Fig. 6

DNA modifications in male embryo genomic DNA of Sciara coprophila. a Percent of adenines or cytosines assigned to a modification class given a minimum coverage level in the PacBio analysis. ModA and ModC are the sets of all adenines or cytosines, respectively, flagged as modified whereas 6mA, 4mC, and 5mC are the subsets therein with those specific classifications. b Methylation frequencies at modification sites in PacBio analysis. c Chi-square standardized residuals (enrichment scores) indicating how many standard deviations away each observation is from expectation for trimers with middle adenines or middle cytosines from PacBio analysis. d Position weighted motifs from sets of 7-mers (where the modified base occurs at position 3) enriched for 6mA, 4mC, or 5mC. e Distributions of ionic current means from Nanopore template reads for 6-mers defined by PacBio motifs in (d). Blue line shows expected distribution given the Nanopore model for each kmer. Red line shows distribution learned from whole E. coli genome PCR data [34] using only canonical nucleotides. Black line shows distribution learned from native Sciara genomic DNA. f As in (e), but showing examples of 6-mers not defined by motifs learned in the PacBio analysis. g Two of the top three trimer motifs learned from the set of all 6-mers with shifted Nanopore signal distributions compared to expected models. h Distributions of distances between neighboring DNA modifications on the same strand