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Box plots of discordance rates between imputed and simulated genotypes using the five different reference panel types. (A) Varying reference panel size, all sites. (B) Varying reference panel size, heterozygous sites with 0 < MAF < 0.1. (C) Varying marker density, all sites. (D) Varying marker density, heterozygous sites with 0 < MAF < 0.1. (E) Varying imputation length, all sites. (F) Varying imputation length, heterozygous sites with 0 < MAF < 0.1.
