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I understand that snp is a single base variation. For example, if person 1 has the sequence in DNA , AAGCCTA the second has AAGCTTA, then the allels are C,T.

My question is what is the meaning of 0,1,2 genotypes under each snp id (rs#) , and how it is related to the snp ?

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    $\begingroup$ I won't post this as an answer, as I really can't find any comprehensive source. Basically you are looking at SNPs from a diploid individual. Therefore it can either be homozygous for an allele or heterozygous. Heterozygous SNPs are encoded by 1. For homozygous ones it is usually 0 if the individual is heterozygous for the major allele (in the population or the one found in the reference in pairwise comparison) and 2 if it is heterozygous for the minor allele. Although this might in fact be different in different formats. 0 and 2 are always homozygous and 1 heterozygous, though. $\endgroup$
    – skymningen
    Jan 31 '17 at 14:38
  • $\begingroup$ Note that there is now a beta bioinformatics stackexchange site where this question might receive answers: bioinformatics.stackexchange.com $\endgroup$
    – bli
    May 24 '17 at 12:38

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