Scoring simulated reads against haploid templates using SAGE. Each row contains the color-coded percentage from the top-score of a read-set mapped against 27 genomic templates. Black: top-score; Red: within 5% of top-score; Orange: ≤ 10%; Yellow: ≤ 20%; White: > 20% below top-score. Sequences are ordered along the rows and columns so that sequences with the same (sub-)type are adjacent to each other. Templates of the same type are indicated by the blue boxes, and those of the same sub-type by light blue boxes.