Table 2 Discordance rates for genotype imputations with different reference panels, using chromosome 20 data with European ancestry in the 1000 Genomes Project
Variant groups
Reference typesAllHeterozygotesMAF (0, 0.1)MAF [0.1, 0.2)MAF [0.2, 0.5]
Most diverse1.023.5310.312.771.92
 Standard deviation0.0040.0190.0760.0190.014
Rank of the most diverse314314
  • Discordance rates are shown as percentages. We split 381 phased diploid individuals into a target sample of 301 target individuals and a reference panel of 160 haplotypes. Shown here are results from one imputation with the most diverse reference panel and the mean and standard deviation of the discordance rates from 50 imputations with randomly selected reference panels. We ranked discordance rates of the most diverse panel together with those of 50 random reference panels from the lowest to the highest value and display the rank of the most diverse panel.