Variants and Allele Counts

Question

[patrick.mackay]

Hi All,

I have a count alleles by Genes table for a vcf. Taking into account that variants stand for the total number of variants for the current sample in each gene and allele count stands for the total number of non-reference alleles for the current sample in each gene, could you please advise me on how to interpret this?

Gene Names # Variants Allele Count # Het # Hemi # HomoVars A1BG 9 13 5 4

I cannot understand how is it possible that in genes the allele count can be major than variants.

Thanks

[GenoMax]

patrick.mackay : Can you clarify if the following edit is appropriate and matches the header?

Gene Names # Variants Allele Count # Het # Hemi # HomoVars 
A1BG               9                 13     5        4

[patrick.mackay]

Hi Genomax.

Yes. This is the right edit.

Thanks for the clarification

[patrick.mackay]

Hi Igor,

i didn't' get it. Could you please advise by explaining with a practical example? I am just entering that field that extremely fascinates me but of course, I am encountering some hurtles.

Thanks in advance

[GenoMax]

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

This comment belongs under @Igor's answer. You could move it there and then come back and delete this instance.

[patrick.mackay]

Hi Igor,

i didn't' get it. Could you please advise by explaining with a practical example? I am just entering that field that extremely fascinates me but of course, I am encountering some hurtles.

[igor]

Let's say your reference sequence is: AAA.

You have two reads: AAG and AAT. Thus, you have a mutation at position 3. That is sometimes counted as 1 mutation since it is 1 position. However, if you look at the alleles, you have 2 (G and T).

Answer 1

[igor]

It depends on how they are counting the variants. They may count each mutated position as a single variant, but there could be multiple alternate alleles at one position.