. 2009 Jan 6;169(4):505–514. doi: 10.1093/aje/kwn359

Table 3.

Deviation From Hardy-Weinberg Equilibrium for Sample Sizes of 5,000, 20,000, and 50,000 and for Allele Frequencies Ranging From 0.05 to 0.95, After Subtracting From the Heterozygote Group a Number Equivalent to 1.96 Standard Deviations

Sample Size	p_true^a	Hz1 True^a	Het True^a	Hz2 True^a	p_false^b	Hz1 Exp^c	Het Exp^c	Hz2 Exp^c	Het Obs^d	No Call^d	χ²^e
5,000	0.05	13	475	4,513	0.0463	11	438	4,511	434	41	0.36
5,000	0.20	200	1,600	3,200	0.1961	190	1,556	3,190	1,535	65	0.86
5,000	0.50	1,250	2,500	1,250	0.5000	1,233	2,465	1,233	2,431	69	0.97
5,000	0.80	3,200	1,600	200	0.8039	3,190	1,556	190	1,535	65	0.86
5,000	0.95	4,513	475	13	0.9537	4,511	438	11	434	41	0.36
20,000	0.05	50	1,900	18,050	0.0482	46	1,826	18,046	1,819	81	0.34
20,000	0.20	800	6,400	12,800	0.1980	779	6,312	12,779	6,271	129	0.85
20,000	0.50	5,000	10,000	5,000	0.5000	4,965	9,931	4,965	9,861	139	0.97
20,000	0.80	12,800	6,400	800	0.8020	12,779	6,312	779	6,271	129	0.85
20,000	0.95	18,050	1,900	50	0.9518	18,046	1,826	46	1,819	81	0.34
50,000	0.05	125	4,750	45,125	0.0488	119	4,634	45,119	4,621	129	0.34
50,000	0.20	2,000	16,000	32,000	0.1988	1,967	15,861	31,967	15,796	204	0.84
50,000	0.50	12,500	25,000	12,500	0.5000	12,445	24,890	12,445	24,781	219	0.96
50,000	0.80	32,000	16,000	2,000	0.8012	31,967	15,861	1,967	15,796	204	0.84
50,000	0.95	45,125	4,750	125	0.9512	45,119	4,634	119	4,621	129	0.34

Abbreviations: Exp, expected; Het, heterozygote; Hz, homozygote; Obs, observed.

p_true are the allele frequencies used to start the simulations. They were also used to estimate the true frequencies of homozygotes (Hz1 True and Hz2 True) and heterozygotes (Het True) assuming Hardy-Weinberg equilibrium.

p_false are the allele frequencies observed after subtracting 1.96 standard deviations from the heterozygote group.

Hz1 Exp, Het Exp, and Hz2 Exp are the expected values of the 3 genotype groups computed from p_false and q_false (1 − p_false).

Het Obs are the observed values for each genotype group after subtracting 1.96 standard deviations from the heterozygote group (which equates to the number presented in the “No Call” column). The observed values of the other 2 genotype groups used to compute the deviations from Hardy-Weinberg equilibrium (Hz1 Obs and Hz2 Obs) are equal to Hz1 True and Hz2 True, respectively.

Hardy-Weinberg equilibrium χ² value.