Genotype Frequency Calculators

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Genotype frequency is the proportion of individuals in a population with a specific genotype at a given locus. In a diploid population with two alleles (A and a) at frequencies p and q, the Hardy-Weinberg principle predicts genotype frequencies: AA = p², Aa = 2pq, aa = q². Genotype frequencies underpin population genetics, carrier frequency estimation for genetic diseases, forensic DNA analysis, and evolutionary biology. Deviations from Hardy-Weinberg expectations indicate selection, non-random mating, population structure, or recent admixture.

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Calculating Genotype Frequencies

Frequency = (count of a specific genotype) / (total individuals genotyped).

Example: 200 individuals — 120 AA, 64 Aa, 16 aa. Frequencies: f(AA) = 0.60; f(Aa) = 0.32; f(aa) = 0.08. Sum = 1.0.

Hardy-Weinberg Expected Frequencies

Allele frequencies from genotypes: p = f(AA) + ½f(Aa) = 0.60 + 0.16 = 0.76; q = 0.24.

HWE expected: f(AA) = p² = 0.578; f(Aa) = 2pq = 0.365; f(aa) = q² = 0.058.

Compare observed to expected via chi-square (df = 1) to test HWE.

Carrier Frequency for Recessive Disease

Disease frequency = q². Therefore q = √(disease freq). Carrier freq = 2pq ≈ 2q for rare alleles. Cystic fibrosis: 1 in 2,500 births → q = 0.02 → carrier freq ≈ 1 in 25.

Multiple Allele Systems

For loci with multiple alleles: homozygotes = pᵢ²; heterozygotes = 2pᵢpⱼ. Forensic DNA profiles use products of genotype frequencies across multiple STR loci, requiring HWE assumptions for each locus.

Glossary

Genotype Frequency
The proportion of individuals with a specific genotype in a population; all genotype frequencies at a locus sum to 1.0.
Hardy-Weinberg Equilibrium (HWE)
Genotype frequencies of p², 2pq, q² for a biallelic locus; maintained in large, randomly mating populations free from selection, mutation, and migration.
Carrier Frequency
The proportion of heterozygous carriers of a recessive disease allele; estimated from disease frequency using 2pq ≈ 2q for rare alleles.

Frequently Asked Questions

Genotype frequency = count of individuals with that genotype / total individuals. For a biallelic locus count AA, Aa, and aa separately, divide each by N. Allele frequencies: p = f(AA) + ½f(Aa); q = f(aa) + ½f(Aa). Check all three genotype frequencies sum to 1.0. Compare observed to Hardy-Weinberg expected values (p², 2pq, q²) using chi-square with df = 1.

Hardy-Weinberg states that in a large, randomly mating population free from selection, mutation, migration, and drift, genotype frequencies remain constant at AA = p², Aa = 2pq, aa = q² (where p + q = 1). It provides a null model — deviations from HWE signal evolutionary forces at work. HWE is also routinely used as a quality control check in GWAS studies to detect genotyping errors, which typically produce strong HWE deviations.

Disease frequency = q². So q = √(disease freq), p = 1 − q, and carrier freq = 2pq. For phenylketonuria (PKU) affecting 1 in 10,000: q² = 0.0001; q = 0.01; p = 0.99; carrier freq = 2 × 0.01 × 0.99 ≈ 0.02 = 1 in 50. This widely used calculation is the basis for estimating population carrier frequencies in genetic counseling and public health planning.

HWE requires five conditions: random mating, large population, no selection, no mutation, no migration. Inbreeding or assortative mating decreases heterozygosity (Ho < He). The Wahlund effect — mixing samples from genetically differentiated subpopulations — also reduces observed heterozygosity. Selection against heterozygotes reduces Aa. Recent admixture can increase heterozygosity above HWE expectations. In GWAS, strong HWE deviation in controls often flags genotyping errors.