Extended Data Fig. 9: Genomic inflation of BOLT-LMM-Mix using LD score based on different LD window sizes and references.
From: A resource-efficient tool for mixed model association analysis of large-scale data
a, Results from simulations based on the simulated genotype data (part 5 of the Supplementary Note) using the same setting as in the (0, 0) case in Fig. 1. The LD scores were computed from the sample using three window sizes; that is, 1 Mb (BOLT-LMM-Mix_wind-1Mb), 10 Mb (BOLT-LMM-Mix_wind-10Mb), and 20 Mb (BOLT-LMM-Mix_wind-20Mb). b, Results from simulations based on real genotypes (part 5 of the Supplementary Note) using the same settings as in the (0, 0) and (≥2nd, 0.1Vp) cases in Fig. 1. Two sets of LD score were tested; LD scores computed from the sample using a window size of 1 Mb (BOLT-LMM-Mix_UKB-LDsc) and LD scores obtained from the BOLT-LMM website (BOLT-LMM-Mix_provided-LDsc). 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.
