Table 3.

Absolute bias and variance for G-REMLadp variance components when HWE was violated, for non-null simulated effects

Parent Corr	MAF Diff	N	${\mathit{\sigma }}_{\mathit{\alpha }}^2$	${\mathit{\sigma }}_{\mathit{\delta }}^2$	${\mathit{\sigma }}_{\mathit{\gamma }}^2$	#Reps	${\widehat{\mathit{\sigma }}}_{\mathit{\alpha }}^2$ Bias	${\widehat{\mathit{\sigma }}}_{\mathit{\alpha }}^2$ Var	${\widehat{\mathit{\sigma }}}_{\mathit{\delta }}^2$ Bias	${\widehat{\mathit{\sigma }}}_{\mathit{\delta }}^2$ Var	${\widehat{\mathit{\sigma }}}_{\mathit{\gamma }}^2$ Bias	${\widehat{\mathit{\sigma }}}_{\mathit{\gamma }}^2$ Var
0.00	0.05	1000	0.017	0.017	0.017	300	1.7e−03	1.0e−03	− 4.8e−04	9.7e−04	2.9e−03	1.0e−03
0.00	0.05	1000	0.033	0.033	0.033	300	1.1e−03	2.4e−03	1.1e−03	2.4e−03	6.6e−04	2.0e−03
0.00	0.05	1000	0.100	0.100	0.100	300	− 1.0e−03	6.6e−03	2.9e−04	6.4e−03	3.1e−04	5.7e−03
0.00	0.05	2000	0.017	0.017	0.017	300	− 1.4e−03	2.5e−04	3.5e−04	3.1e−04	− 1.8e−05	2.8e−04
0.00	0.05	2000	0.033	0.033	0.033	300	9.4e−04	5.4e−04	1.6e−03	5.2e−04	3.0e−04	4.8e−04
0.00	0.05	2000	0.100	0.100	0.100	300	2.2e−03	1.6e−03	− 5.2e−04	1.6e−03	6.9e−04	1.6e−03
0.00	0.05	4000	0.017	0.017	0.017	300	1.9e−04	7.2e−05	− 6.7e−04	6.9e−05	− 9.4e−04	8.1e−05
0.00	0.05	4000	0.033	0.033	0.033	300	− 6.3e−04	1.5e−04	8.3e−04	1.8e−04	− 8.2e−04	1.5e−04
0.00	0.05	4000	0.100	0.100	0.100	290	− 2.1e−03	4.9e−04	1.7e−03	5.6e−04	− 2.0e−04	4.3e−04
0.25	0.00	1000	0.017	0.017	0.017	300	6.1e−04	8.2e−04	1.5e−03	1.6e−04	− 1.4e−03	1.1e−03
0.25	0.00	1000	0.033	0.033	0.033	290	1.9e−03	1.6e−03	1.9e−03	2.5e−04	− 6.8e−03	2.0e−03
0.25	0.00	1000	0.100	0.100	0.100	290	1.7e−03	5.6e−03	2.1e−03	9.8e−04	− 2.5e−02	8.3e−03
0.25	0.00	2000	0.017	0.017	0.017	300	− 1.3e−04	2.0e−04	− 3.5e−04	5.6e−05	− 5.4e−03	2.8e−04
0.25	0.00	2000	0.033	0.033	0.033	300	2.0e−03	3.9e−04	− 9.0e−05	1.0e−04	− 6.9e−03	6.5e−04
0.25	0.00	2000	0.100	0.100	0.100	300	3.6e−03	1.5e−03	4.5e−03	3.8e−04	− 2.5e−02	2.2e−03
0.25	0.00	4000	0.033	0.033	0.033	300	2.3e−04	1.2e−04	4.0e−04	4.6e−05	− 7.1e−03	1.3e−04
0.25	0.00	4000	0.100	0.100	0.100	300	1.3e−03	3.6e−04	1.7e−03	1.4e−04	− 2.3e−02	4.7e−04
0.25	0.05	1000	0.017	0.017	0.017	130	− 4.1e−03	8.4e−04	3.5e−03	3.6e−04	− 3.4e−03	1.3e−03
0.25	0.05	1000	0.033	0.033	0.033	160	− 1.2e−03	1.7e−03	2.1e−04	5.6e−04	− 1.5e−02	2.5e−03
0.25	0.05	1000	0.100	0.100	0.100	220	− 9.1e−04	5.2e−03	7.1e−03	2.6e−03	− 3.1e−02	8.2e−03
0.25	0.05	2000	0.017	0.017	0.017	280	− 9.5e−04	1.9e−04	4.4e−05	1.1e−04	− 4.7e−03	3.2e−04
0.25	0.05	2000	0.033	0.033	0.033	300	8.4e−05	3.8e−04	2.0e−03	2.8e−04	− 8.6e−03	5.4e−04
0.25	0.05	2000	0.100	0.100	0.100	300	5.2e−03	1.4e−03	1.2e−03	7.4e−04	− 2.1e−02	1.8e−03
0.25	0.05	4000	0.033	0.033	0.033	300	− 2.9e−04	1.3e−04	1.5e−03	7.8e−05	− 7.8e−03	1.6e−04
0.25	0.05	4000	0.100	0.100	0.100	300	2.2e−03	3.1e−04	3.5e−03	2.5e−04	− 2.3e−02	4.8e−04

Parent Corr average correlation of parental genotypes, MAF Diff average difference in parental MAFs. Proportion of phenotypic variance explained by additive effects is given in the ${\mathit{\sigma }}_{\mathit{\alpha }}^2$ column, by dominance effects in the ${\mathit{\sigma }}_{\mathit{\delta }}^2$ column, and by parent-of-origin effects in the ${\mathit{\sigma }}_{\mathit{\gamma }}^2$ column. N number of simulated phased genotypes, #Reps number of simulated replications, “Bias” is absolute bias of estimates across simulated replications, “Var” is variance of estimates across simulated replications