Table 1.

Estimated Rejection Rates by Test^[Note]

1A. Discrete Populations
p1, p2	STRAT	TDT	χ2
P=.05
.5, .5	.050	.050	.049
.1, .1	.048	.049	.049
.5, .1	.050	.050	.437
.9, .1	.049	.050	.769
P=.01
.5, .5	.011	.010	.011
.1, .1	.009	.010	.009
.5, .1	.009	.010	.260
.9, .1	.010	.009	.649
P=10-3
.5, .1	0.83×10-3	0.98×10-3	.112
.9, .1	0.83×10-3	0.90×10-3	.506
P=10-4
.5, .1	0.97×10-4	0.95×10-4	.046
.9, .1	0.80×10-4	0.76×10-4	.370
1B. Admixed Populations
p1, p2	STRAT	TDT	χ2
P=.05
.5, .5	.048	.049	.054
.1, .1	.050	.049	.051
.5, .1	.044	.050	.623
.9, .1	.033	.050	.998
P=.01
.5, .5	.010	.010	.010
.1, .1	.010	.009	.010
.5, .1	.008	.010	.370
.9, .1	.005	.010	.979
P=10-3
.5, .1	0.83×10-3	0.86×10-3	.156
.9, .1	0.45×10-3	1.06×10-3	.874
P=10-4
.5, .1	0.85×10-4	0.38×10-4	.050
.9, .1	0.61×10-4	0.92×10-4	.662

Note.—Rejection rates under the null hypothesis at a biallelic candidate marker whose allele frequencies in subpopulations 1 and 2 are given by p₁ and p₂, respectively. We show estimated rejection rates at the .05, .01, 10⁻³ and 10 ⁻⁴ significance levels for the STRAT, the TDT, and the standard χ² test. The χ² test is valid where p₁=p₂. Results are based on at least 50,000 replicates (P=.01, .05), 200,000 replicates (P=10^-3), and 350,000 replicates (P=10^-4).