Fig. 4

EpiTEome detects new TE insertions in repetitive crop genomes. a, b Bar plot of sensitivity of detection for simulated TE insertions at three different potential TE insertion contexts (gene, intergenic, TE) in the maize (a) or rice (b) genomes using in silico generated bisulfite-converted reads. Results are divided by TE copy number. c FDR of epiTEome calculated from the same simulated data as part A. Error bars in (a)–(c) represent the 95% CI generated using five replicates. d Genome browser visualization of a non-reference (not in the reference B73 genome) LTR retrotransposon TE insertion into the PFK5 GRMZM2G127717 gene in the Oh43 inbred line identified by epiTEome