Table 1. Estimated Type I Error Rate and Statistical Power.

		Type I error rate			Statistical power
Distra	Methodb	α = 0.10	α = 0.05	α = 0.01	α = 0.10	α = 0.05	α = 0.01
Exp	Permut	0.191***	0.113***	0.028***	0.493	0.387	0.235
	Bootstr	0.145***	0.078***	0.022***	0.451	0.360	0.235
	GeneDr	0.108	0.045	0.009	0.402	0.312	0.164
	GRAIP	0.116*	0.052	0.012	0.416	0.315	0.164
Norm	Permut	0.129***	0.059	0.012	0.478	0.379	0.241
	Bootstr	0.090	0.048	0.007	0.409	0.343	0.223
	GeneDr	0.090	0.051	0.010	0.416	0.355	0.239
	GRAIP	0.086*	0.044	0.010	0.418	0.342	0.217
Unif	Permut	0.136***	0.079***	0.014	0.488	0.397	0.241
	Bootstr	0.104	0.057	0.011	0.435	0.352	0.219
	GeneDr	0.104	0.062*	0.011	0.429	0.351	0.220
	GRAIP	0.105	0.060	0.011	0.430	0.352	0.246

Allele (A/a) frequencies at the founder generation: 3/1 for F₂₆ vs. 1/3 for F₃₄. Estimated from 1200 simulations at genome-wide significance level α = 0.10, 0.05 or 0.01. *, **, and *** indicate that the estimated type I error rate is significantly different from the expected significance levels 0.10, 0.05, and 0.01, respectively.

^aResidual distribution: exponential (Exp), normal (Norm), or uniform (Unif).

^bPermuting marker data (Permut), bootstrapping phenotypic data (Bootstr), or gene dropping (GeneDr).