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Allele Frequency from Genotypes Calculator

Compute allele frequencies p and q from observed genotype counts, and compare the observed genotype frequencies against the Hardy-Weinberg expectation.

Homozygous dominant (AA) count

Heterozygous (Aa) count

Homozygous recessive (aa) count

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How it works

p = (2·AA + Aa) ÷ (2·N) · q = (2·aa + Aa) ÷ (2·N) · N = AA + Aa + aa · expected: AA = p², Aa = 2pq, aa = q²

Each individual carries two alleles, so counting alleles directly gives allele frequencies: every AA contributes two dominant alleles, every heterozygote one of each, and every aa two recessive alleles. Dividing the dominant-allele count by the total number of alleles (2N) gives p, and the recessive count gives q, with p + q = 1. Comparing the observed genotype frequencies against the Hardy-Weinberg predictions p², 2pq and q² is the first step in testing whether a population is evolving at that locus.

Worked example

With 320 AA, 160 Aa and 20 aa (500 individuals, 1000 alleles): p = (640 + 160) ÷ 1000 = 0.80 and q = (40 + 160) ÷ 1000 = 0.20. The Hardy-Weinberg expectation is AA = 0.64, Aa = 0.32, aa = 0.04 — close to the observed 0.64 / 0.32 / 0.04.

Sources: Allele frequency — Wikipedia

Frequently asked questions

Why multiply by 2 in the formula?

Because every individual has two alleles at the locus, the total number of alleles in the population is twice the number of individuals (2N). Counting how many of those alleles are dominant and dividing by 2N gives p.

How do I test for Hardy-Weinberg equilibrium?

Compare the observed genotype counts with the expected counts (p²·N, 2pq·N, q²·N) using a chi-square goodness-of-fit test. Close agreement is consistent with equilibrium; a large deviation suggests selection, migration or non-random mating.

What if I only know the recessive count?

Then you cannot separate AA from Aa directly and must assume equilibrium to estimate q as √(aa/N). Use the Hardy-Weinberg equilibrium calculator for that case; this tool needs all three genotype counts.

Related calculators

Allele Frequency Calculator

Count homozygous and heterozygous individuals to get the dominant and recessive allele frequencies and the genotype frequencies of a population.

Hardy-Weinberg Equilibrium Calculator

Work out allele and genotype frequencies under Hardy-Weinberg equilibrium from a dominant allele frequency p or from the frequency of the recessive phenotype q².

Hardy-Weinberg Equilibrium Calculator

Estimate allele frequencies p and q and the expected genotype counts under Hardy-Weinberg equilibrium from the number of recessive (homozygous) individuals in a population.

Punnett Square Calculator

Cross two parent genotypes for a single gene and get the offspring genotype ratio, phenotype ratio and the odds of dominant versus recessive traits.

Educational estimate, not medical or laboratory advice — verify formulas, units and assumptions for your specific protocol.