For very rare variants with MAF <0.05%, we observed ~22.1X (5.8X) and ~11.8X (10.7X) increases in the number of well-imputed variants, with 6% (5%) and 13% (11%) increases in average true R2, in JHS (HCHS/SOL), compared with 1000G and HRC respectively. Mismatch rates between true and imputed genotypes were low; using the program CalcMatch, the mean concordance for heterozygote individuals (generally the hardest to impute) for Jackson Heart Study is 97.5% for all well imputed variants in Table 1, 96.6% for MAF <0.5%, and 97.6% for MAF < 0.05%. For HCHS/SOL, the mean concordance is 98.2% for all well imputed variants, 92.9% for MAF <0.5%, and 83.8% for MAF < 0.05%. Most well-imputed variants from 1000G and HRC were also included in TOPMed freeze 5b imputation results (S2 Fig).
