Figure 4.

Effect size heterogeneity in the context of polygenicity

(A) Boxplot of type I error for Tractor and a standard GWAS split by non-differentiated (MAF difference $\le$ 0.2) and differentiated (MAF difference > 0.2) SNPs.

(B) Boxplot of power for Tractor and a standard GWAS in the case of no effect size heterogeneity split by non-differentiated and differentiated SNPs.

(C) Boxplot of power for Tractor and a standard GWAS in the case of effect size heterogeneity split by non-differentiated and differentiated SNPs.

(D) Boxplot of power for Tractor and a standard GWAS in the case of opposite effect sizes split by non-differentiated and differentiated SNPs.

All simulations used real UKBB admixed genotypes and simulated phenotypes with 100 causal SNPs and a total additive genetic heritability of $h^2$ = 0.5 (see subjects and methods). “^∗” indicates a nominally significant p value (<0.05). “^∗∗” indicates a Bonferroni-corrected significant p value (<1.28 × 10⁻³). The boxes show the inter-quartile range while the whiskers show the rest of the distribution (not including outliers).