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Median Allelic R2 and Minor-Allele Frequency
Genotypes for markers on the Illumina 550K chip, but not the Affymetrix 500K chip, were imputed with two different reference panels in a sample of 1088 individuals genotyped on the Affymetrix 500K chip. For each minor-allele frequency, x = 0.01, 0.02, …, 0.5, the median allelic R2 for imputed markers with minor-allele frequency between x − 0.01 and x + 0.01 is plotted.
