Allele Frequency - Calculation of Allele Frequencies From Genotype Frequencies

Calculation of Allele Frequencies From Genotype Frequencies

If, and are the frequencies of the three genotypes at a locus with two alleles, then the frequency p of the A-allele and the frequency q of the a-allele are obtained by counting alleles. Because each homozygote AA consists only of A-alleles, and because half of the alleles of each heterozygote Aa are A-alleles, the total frequency p of A-alleles in the population is calculated as

Similarly, the frequency q of the a allele is given by

It would be expected that p and q sum to 1, since they are the frequencies of the only two alleles present. Indeed they do:

and from this we get:

and

If there are more than two different allelic forms, the frequency for each allele is simply the frequency of its homozygote plus half the sum of the frequencies for all the heterozygotes in which it appears. Allele frequency can always be calculated from genotype frequency, whereas the reverse requires that the Hardy–Weinberg conditions of random mating apply. This is partly due to the three genotype frequencies and the two allele frequencies. It is easier to reduce from three to two.