Fig. 3

Validation of epiTEome using published MethylC-seq data. a Venn diagram comparing three independent programs created to identify TE insertion sites in the Arabidopsis ecotype Ha-0. EpiTEome is the only program that utilizes MethylC-seq data. Color codes are maintained throughout panels (b)–(d). Split-reads identify the insertion and target site duplication of a TE insertion detected by all three programs (b) and a TE insertion specifically detected by epiTEome (c). The split-read analysis is confirmed by the decrease in coverage of un-split MethylC-seq reads in Ha-0 (insertion present) vs. the ecotype Rou-0 (insertion absent). d Meta-plot of MethylC-seq un-split read coverage at the TE insertion sites and flanking regions uniquely detected by each program or detected by all three. e MethylC-seq un-split read coverage z-score for each of the 175 TE insertions uniquely identified by epiTEome, plus the 16 detected by all three programs (asterisks). Seven percent of the insertion sites with high un-split read coverage (bracket) at the TE insertion site are likely false positives (FP)