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Imputation quality metrics evaluation HapMap. a Boxplots of the MACH Rsq in function of the MAF of the imputed SNPs. b Imputation quality distribution per MAF category. Blue and green denotes the poorly and well imputed SNPs based in a 0.3 quality score as threshold. 88,625 out of 3,021,329 (2.93 %) are poorly imputed SNPs (Rsq < 0.3). (Color figure online)
