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Imputation accuracy (Dosage Rsq) values vs MACH Rsq values for masked SNPs at 5% masking rates using panels from the 1000 Genomes (1KG) Project. Plots for HapMap-based imputations were similar. Blue points are SNPs polymorphic only in CEU, and cyan points are SNPs polymorphic only in YRI. Black line is where MACH Rsq equals Dosage Rsq. Red line is the regression line. Vertical dashed line is the filtering rule that we used. Note MER equals YRI plus blue points from CEU.
