genotype frequency

If allele frequency counts the individual cards, genotype frequency counts the hands. Each diploid individual carries two alleles at a locus, forming a pairing such as AA, Aa, or aa. Genotype frequency is the share of the population holding each particular pairing.

It is the proportion of individuals in a population that have a specified genotype. For a locus with alleles A and a, the three genotype frequencies—of AA, Aa, and aa—must sum to one, because every individual must be one of them.

Genotype and allele frequencies are linked but not the same. From genotype frequencies you can always recover allele frequencies by counting copies. Going the other way, predicting genotype frequencies from allele frequencies, requires an assumption about how alleles pair up, which is exactly what the Hardy–Weinberg principle supplies.

Comparing observed genotype frequencies with those expected under random mating is a standard first check: a mismatch hints at inbreeding, selection, population structure, or other interesting forces at work.