imputation R2 in N≈12,000 curated British samples at the masked and imputed SNPs, computing means and standard errors across MAF strata as before (treating R2 from different SNPs as approximately independent given that each MAF bin contained <1 SNP per cM). We further assessed imputation R2 in UK10K-imputed 1000 Genomes GBR samples (N=89); since sequence data was available for these samples, we computed R2 at all UK10K-imputed SNPs in the 1000 Genomes data set. We computed means of R2 across MAF strata and estimated standard errors using a 100-block jackknife to account for linkage disequilibrium among SNPs.
