To evaluate the quality of imputed genotypes, we contrasted our estimates of the most likely genotypes and the expected number of copies of the minor allele with actual genotype data for three sets of markers: 521 SNP markers in a region of chromosome 14 previously examined to fine-map a candidate linkage region [Willer et al., 2006], 1,234 SNP markers selected to augment coverage of the Illumina 317K panel in regions surrounding 222 candidate genes [Gaulton et al., 2008] and 12,702 markers with MAF <5% not included in the set of 290,690 markers used for imputation. We expected the last two panels of markers to be harder to impute, because they represent SNPs that are not well tagged by the Illumina 317K SNP chip or that have lower MAF. We observed that 98.60% of imputed alleles matched actual genotyped alleles in the fine-mapping panel, 96.24% in the candidate gene panel, and 98.73% in the low MAF SNP panel. Furthermore, the average r2 between imputed genotypes and actual genotypes was 90.4, 79.1, and 74.0% in the three SNP panels, respectively. This represents
