Figure 3
Calibration of posterior probabilities. The posterior probabilities were, in general, well calibrated, although there were a few deviations from the expected accuracy (a). For common and low-frequency variants (b and c), we observed a strong correlation (r2 0.97 and 0.91, respectively) between the impute2 info metric and the observed r2. However, for the rare variants (d), the relation between predicted and observed quality was less profound. We also observed a correlation of 0.70 and several large deviations from the diagonal.
