Allele Frequency Calculator
Enter the number of individuals with each genotype (AA, Aa, aa) in your sample to calculate the observed frequency of each allele.
Last updated: September 25, 2026
Frequently asked questions
Why does AA count for 2 in the formula but Aa only counts for 1?
Each individual carries 2 alleles at the gene locus. An AA individual has two copies of allele A, so it contributes 2 to A's count. An Aa individual has one copy of each allele, contributing 1 to A's count and 1 to a's count. Summing these contributions and dividing by the total allele count (2N) gives each allele's frequency.
Why should p + q always equal 1?
Because every allele counted in the sample is classified as either A or a - there's no third option in this two-allele model, so their frequencies must sum to the whole (1, or 100%). If your result is slightly off from exactly 1, that's normal rounding in the displayed decimals, not a calculation error.
Is this the same as a Hardy-Weinberg calculator?
No - this tool goes from real, observed genotype counts to observed allele frequencies (p and q). A Hardy-Weinberg calculator instead starts from an assumed allele frequency and predicts what the genotype frequencies would be under equilibrium (no selection, mutation, migration, or drift). Use this calculator first to find your sample's actual p and q from real counts, then use a Hardy-Weinberg calculator to see whether your observed genotype counts match what equilibrium would predict.
Can this handle a sample with only two genotypes present, like no aa individuals?
Yes - enter 0 for any genotype not observed in your sample. The formulas still work correctly; a genotype count of 0 simply contributes nothing to that allele's tally.
What if I only have genotype frequencies (percentages) instead of raw counts?
Multiply each frequency by your total sample size to get counts, or simply enter frequencies scaled to a convenient total (like frequencies × 100, treating them as counts out of 100) - the formula produces the same p and q either way since it works with relative proportions.
Does this assume the population is in Hardy-Weinberg equilibrium?
No - calculating allele frequencies from genotype counts is a direct tally and makes no equilibrium assumption. It works whether or not the population is actually in Hardy-Weinberg equilibrium; that assumption only comes into play if you go on to compare these frequencies against Hardy-Weinberg-predicted genotype ratios.