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 predictors of false-positive associations derived from imputed allelic frequencies, since the bias between empiric and imputed association statistics was randomly distributed or clustered in markers showing high calling probabilities or very close to HW equilibrium.
