criteria thresholds for MAF (minor allele frequencies), calling probabilities and Hardy Weinberg equilibrium deviation and analyzed the overall correlation between minus log transformed P-values of empiric and imputed allelic frequencies under a log-additive model of inheritance. We used a combined quality criteria of markers showing MAF > 0.01 and calling probability higher than 0,95 and filtered markers showing a considerably higher accuracy between association statistics using imputed and empiric frequencies (Figure 1). Using a minimum association threshold of 10 -5, we identified a total of 73 imputed markers clamming association and among those, only 38 (52%) would be considered associated based on their empiric (directly genotyped) association statistics (i.e., nearly a half of imputed markers would be erroneously considered associated to the phenotype under study). The same pattern was observed when different and more stringent significance thresholds were used (10 -6 and 10 -7).This result suggests that imputation methods are prone to inflate the number of markers considered associated in any of the evaluated thresholds in this report. These results are not a contradiction to the overall high accuracy for predicting genotype status previously described. These few highly deviated markers would be considered associated even when using highly stringent significance
