Fig. 3: Imputation performance of five reference panels in the Han Chinese.

a The average R-square (Rsq) and number of well-imputed (Rsq ≥ 0.8) variants in shared sites of five reference panels (729,958 SNPs). All shared variants were grouped into nine MAF bins. b, c The cumulative number and proportion of well-imputed variants in shared sites of five panels, there were 729,958 shared SNPs in total. d Non-reference allele (NR-allele) concordance rate distribution (imputed variants vs. array variants). Each dot represents an individual. The plots on the top and right are the corresponding density distributions. e, f The NR-allele genotype concordance rate for rare, low-frequency, and common variants and overall variants (imputed variants vs. WGS variants). A total of 184 unrelated samples with both sequencing and genotyping data were used for the evaluation. The concordance rates for each variants group with mean value ± SEM, and quartile for each panel were plotted. The 1KG means 1000G Phase 3 and EAS means East Asian group in 1000G Phase 3. All imputations were conducted on chromosome 2. Source data are provided as a Source Data file.