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

Table 2.

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 Homozygote 1 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	Hz1 Obs^d	No Call^d	χ²^e
5,000	0.05	13	475	4,513	0.0487	12	462	4,519	6	7	3.65
5,000	0.20	200	1,600	3,200	0.1956	190	1,565	3,217	173	27	2.48
5,000	0.50	1,250	2,500	1,250	0.4939	1,205	2,470	1,265	1,190	60	0.75
5,000	0.80	3,200	1,600	200	0.7973	3,136	1,595	203	3,133	67	0.06
5,000	0.95	4,513	475	13	0.9496	4,471	475	13	4,471	41	0.00
20,000	0.05	50	1,900	18,050	0.0493	49	1,875	18,063	36	14	3.55
20,000	0.20	800	6,400	12,800	0.1978	781	6,330	12,835	746	54	2.42
20,000	0.50	5,000	10,000	5,000	0.4970	4,910	9,940	5,030	4,880	120	0.73
20,000	0.80	12,800	6,400	800	0.7987	12,672	6,389	805	12,667	133	0.06
20,000	0.95	18,050	1,900	50	0.9498	17,968	1,900	50	17,968	82	0.00
50,000	0.05	125	4,750	45,125	0.0496	123	4,710	45,145	103	22	3.52
50,000	0.20	2,000	16,000	32,000	0.1986	1,969	15,890	32,055	1,914	86	2.40
50,000	0.50	12,500	25,000	12,500	0.4981	12,358	24,905	12,548	12,310	190	0.73
50,000	0.80	32,000	16,000	2,000	0.7992	31,798	15,983	2,008	31,790	210	0.06
50,000	0.95	45,125	4,750	125	0.9499	44,995	4,749	125	44,995	130	0.00

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 homozygote 1 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).

Hz1 Obs are the observed values for each genotype group after subtracting 1.96 standard deviations from the homozygote 1 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 (Het Obs and Hz2 Obs) are equal to Het True and Hz2 True, respectively.

Hardy-Weinberg equilibrium χ² value.