Figure 3.

Regional variability in TOPMed reference panel imputation quality

(A) Observed imputation r² by genomic position (Mb) of common (MAF > 0.05) bi-allelic SNVs on chromosome 20. Sequenced bi-allelic SNVs not present in reference panels were assigned r² = 0. The horizontal line at r² = 0.8 corresponds to the threshold used to determine well-imputed variants.

(B) Cumulative distribution of the number of consecutively well-imputed (r² > 0.8) bi-allelic SNVs in each MAF category: common (MAF ≥ 0.05), low frequency (0.005 ≤ MAF < 0.05), and rare (MAF < 0.005), as calculated separately in each study. For common variants, European and Finnish curves appear to overlap and African and Hispanic/Latino curves appear to overlap.