Figure 3 shows the proportion of incorrectly imputed alleles in each of the populations. Results are presented using a single HapMap analysis panel as a reference (either the CEU, YRI, or CHB+JPT) or using all HapMap samples as a larger reference panel. For each of the populations, the reference panel that resulted in the smallest overall error rate is highlighted. Overall, African samples were the most difficult to impute, with error rates ranging between 5.13% for the Yoruba and 11.86% for the San when the HapMap YRI panel was used as a reference. In other parts of the world, we generally observed that the HapMap CEU provided a good reference panel for European populations and that the HapMap CHB+JPT provided a good reference panel for East Asian populations, resulting in error rates of <3.34 and <2.89%, respectively. Outside Europe and East Asia, when imputation was applied to populations from the Middle East, Central and South Asia, the Americas or Oceania, it was generally better to use the combined HapMap sample as a reference than to use any single HapMap analysis
