Scoring simulated reads against diploid templates. Each row of a matrix represent scores from the same read sets mapped to different prediction templates. The scores are normalized so that the second best score in each row is equal to 1 and the worst score is equal to 0. We normalize with respect to the second best score since it would be used to predict the haplotype in the absence of the best scoring (and presumably correct) template. Furthermore, the entries are color-coded accordingly- Black: top-score; Red: second top-score; Orange: within 10% of second top-score; Light Orange: ≤ 20%; Yellow: ≤ 30%; White: > 30% below top-score. Both matrices are ordered according to template sub-types. Templates of the same type are indicated by the blue boxes. (a) SAGE scores (b) Bowtie scores.