Mutation filtering for sequencing libraries of Escherichia coli rRNA probed in vivo with ETC. (A) Violin plots of background-subtracted mutation rates of paired and unpaired Us and Gs separated by the three possible single-nucleotide mismatches. These and other mutation types are provided in Supplemental Figure S8. The significance of Wilcox test is denoted with asterisks comparing the paired and unpaired residues. Medians are provided in Supplemental Tables S12 and S14, P-values are provided in Supplemental Tables S13 and S15. (B) ROC curve of U and G reactivities with ETC; filtered (+) and unfiltered (−). (C) ROC curve of C and A reactivities with filtered DMS. (D) Example per nucleotide reactivity distributions for unfiltered ETC, filtered ETC, and filtered DMS. Nucleotides with reactivity of >1.5 are marked with an asterisk, and reactivity values clipped of >4 are annotated on the plot. A–C are across all three rRNAs, whereas D is for the 16S rRNA 3′ major domain.
