Allele Frequency Calculator
Allele frequency is the relative proportion of a specific allele in a population. For a diploid organism with two alleles (A and a) at a locus, each individual carries two copies. If you know the genotype counts (number of AA, Aa, and aa individuals), allele frequency p (for A) = (2 x n_AA + n_Aa) / (2 x total), and q (for a) = 1 - p. This calculator takes observed genotype counts and returns allele frequencies p and q, genotype frequencies, and total allele counts. These values are the starting point for Hardy-Weinberg equilibrium testing and population genetic analysis.
Allele frequency formula
p (freq. of A) = (2 x n_AA + n_Aa) / (2 x N)
q (freq. of a) = (2 x n_aa + n_Aa) / (2 x N)
p + q = 1
N = n_AA + n_Aa + n_aa (total individuals)
For the worked example (49 AA, 42 Aa, 9 aa, N = 100): p = (98 + 42) / 200 = 0.70; q = (18 + 42) / 200 = 0.30.
From allele frequencies to Hardy-Weinberg
- Under Hardy-Weinberg equilibrium, expected genotype frequencies are: AA = p^2, Aa = 2pq, aa = q^2.
- Compare observed to expected counts with a chi-square test to detect departure from H-W equilibrium.
- Significant departure suggests selection, inbreeding, non-random mating, or recent admixture.
Frequently asked questions
What is allele frequency?
Allele frequency is the proportion of a particular allele among all allele copies in a population at a specific locus. For a diploid population with N individuals, there are 2N total allele copies. Frequency of allele A = (2 x count of AA + count of Aa) / (2N).
How do I calculate allele frequency from genotype counts?
For allele A: p = (2 x n_AA + n_Aa) / (2 x total individuals). For allele a: q = (2 x n_aa + n_Aa) / (2 x total individuals). Alternatively, q = 1 - p. The sum p + q always equals 1.
What is the difference between allele frequency and genotype frequency?
Genotype frequency is the proportion of a particular genotype (AA, Aa, or aa) in the population. Allele frequency is derived from genotype frequencies by counting alleles. Hardy-Weinberg equilibrium predicts genotype frequencies from allele frequencies.
Why is allele frequency important in population genetics?
Allele frequencies change over time due to natural selection, genetic drift, mutation, and gene flow. Tracking allele frequencies reveals evolutionary dynamics, helps identify disease-associated variants, and informs conservation genetics for endangered species.
What does it mean for an allele to be at fixation?
An allele is fixed when its frequency reaches 1.0 (100%), meaning all individuals in the population carry that allele. The alternative allele is lost (frequency = 0). Fixation can occur by selection, drift (especially in small populations), or a population bottleneck.
Official sources
- NCBI dbSNP: dbSNP variant allele frequency database.
- NHGRI: Allele Frequency definition.
Reviewed by the CalculatorHub team, edited by James Graham, 15 June 2026. See our methodology.