Allele and genotype encoding

AlphaPeel works with bi-allelic loci; reference (major) allele a and alternative (minor) allele A. The terms major and minor indicates their frequency in a population, but this is not a requirement for AlphaPeel. These alleles are respectively numerically encoded as 0 and 1.

Combining two alleles in a diploid individual gives three possible genotypes:

  • reference homozygote a/a encoded as 0 (from 0+0),

  • heterozygote a/A or A/a encoded as 1 (from 0+1 or 1+0), and

  • alternative homozygote A/A encoded as 2 (from 1+1).

The codes 0 and 1 for alleles, and 0, 1, and 2 for genotypes represent the number (dose) of alternative alleles and are hence called allele dosage or just dosage.

Missing or uncertain alleles and genotypes are numerically encoded as 9.

When the origin of alleles that an individual inherited is known, we have four phased genotypes: aa, aA, Aa, and AA, where the paternal allele is listed first and the maternal allele is listed second.

Related to phased genotypes is the concept of a haplotype, which represents a sequence of alleles an individual inherited together from one parent. For example, individual with genotypes at three loci of a/a, a/a, and A/A has haplotypes [a,a,A] and [a,a,A], which we numerically encode as [0,0,1] and [0,0,1].

When working with the X chromosome:

(1) heterogametic genotypes (for males in mammals (XY) and for females in birds (ZW)) should be coded as: 0 (reference allele a on the X chromosome of the XY genotype), 1 (alternative allele A on the X chromosome of the XY genotype), or 9 (missing) and

(2) Homogametic genotypes (females in mammals (XX) and males in birds (ZZ)) should be coded as described above for autosomes (since they have the XX genotype).