At the HapMap SNPs (settings 1 and 2), imputation using the 1000G reference achieved slightly lower quality compared with using the HapMap reference. This is probably because microarray-based genotyping is still more reliable than the low-coverage, next-generation sequencing used in the 1000 Genomes Project pilot 1 study. At the non-HapMap sites, 1000G imputation still achieved high quality, but the reduction of imputation accuracy was more noticeable. For rare variants (MAF > 1%), average R2 remained above 0.6. The relationship between imputation quality and allele frequency does not change if we used allele frequencies from the reference panel (Fig. 3B).
