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Genotype representation with 0, 1, 2 - what do they mean?

Hello all, I am currently learning about phasing and imputation, and I have come across a few ways of representing genotypes. As I understand it, 0 refers to the reference allele while 1 the alternate allele. 0/0 refers to homozygous for the reference allele, 1/1 would be homozygous for the alternate allele, while 0/1 and 1/0 would be the heterozygotes.

However, I have also come across genotypes represented by a single 0, 1 or 2, and here is where I am confused. It's a bit hard to find info for this, but it seems that 0 and 1 refers to the homozygote genotypes, while 2 refers to the heterozygote genotypes, is this correct?

Which of 0 or 1 would be homozygous for the reference and which for the alternate allele? When denoting a genotype as 2, would it not matter if its 0/1 or 1/0? Thanks very much!

genotype representation phasing imputation gwas
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updated by far • far • written by Volka Volka

I have also come across genotypes represented by a single 0, 1 or 2

in a VCF these are haploid regions. For a diploid organism that could be a haploid region where there is a deletion.

for the other formats & diploid organism, it's usually: 0:HOM_REf, 1:HET 2: HOM_VAR

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written by Pierre Lindenbaum Pierre Lindenbaum

2 answers

this might help anyone with the same question: https://mr-dictionary.mrcieu.ac.uk/term/genotype/

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written by far • far

My response is certainly late, but it might benefit someone... I have come across that coding with respect to dosage of the minor allele e.g. If we have a biallelic loci with T and G, and say G is a minor allele, the 3 possible genotypes will be coded as follows: TT=0, TG=1, and GG = 2

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written by Mwangana • Mwangana

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