by mangfu100730

In this context, allele frequency refers to the proportion of reads that contain a variant. So if at a site you had 100x coverage and more than 75 of the reads contained a variant, the sample would be considered homozygous for the variant. I wonder if you are confusing this with allele frequency in a population of individuals, which I think is the more common use of the phrase.

ADD REPLYlink written 6.2 years ago by Katie D'Aco1.0k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1198 users visited in the last hour