Figure 1

Distribution of estimates for a common tag SNP and a common causal SNP. Boxplot of estimates of genetic effect at a tag SNP (GWAS stage 1) and causal SNP C6S5380 (sequencing stage 2) on quantitative trait Q2 over 200 replicates with and without selection at a stage 1 tag SNP for additive genetic effect using a selection threshold p < 0.05. p _C is the MAF of the causal SNP, p _T is the MAF of the tag SNP, ρ _TC is the correlation between the tag SNP and the causal SNP. Horizontal lines are the null effect size (zero) and the mean of causal SNP genetic effect estimates without selection. Because of sampling variation, the mean is different from the median (band in middle of boxplots).