Meaning Of Genotype 2/0 And 2/1

Question

[stat.1405]

Dear all Could you please explain the meaning of this 2/0 2/1 2/2 also 3/0 3/1 3/2 imagine that I have

CHROM        POS         REF              ALT                ALT1
1             2078          A                ACACAC              ACAC

You can give an example from you to illustrate that.

Answer 1

[Devon Ryan]

0: Reference
1: Alternate allele
2: Second alternate allele
3: Third alternate allele

So 2/0 is ACAC/A and 2/1 is ACAC/ACACAC. You only have two alternate alleles shown, so there should be no 3/? in there. This is basically a modified VCF format.

[stat.1405]

so if I have a third alt allele for example G. 3/1 will be G/A 3/2 will be G/ACAC 3/3 will be G/G so if I have more than tow alleles there is no Homzygous in REF,

[Devon Ryan]

3/1 would be G/ACACAC, 3/2 would be G/ACAC and so on. It's always possible to have a homozygous reference allele, regardless of the number of alternate alleles.

[stat.1405]

thank you so much

Answer 2

[Giovanni M Dall'Olio]

Note that in a valid VCF the ALT1 column would not exist, so your example would not be correct.

According to the VCF format specification, all the Alternate alleles are defined in the "ALT" column, separated by commas.

For example, your example would be:

CHROM        POS         REF              ALT
1            2078        A                ACACAC,ACAC

In this case, a genotype of 1 would mean ACACAC, and a genotype of 2 would represent ACAC.

In general, SNPs should always be bi-allelic variations, e.g. only two alleles are commonly found. In the close past, tri-allelic SNPs were generally filtered out, in order to simplify he downstream analysis. However, recently I've seen some tri-allelic SNPs being used in public datasets, so this may create some confusion in the future.