In this report, we comprehensively tested several genotyping and imputation quality criteria, haplotypic information and chromosomal location as predictors of the quality of association statistics derived from imputed markers. As demonstrated in other reports dealing with the accuracy of genotypic determination, when the MAF of imputed markers are close to 50% [10] imputation accuracy greatly diminishes. We further analyzed a subset of markers that were selected based on their extreme minor allele frequencies (MAF > = 0, 49) to determine the validity of the evidence provided by this allelic condition for the identification of biased imputed markers. Indeed this allelic condition greatly predisposes imputed markers to have biased association statistics, but it can not be considered a good predictor since the majority of markers in this allelic condition show good agreement with directly genotyped ones in terms of association statistics. Imputed markers showing these specific allelic frequencies should be annotated and their use in follow-up studies should be done carefully. The other analyzed quality criteria, such as calling probabilities and Hardy-Weinberg Equilibrium deviation showed an even more limited use as
