Figure 2. The receiver operating characteristic (ROC) curves; Datasets in (A) 100 bp and (B) 76 bp read lengths.

Each point represents the total numbers of alignments whose mapping qualities are greater than the indicated value. MOSAIK has a relatively smooth curve, ensuring that downstream tools that employ mapping quality cutoffs (i.e. ignoring all reads with mapping qualities less than the cutoff) do not incur extremely large changes in the number of reads while progressively increasing the cutoff.