Figure 4A shows the results for all Illumina-only SNPs imputed from Affymetrix genotypes, and Figure 4B shows the equivalent results for Affymetrix-only SNPs imputed from Illumina genotypes. One striking difference between these plots is that the imputations based on Illumina genotypes (Figure 4B) are generally more accurate. There are a number of possible explanations for this trend: the Illumina chip has a higher SNP density, and imputation generally improves as more SNPs are observed; the Affymetrix chip contains a larger proportion of rare SNPs, which are easier to impute on the whole, as we discuss below; and, while the Illumina SNPs were specifically chosen to predict, or “tag”, many of the common Affymetrix SNPs via the HapMap, the reverse is not true.
