Extract DNA and RNA from the same E. coli culture High-throughput sequencing and alignment to the E. coli Genome RNA editing detection ≥1% Total coverage ≥30× Editing frequency G ≥5× No strand bias Forward Reverse DNA TGCTACGA GCTACGAA CTGCTACG CTACGAAT RNA TGCTACGA GCTGCGAA CTGCTGCG CTACGAAT TGCTGCGA AGGA Supplemental Fig S1. Detecting RNA editing in E. coli. In order to detect RNA editing in E. coli DNA and RNA are purified from the same sample, subjected to high-throughput sequencing, and aligned to the genome. Only sites harboring a mixture of nucleotides in the RNA but not DNA samples, having at least five forward and reverse reads which display a non-DNA allele and are covered by more than 30 reads in total are considered true editing sites.