Fig. 1

Identification of A-to-I editing sites with various analysis pipelines. A Distribution of mismatch types at different steps of the separate samples analysis workflow. Each two-letter combination, XY, indicates X-to-Y mismatch. Altogether, there are 12 possible mismatch types. The first histogram shows the raw output from REDItools, while the second histogram shows the distribution after elimination of genomic SNPs. “Remove multi-mismatches” means that variants with other types of mismatches in their vicinity are discarded. The last filter, labeled as “min 2 same-type sites”, selects for clustered editing events, which are characteristic of ADAR targets. MHT refers to the datasets generated in this study. A total of 36 samples were analyzed. B Venn diagram indicating the number of isolated editing sites recovered in the separate samples analysis workflow due to their detection in at least two different studies. C Distribution of mismatch types at different steps of the pooled samples analysis workflow. D Venn diagram indicating the number of isolated editing sites recovered in the pooled samples analysis workflow due to their detection in at least two different studies. E Distribution of mismatch types at different steps of the hyper-editing analysis workflow. The last filter, “min 2 same-type sites”, is unnecessary here as hyper-edited loci often occur in clusters. F Venn diagram showing the number of editing events detected using regular read alignment and REDItools or the hyper-editing pipeline where mapping was done with all As converted to Gs. G Venn diagram showing the number of A-to-I editing sites found in each of the three studies, which are indicated by the initials of the corresponding authors. DR refers to the datasets reported by Daniel Rokhsar [12], while MK refers to the datasets reported by Marc Kirschner [15]. H ADAR motif in X. laevis based on our curated list of editing sites. I Editing in repetitive regions of the X. laevis genome. Unlike human and mouse, minority of the frog ADAR targets were found in repeats. The pie chart shows the distribution of A-to-I editing sites in various repeat families. Fourteen annotated repeat families contained comparatively few editing events and thus were grouped together in a single slice of the pie chart. J Genomic locations of editing sites in X. laevis. Most sites resided in non-coding regions of the genome, such as introns and 3’UTRs