Fig. 2

Individual validation of predicted insertions. Black boxes represent TE annotations in Nipponbare IRGSP (green rectangle) and MH63 (blue rectangle) assembled genomes. Examples of shared (reference) and MH63-specific (non-reference) insertions are shown in a. Insertions predicted by each tool (shown as arrows in b) were intersected with windows of 500 bp spanning the entire Nipponbare IRGSP genome, and windows having an intersection (red boxes, b) were aligned to MH63 genome. True positive reference insertions (TP ref.) were those having full-length alignments with an MH63 region where a MITE or LTR-retrotransposon was annotated. False positives (FP) have high-quality alignments (MAQ > 30) to regions were no MITE or LTR-retrotransposon was present. True positive non-reference insertions (TP non-ref) alignments were those having a spliced alignment in which the two hits were separated by a region that overlaps with a MITE or LTR-retrotransposon annotated in MH63