1. A method in a computer for determining the quality of predicted DNA base identifications, the method comprising: receiving a training data set, the training data set comprising a plurality of predicted DNA base identifications; defining a group of subsets; comparing the predicted DNA base identifications with actual DNA base identifications for training data within each subset of the group; determining a sampling characteristic for each subset of the group based on training data within the respective subset; and determining, with a processor, 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.