Allele Frequency Calculator

Calculate allele and genotype frequencies using the Hardy-Weinberg equilibrium. Supports 2-allele and 4-allele models with flexible input options.

Choose your known input:

Disease Prevalence (q²) - value between 0 and 1

Results

Parameter	Value	Percentage

Enter the frequency for each of the 4 alleles (must sum to 1):

Allele p frequency

Allele q frequency

Allele r frequency

Allele s frequency

Results — 10 Genotype Frequencies

Genotype	Formula	Frequency	Percentage

What is Allele Frequency?

Allele frequency, also called gene frequency, describes how common an allele is in a population. It is defined as the proportion of all copies of a gene in a population that are of a particular allele type. For example, if there are 100 copies of a gene in a population, and 40 of them are allele "A", then the frequency of A is 0.40 or 40%.

Allele frequencies are fundamental to population genetics and evolutionary biology. They help scientists understand genetic diversity, track evolutionary changes, and predict the distribution of genetic traits in future generations.

The Hardy-Weinberg Equilibrium

The Hardy-Weinberg principle states that allele and genotype frequencies in a population will remain constant from generation to generation in the absence of other evolutionary influences. These influences include:

Natural selection
Genetic drift
Gene flow (migration)
Mutation
Non-random mating (assortative mating)

The mathematical framework consists of two equations:

Allele frequency equation: p + q = 1
Genotype frequency equation: p² + 2pq + q² = 1

Where p = frequency of dominant allele (A), q = frequency of recessive allele (a).

The three genotype frequencies represent:

p² = frequency of homozygous dominant (AA) individuals
2pq = frequency of heterozygous (Aa) individuals
q² = frequency of homozygous recessive (aa) individuals

How to Calculate Allele Frequency

Step-by-step method:

Count the number of each allele type in the population
Divide each count by the total number of alleles
Verify: all frequencies should sum to 1

Alternative: Using disease prevalence

If a recessive disease affects 1% of the population, q² = 0.01
q = √0.01 = 0.1
p = 1 − 0.1 = 0.9
Carrier frequency (2pq) = 2 × 0.9 × 0.1 = 0.18 = 18%

Extending to Multiple Alleles

For genes with more than two alleles (like ABO blood types with 3 alleles), the Hardy-Weinberg equation expands:

For 4 alleles: p + q + r + s = 1
Genotype frequency: (p+q+r+s)² = p² + 2pq + 2pr + 2ps + q² + 2qr + 2qs + r² + 2rs + s² = 1

Real-World Applications

Genetic counseling: Predicting carrier frequencies for genetic diseases
Forensic science: DNA profile frequency calculations
Conservation biology: Assessing genetic diversity in endangered species
Medical genetics: Estimating disease risk in populations
Evolutionary biology: Detecting natural selection

Example Calculations

Example 1: Cystic fibrosis affects 1 in 2,500 people

q² = 1/2500 = 0.0004
q = √0.0004 = 0.02
p = 1 − 0.02 = 0.98
Carrier frequency = 2pq = 2(0.98)(0.02) = 0.0392 ≈ 4%

Example 2: Given 500 individuals — 320 AA, 160 Aa, 20 aa

Total alleles = 1000
p = (2×320 + 160)/1000 = 800/1000 = 0.80
q = (2×20 + 160)/1000 = 200/1000 = 0.20

Frequently Asked Questions

Q: How do you calculate P and Q allele frequency?

Count each allele type and divide by total alleles. Or use p + q = 1 if you know one frequency. For example, if you know the frequency of the dominant allele p = 0.7, then q = 1 - 0.7 = 0.3.

Q: What do P and Q mean in allele frequency?

p represents the dominant allele frequency (A), and q represents the recessive allele frequency (a). Together they always sum to 1 in a two-allele system.

Q: How to calculate minor allele frequency?

The minor allele frequency (MAF) is the frequency of the second most common allele. Use the same Hardy-Weinberg calculation. The minor allele is whichever of p or q is smaller.

Q: What are the allele frequencies if 1% of people have a disease?

If a recessive disease affects 1% of the population, then q² = 0.01, so q = 0.1 and p = 0.9. About 18% of the population are carriers (2pq = 0.18).

Q: What does Hardy-Weinberg equilibrium mean?

It describes a theoretical population where allele frequencies don't change over generations, serving as a null model to detect evolution. When observed genotype frequencies deviate from expected Hardy-Weinberg frequencies, it suggests evolutionary forces are at work.