Distribution of imputation accuracies when 1% of the SNPs were randomly selected from chromosome 21 and their genotype data completely removed in the NNC set. The results for other proportion of missing SNPs are in the supplementary material. In each of the 1,000 simulations we randomly selected 1% of the SNPs to be removed from the data and their genotype data to be imputed. The chromosome is tagged by approximately 5,900 SNPs, so that 59 SNPs were removed in each run, and 59,000 SNPs had to be imputed across all 1,000 simulations. The x-axis reports the accuracy of each of the 59,000 SNPs that were imputed in the 1,000 simulations. The y-axis reports the frequency of different imputation accuracies.
Zhao et al. BMC Genetics 2008 9:85 doi:10.1186/1471-2156-9-85