Correlations between the SBayesRC estimated and true effect sizes at SNPs with posterior inclusion probability (PIP) greater than a threshold. Results were from simulations ( n = 10 independent replicates) with trait heritability h 2 = 0.5 (the upper bound of the prediction accuracy). See Extended Data Figs. 2 and 3 and Supplementary Figs. 3 – 5 for results from the simulation with h 2 = 0.1. Each box plot in a – c shows the spread of data; the line is the middle (median), the box covers the middle half (IQR), the whiskers extend to 1.5 times the IQR, and dots show outliers. Data in d – f are presented as mean values (center point) ± standard error of the mean (s.e.m.) (error bar) in each PIP bin.
