False negative (FN) and false positive (FP) minor allele call rates at rare SNPs (MAF<5%) in Scenario B.

The two columns on the left show results for Illumina-only genotypes imputed from Affymetrix 500 K data in the study sample, and the two columns on the right show results for Affymetrix-only genotypes imputed from Illumina 550 K data. The FN rates are expressed as percentages of genotypes that are truly heterozygous and the FP rates as percentages of genotypes that are truly homozygous common.
*Unlike the other methods, IMPUTE v1 was not provided with the diploid reference panel. Consequently, these numbers are based on using a reference panel of 120 chromosomes to impute a study sample of 459 individuals.