Comparison of empirical evaluations of imputation quality to IQS in European Americans.

The sample is based on 2,597 European Americans that were randomized to cases and controls. Cases used genotypes from the Illumina 550 K platform and were imputed to the 1 M platform and controls were genotyped on the 1 M platform. Genome-wide significance is set as p<5×10−8. There were 792,563 SNPs available. False positives refer to the absolute number of SNPs that reached genome-wide significance despite the filter. The retained percentage is the proportion of SNPs that passed the filter.