Fig. 4.

Visualizing bisulfite sequencing data. (a) Bismark output file from an Arabidopsis bisulfite sequence experiment. Peaks indicate regions containing many methylated cytosine residues. (b) Zoomed in view of (a). A user-defined threshold shows that most cytosines in the first intron are methylated. (c) Zoomed in view of (b), showing the positive and negative strand aligned reads. Thymines are colored white, and cytosines red. Unmethylated cytosines that were converted to thymines appear as white columns occupying the same base pair position as a mark below the sequence axis, which indicate cytosines in the reference sequence. The highly-methylated region on the left contains many marks and few white columns