Allele Counting Calculators

0 calculators tagged with “Allele Counting”

Allele counting is the process of tabulating the number of each allele variant at a genetic locus across a sample of individuals. Because diploid organisms carry two alleles per locus, a sample of N individuals contains 2N alleles in total. Allele frequency = count of a specific allele / total allele count (2N). Allele counting is the foundation of population genetics — it provides the raw data for Hardy-Weinberg equilibrium tests, F-statistics, FST, and evolutionary analyses. Next-generation sequencing (NGS) allows allele counting at millions of SNP loci simultaneously across entire genomes.

All Calculators

No calculators found for this topic.

Allele Counting from Genotype Data

For diploid organisms: each individual contributes 2 alleles per locus. Sample of N individuals: 2N total alleles. Example: 50 individuals at a biallelic SNP (A/a): 12 AA; 26 Aa; 12 aa. Count of A allele: (12×2) + (26×1) = 24 + 26 = 50 copies. Count of a allele: (12×2) + (26×1) = 24 + 26 = 50 copies. Total alleles: 2 × 50 = 100. Allele frequencies: p(A) = 50/100 = 0.50; q(a) = 50/100 = 0.50.

Hardy-Weinberg Expected Genotype Frequencies

Expected: AA = p² = 0.25 (12.5 individuals); Aa = 2pq = 0.50 (25); aa = q² = 0.25 (12.5). Observed matches well → population in HWE.

Multiple Alleles

For multiallelic loci (k alleles): pᵢ = count of allele i / (2N). Σpᵢ = 1. Example: blood group ABO. Microsatellite loci: many alleles (5–20+); each allele counted separately.

NGS Allele Counting

Read depth at SNP locus: count reads carrying each allele. Allele frequency = reads with allele A / total reads. Error threshold: minimum allele frequency above sequencing error rate (~0.1–1% for Illumina).

Glossary

Allele Frequency
Count of a specific allele / total allele count (2N for diploids); p + q = 1 for biallelic loci; foundation of population genetics analyses including HWE, FST, and GWAS.
Hardy-Weinberg Equilibrium (HWE)
Expected genotype frequencies (AA = p², Aa = 2pq, aa = q²) in a randomly mating population with no evolutionary forces; tested by chi-square from observed vs. expected genotype counts.
Minor Allele Frequency (MAF)
Frequency of the less common allele at a biallelic locus; GWAS typically requires MAF ≥ 0.05; catalogued in gnomAD across global populations; used to classify variants as common, low-frequency, or rare.

Frequently Asked Questions

For diploid organisms each individual carries 2 alleles per locus. For N individuals: total alleles = 2N. Count each allele by multiplying genotype count by allele contribution: Homozygotes contribute 2 copies; heterozygotes contribute 1 copy. Example: 100 individuals; 36 AA; 48 Aa; 16 aa. Count of A: (36×2) + (48×1) = 72 + 48 = 120. Count of a: (16×2) + (48×1) = 32 + 48 = 80. Total: 120 + 80 = 200 = 2×100 ✓. Frequencies: p(A) = 120/200 = 0.60; q(a) = 80/200 = 0.40.

Hardy-Weinberg equilibrium (HWE) predicts genotype frequencies from allele frequencies in a randomly mating population with no selection, drift, mutation, or migration. Expected genotype frequencies: AA = p²; Aa = 2pq; aa = q². Chi-square test: H₀ = population is in HWE. χ² = Σ(O−E)²/E; df = 1 (for biallelic locus). Example: p = 0.60, q = 0.40, N = 100: Expected: AA = 36; Aa = 48; aa = 16. Observed: 30 AA; 60 Aa; 10 aa. χ² = (30−36)²/36 + (60−48)²/48 + (10−16)²/16 = 1.00 + 3.00 + 2.25 = 6.25. p < 0.05 → reject HWE → evidence of non-random mating or population structure.

In NGS data (from WGS or amplicon sequencing): sequence reads aligned to a reference genome; at each SNP position, reads are counted for each allele. Allele depth: number of reads carrying the reference allele (REF) and each alternate allele (ALT). Allele frequency (AF) = ALT count / total read depth. Example: at a SNP position, 23 reads show 'A' (REF) and 17 reads show 'T' (ALT): total depth = 40; AF(T) = 17/40 = 0.425. In tumor sequencing: AF < 0.50 for somatic mutations (due to tumor heterogeneity and normal cell contamination). In population studies: AF is used to call SNPs and calculate population genetics statistics.

Minor allele frequency (MAF) = the frequency of the less common (minor) allele at a biallelic locus. If p = 0.75 and q = 0.25: MAF = 0.25. Significance: GWAS (genome-wide association studies) typically require MAF ≥ 0.01 (1%) or ≥ 0.05 (5%) for statistical power — very rare variants require much larger samples to detect associations. Common variant: MAF ≥ 0.05. Low-frequency variant: 0.01 ≤ MAF < 0.05. Rare variant: MAF < 0.01. gnomAD database: catalogues allele frequencies at millions of SNP loci across diverse human populations — essential reference for variant interpretation in clinical genetics.