Figure 2.
Imputation Accuracy and Reference Panel Sample Size
Genotypes for markers on the Illumina 550K chip, but not the Affymetrix 500K chip, were imputed in a sample of 188 individuals with five different reference panels: 60 phased individuals and 100, 300, 600, and 1200 unphased individuals. For each reference panel, the proportion of imputed markers whose allelic R2 (see Material and Methods) exceeds each threshold is given. The allelic R2 for each imputed marker is calculated with the assumption that the Illumina genotypes are the true genotypes.