Figure 5.

Boxplots of the absolute bias of heritability estimates $(|E({\hat{h}}_{\mathit{\text{SNP}}}^2)-h^2|)$ across all simulated phenotypes from Supplementary Figures 24 & 26 using WGS data to estimate GRMs (top), and from Figures 3–4 using imputed variants to estimate the GRMs (bottom). X axis indicates the parameters for the estimation model, including the MAF scaling factor, α, and the assumed effect size distribution, β_k, specified in the GRM and whether imputation scores (r²) were used in the GRM estimation. All used a single GRM except for LD- & MAF-stratified GREML (LDMS), which used 16 GRMs (α=−1) stratified by MAF and either regional (-R) or individual SNP (-I) LD score. * Typical GREML-SC parameters. † Typical LDAK-SC parameters. Boxplots show the median and interquartile, with whiskers extending 1.5 times the quartiles and more extreme points shown for N=22 (WGS) and 26 (imputed) mean estimates of heritability.