1. A system for determining the quality of predicted DNA base identifications, the system comprising a processor configured to: receive a training data set, the training data set comprising a plurality of predicted DNA base identifications; define a group of subsets; compare the predicted DNA base identifications with actual DNA base identifications for training data within each subset of the group; determine a sampling characteristic for each subset of the group based on training data within the respective subset; and determine a quality characterization for predicted DNA base identifications within at least one of subset of the group based on the comparison and determined sampling characteristic; wherein the sampling characteristic comprises a confidence value comprising a binomial proportion confidence interval value; and detect nucleotides based on the quality characterization.