Fig. 5: RNA modification detection across seven human cell lines.

a, Number of m6A sites found in each cell line that occur in the m6A-Atlas v.2 pTPs. Solid bars indicate the number of sites found with the default probability threshold 0.9, and shaded bars indicate the count at threshold where the putative positive predictive values (pPPV) is 85%. Uncalled4 with NA12878 has reduced recall at 85% pPPV, as indicated by dashed line. b, Coverage distribution of true positive (pTP) sites (top) and pPPV of sites within coverage bins. c, Number of sites shared by Uncalled4, Nanopolish and m6A-atlas v.2 across all cell lines. d, Difference in per-gene m6A count found by Uncalled4 and Nanopolish across all seven cell lines. e, Difference in aggregated gene m6A count found by Uncalled4 versus Nanopolish alignments, limited to COSMIC tier 1 genes where at least one m6A modification is found in every cell line by either tool (51 genes). Negative (green) values indicate genes where more m6A sites were found by Nanopolish, and positive (purple) values indicate more m6A sites found by Uncalled4. f, Transcript-level m6A calls in an ABL1 transcript alongside BCR fusion. g, Gene-level m6A calls in the TTC4 gene.