Under some population genetic assumptions such as minimal inbreeding, genotype frequencies for a biallelic variant can be expected to follow the Hardy-Weinberg proportions \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document} $$\begin{aligned} &\text{freq} (A_{1}A_{1}) = p^{2} \qquad \text{freq} (A_{1}A_{2}) = 2pq\qquad\\ &\text{freq} (A_{2}A_{2}) = q^{2} \end{aligned} $$ \end{document}freq(A1A1)=p2freq(A1A2)=2pqfreq(A2A2)=q2 where p is the frequency of allele A1 and q=1−p is the frequency of allele A2 [12]. It is now common for bioinformaticians to use an exact test for deviation from Hardy-Weinberg equilibrium (HWE) to help detect genotyping error and major violations of the Hardy-Weinberg assumptions.
