Fig. 3

NT-seq simultaneously detects three types of methylation motifs in bacteria. a A to G frequency at known 6mA sites (G6mATC, A6mACN₆GTGC, and GC6mACN₆GTT) and unmethylated A sites in E. coli MG1655 genome from native and PCR amplified DNA. b C to T frequency at known 4mC sites (T4mCTTC and 4mCCGG) and unmethylated C sites in H. pylori JP26 genome from native and PCR amplified DNA. c–e Negative log normalized A to G ratio of different 6mA motifs in E. coli WT strain MG1655 (a), hsdM deleted strain (b), and dam/dcm/hsdR mutated strain (c). 6mA position was underlined. f Negative log normalized C to T ratio of different 4mC motifs in H. pylori JP26. g Negative log normalized C to T ratio of 4mC sites identified by SMRT-seq in E. coli strain MG1655. h Negative log normalized C to T ratio of different 5mC motifs in H. pylori JP26. Only motifs with sequencing depth larger than 25× were considered for violin plots. Statistic test were performed by two-sided Mann-Whitney-Wilcoxon (MWW) test with Bonferroni correction (ns: P > 1.0e-3; ****: P ≤ 1.0e−6)