Allele Frequency

Allele frequency measures how common a particular version of a gene — an allele — is among all copies of that gene present in a population. For a gene with two alleles, a dominant version conventionally labeled "A" (frequency p) and a recessive version labeled "a" (frequency q), the two frequencies always sum to 1 (or 100%), since every gene copy in the population must be one allele or the other: p + q = 1.

Allele frequency is distinct from genotype frequency. An individual's genotype is the specific pair of alleles they carry (AA, Aa, or aa), while allele frequency looks at the population level, pooling every individual's two allele copies together and asking what fraction are A versus a. This is exactly what the Allele Frequency Calculator computes — given genotype counts across a population, it returns p and q.

Allele frequency is the foundation of population genetics and is central to the Hardy-Weinberg Equilibrium, which predicts expected genotype frequencies (p², 2pq, q²) from allele frequencies under specific idealized conditions. Comparing observed genotype counts to Hardy-Weinberg predictions — computed by the Hardy-Weinberg Calculator — lets biologists detect whether evolutionary forces like selection or migration are acting on a population. Allele frequency also connects back to individual crosses modeled by a Punnett Square: while a Punnett square predicts outcomes for one pair of parents, allele frequency extends the same logic across an entire population.

p + q = 1

Where p is the frequency of the dominant allele and q is the frequency of the recessive allele. Calculated from genotype counts in a population of N individuals:

p = (2 × AA count + Aa count) / (2 × N) q = (2 × aa count + Aa count) / (2 × N)

A population of 100 individuals is genotyped for a single gene with two alleles: 64 are homozygous dominant (AA), 32 are heterozygous (Aa), and 4 are homozygous recessive (aa).

Total alleles = 2 × 100 = 200.

Dominant allele count (A) = (64 × 2) + 32 = 128 + 32 = 160, so p = 160 / 200 = 0.80

Recessive allele count (a) = (4 × 2) + 32 = 8 + 32 = 40, so q = 40 / 200 = 0.20

Check: p + q = 0.80 + 0.20 = 1.0, confirming the calculation is consistent.

• Allele frequency is always between 0 and 1: a frequency of 1 means every gene copy in the population is that allele (fixed), while 0 means the allele is absent entirely.
• Allele frequency drives the Hardy-Weinberg Equilibrium: once p and q are known, expected genotype frequencies (p² for AA, 2pq for Aa, q² for aa) can be predicted assuming no evolutionary pressures are acting.
• Population-level, not individual-level: allele frequency describes a whole population's gene pool, in contrast to a Punnett square, which predicts the outcome of one specific cross between two known parents.
• Changes in allele frequency over time define evolution: natural selection, genetic drift, mutation, and migration all shift p and q generation to generation, making allele frequency tracking a core tool in evolutionary biology.
• Heterozygotes contribute to both allele counts: an individual with genotype Aa contributes one copy to the dominant allele count and one copy to the recessive allele count, which is why the Aa count appears in both the p and q formulas above.