Figure 2

M-Bias plots are useful for quality control. The methylation level averaged per position in the reads should be nearly constant, but often shows bias at the 5′ and/or 3′ end of reads. The first (red) and second (blue) read in each pair is plotted separately. Likewise, results of reads mapping to the original top (OT, left) strand and original bottom (OB, right) are kept separate. When a non-directional library is used, graphs for the complementary to original top (CTOT) and complementary to original bottom (CTOB) are also produced. Vertical lines indicate the suggested bounds of the region for inclusion during methylation extraction.