What is Hardy-Weinberg equilibrium?

Hardy-Weinberg equilibrium (HWE) describes a theoretical state in which allele and genotype frequencies remain constant from generation to generation in the absence of evolutionary forces such as mutation, selection, migration, genetic drift, and non-random mating.

How are allele frequencies p and q calculated?

Given counts of AA (n_AA), Aa (n_Aa), and aa (n_aa), the frequency of allele A is p = (2·n_AA + n_Aa) / (2·N) and q = 1 − p, where N is the total number of individuals.

What does the chi-square test tell me?

The chi-square test compares the observed genotype counts to the counts expected under HWE. A p-value above 0.05 (chi-square < 3.841 with 1 degree of freedom) suggests the population does not significantly deviate from HWE.

What is the minimum sample size required?

The chi-square approximation is reliable when all expected genotype counts are at least 5. For smaller samples, consider exact tests. This calculator warns you when expected counts fall below this threshold.

Can I use this for more than two alleles?

This tool handles the classic biallelic case (two alleles, three genotypes). For multi-allelic loci you would need to extend the HWE model, which is beyond the scope of this calculator.

What does a significant chi-square result mean biologically?

A significant deviation from HWE may indicate natural selection on the locus, population stratification, inbreeding, genotyping error, or recent admixture. It does not identify which force is responsible.

Allele Frequency Calculator

Name: Allele Frequency Calculator
Availability: InStock
Author: Nham Vu

Enter observed genotype counts to calculate allele frequencies and expected Hardy-Weinberg equilibrium genotype frequencies.

Observed Genotype Counts

Enter the number of individuals for each genotype.

Homozygous dominant — AA

Heterozygous — Aa

Homozygous recessive — aa

Allele Frequencies

Frequency of A (p)

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Frequency of a (q)

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HWE Genotype Frequencies & Counts

Genotype	Observed	Expected freq.	Expected count
Enter counts and click Calculate

Chi-Square Test for HWE

Chi-square (χ²)

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Degrees of freedom

Summary

Enter observed genotype counts to calculate allele frequencies and expected Hardy-Weinberg equilibrium genotype frequencies.

How it works

Enter the observed counts for each genotype (AA, Aa, and aa).
The tool calculates the frequency of allele A (p) and allele a (q) from the genotype counts.
Using p and q, expected HWE genotype frequencies are computed: p² (AA), 2pq (Aa), q² (aa).
Expected genotype counts are derived by multiplying frequencies by the total sample size.
A chi-square test compares observed vs. expected counts to determine if the population is in HWE.
Results show whether to accept or reject the HWE hypothesis at the 0.05 significance level.

Use cases

Determine whether a population is in Hardy-Weinberg equilibrium.
Calculate carrier frequency for recessive genetic disorders.
Estimate disease allele prevalence from known genotype data.
Analyze SNP genotyping data in association studies.
Support population genetics homework and exam problems.
Evaluate evolutionary forces such as selection or genetic drift.
Validate genotyping quality control in genome-wide studies.
Teach and demonstrate population genetics concepts interactively.

Frequently Asked Questions

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Last updated: 2026-05-23 · Reviewed by Nham Vu