Relationship between quality of estimated allelic dosage from IMPUTE2 imputation and predictors of imputation quality.

Data are estimated from 10% of the original chip (59808 SNPs) masked from imputation. Discordance of predicted allelic dosage (y axis) is the fraction difference between dosage computed from imputation probabilities and dosage based on masked genotype data: for example, if the true genotype is reference homozygote and the allelic dosage from imputation is 1.4, the discordance is . Left panel: imputation quality greater than 0.9; right panel: quality between 0.8 and 0.9. Clusters correspond to minor allele frequencies of 10%; individual bars represent quality stratified by masked genotype. “Predicted” bars correspond to expected concordance assuming independence of individual haplotypes. Error bars represent 95% confidence intervals of mean discordance estimate.