Figure 2.

Comparison of the read probability calculation methods for S. aureus with 4,788,174 reads. Each mark on the plot represents a single read. The read’s position is determined by the probability calculated from our dynamic programming method (y-axis) and Bowtie 2 (x-axis). Points on the line y = x denote reads that were given the same probability by both methods. Since Bowtie 2 only finds the best alignment, it usually reports a slightly lower probability. A probability threshold of 1e-30 is shown for the dynamic programming method. The read probabilities that fall below this threshold would be rounded up to 1e-30 during LAP computation.