Table 1.

Overview of simulations

Scenario	Allele frequency	N	Population structure	Sequencing depth and phenotype	Simulated phenotype mean
1	0.45	1,000	No	Correlated	0
2	0.45	1,000	No	Not correlated	$\beta ·g$
3	$(0.9,0.1)$	1,000	Yes	Correlated	$q·\gamma$
4	$(0.9,0.1)$	1,000	Yes	Not correlated	$\beta ·g+q·\gamma$
5	0.45	1,000	No	Correlated	$\beta ·g$
6	$(0.9,0.1)$	1,000	Yes	Correlated	$\beta ·g+q·\gamma$

We simulate under a standard additive model with a normally distributed phenotype with a mean given in the last column, and SD 1, according to Equation (5). N is the number of individuals, g is the genotype with effect size β and q is the ancestry proportion with effect sizeγ. In scenarios 1 and 3, there is no effect of the genotype. In scenarios 3, 4, and 6, there is population structure with two ancestral populations with allele frequency of 0.9 and 0.1. The sequencing depth and phenotype correlation are simulated using (Equation 5;Supplementary Methods).