Extended Data Fig. 6: Genomic inflation and power of fastGWA with the sparse GRM thresholded at different genetic relatedness cut-off values.

This simulation was performed based on real genotypes from the UKB (see simulation settings in part 5 of the Supplementary Note). We constructed different sparse GRMs by setting off-diagonal elements below a certain threshold (varying from 0.03 to 0.10) to 0 and performed fastGWA analyses using these sparse GRMs. Each boxplot represents the distribution of estimates (that is, median λ, or mean χ²) across 100 simulation replicates. The line inside each box indicates the median value, notches indicate the 95% confidence interval of the median, the central box indicates the interquartile range (IQR), and whiskers indicate data up to 1.5 times the IQR.