Three Allele Frequencies
Estimate allele frequencies p1, p2 and p3 from three-allele genotype counts using gene counting: pi = (2*nii + sum of heterozygote counts with allele i) / (2*N).
Description
Estimate allele frequencies p1, p2 and p3 from three-allele genotype counts using gene counting: pi = (2*nii + sum of heterozygote counts with allele i) / (2*N).
Three Allele Frequencies is a focused biology tool that estimate allele frequencies p1, p2 and p3 from three-allele genotype counts using gene counting: pi = (2*nii + sum of heterozygote counts with allele i) / (2*N). It calculates locally from the values you enter and exposes the result without changing the source observations.1
When to use Three Allele Frequencies
Use Three Allele Frequencies when you need to estimate allele frequencies p1, p2 and p3 from three-allele genotype counts using gene counting: pi = (2*nii + sum of heterozygote counts with allele i) / (2*N). Enter Genotype 1/1 count, Genotype 1/2 count, Genotype 1/3 count, Genotype 2/2 count, Genotype 2/3 count, and Genotype 3/3 count using the definitions and units below so the result can be reproduced.
- Genotype 1/1 count
- An integer count or setting greater than or equal to 0.
- Genotype 1/2 count
- An integer count or setting greater than or equal to 0.
- Genotype 1/3 count
- An integer count or setting greater than or equal to 0.
- Genotype 2/2 count
- An integer count or setting greater than or equal to 0.
- Genotype 2/3 count
- An integer count or setting greater than or equal to 0.
- Genotype 3/3 count
- An integer count or setting greater than or equal to 0.
How Three Allele Frequencies calculates the result
The published tool contract uses this rule: Estimate allele frequencies p1, p2 and p3 from three-allele genotype counts using gene counting: pi = (2*nii + sum of heterozygote counts with allele i) / (2*N).
- Allele frequency p1
- The calculated allele frequency p1.
- Allele frequency p2
- The calculated allele frequency p2.
- Allele frequency p3
- The calculated allele frequency p3.
Limitations of Three Allele Frequencies
The output is an estimate tied to the stated model and coefficients; it is not a direct measurement and should retain that label when reported.
Alternative or Complementary measurements
Retain the original Genotype 1/1 count, Genotype 1/2 count, Genotype 1/3 count, Genotype 2/2 count, Genotype 2/3 count, and Genotype 3/3 count values and their units alongside the result. Allele Frequency p is useful when you instead need to estimate dominant allele frequency p from genotype counts using p = (2*AA + Aa) / (2*total). Genotype Frequencies provides another view by helping you compute expected Hardy-Weinberg genotype frequencies p^2, 2pq, and q^2 from an allele frequency.
References
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Hardy–Weinberg principle — Wikipedia contributors
Similar or alternative tools
- Allele Frequency p
Estimate dominant allele frequency p from genotype counts using p = (2*AA + Aa) / (2*total).
- Genotype Frequencies
Compute expected Hardy-Weinberg genotype frequencies p^2, 2pq, and q^2 from an allele frequency.
- HW Chi-Square
Compute a chi-square statistic comparing observed genotype counts against Hardy-Weinberg expectations derived from an allele frequency.