Genetic Variation and Allele Proportion Analysis
Understanding allele distribution within a population is central to evolutionary biology, medical genetics, and breeding programs. The allele frequency calculator estimates the proportion of each allele from genotype counts and evaluates expected genotype frequencies under Hardy–Weinberg equilibrium. These calculations help quantify genetic diversity, assess population structure, and detect deviations caused by selection or drift.
How Allele Frequencies Are Calculated
For a two-allele system (A and a), allele frequencies are computed directly from genotype counts:
- p (A): (2 × AA + Aa) ÷ (2N)
- q (a): (2 × aa + Aa) ÷ (2N)
The values p and q describe the relative abundance of alleles and always sum to 1 unless rounding discrepancies occur.
Hardy–Weinberg Equilibrium Expectations
Under equilibrium assumptions (random mating, no migration, infinite population size, no selection, no mutation), genotype frequencies follow:
- p²: expected frequency of AA
- 2pq: expected frequency of Aa
- q²: expected frequency of aa
Applications of Allele Frequency Estimates
- Evolutionary and population genetics studies
- Genetic association and disease-risk modeling
- Breeding program allele selection
- Monitoring allele shifts across generations
- Estimating heterozygosity and genetic diversity
Best Practices for Genotype-Based Calculations
- Ensure genotype counts are accurate and representative.
- Avoid small population sizes that introduce sampling bias.
- Check for deviations between observed and expected heterozygosity.
- Use consistent criteria when scoring genotypes.
FAQ
Population Genetics & Allele Frequency Questions
Core concepts for genotype interpretation and Hardy–Weinberg analysis.
Allele frequency is the proportion of a particular allele in a population, usually expressed as a decimal or percentage.
It computes allele frequencies from genotype counts and can estimate Hardy–Weinberg genotype proportions using p and q values.
Allele frequencies are calculated as: p = (2AA + Aa) ÷ (2N), q = (2aa + Aa) ÷ (2N), where N is total individuals.
Yes. The tool supports diploid systems with two alleles (A and a).
Yes. Expected genotype frequencies p², 2pq, and q² are displayed when allele frequencies are computed.
Any diploid organism, including humans, animals, plants, and many model systems.
You can input any set of AA, Aa, and aa values as long as they sum to a valid population size.
Yes. Frequencies are displayed as decimals and percentages.
Yes. Observed and expected heterozygosity (2pq) can be derived from allele frequencies.
This indicates rounding or inconsistent genotype counts; the calculator highlights such inconsistencies.