Fig. 2

5hmU peaks in L. major obtained by DIP and chemical pull down. a Percentage of 5hmU peak lengths overlapped with genomic features. b Overlaps of 5hmU peaks and base J peaks in length (kb) and peak numbers (in parentheses). High confidence peaks were defined as peaks supported by at least two replicates out of three for each modification. Then the set of high confidence peaks were intersected to obtain consensus peaks for both 5hmU and base J. c An example of peaks in chromosome 23 (200–400 kb). 5hmU read counts (top) and base J read counts (bottom) with genes on the forward strand are shown in red and genes in the reverse strand are shown in blue. Red arrows indicate 5hmU loci. d Enrichment of peaks to each genomic feature. Values are shown with 95% confidence interval. e GC content (percentage) within peaks of T-modified loci and in the ±2kb flanking regions