Fig. 1

Chromosomal overview of rearrangements called by long-reads and novel transposable element insertions. A Chromosomal overviews showing local duplication calls, read coverage (white line shows autosome or sex chromosome median and shadings toward the centromere denote repetitive regions in which read coverage was not used to compile the coverage profile), large-scale (> 100 kbp breakpoint distance) rearrangements (deletions, inversions, duplications; shown in black, and translocations; shown in red), and repetitive sequence density in 100 kbp bins (red blocks above the line denote reference genome annotations; blue blocks below the line denote novel insertions) of all repeat annotations and Gypsy elements. Unresolved large-scale rearrangements (not spanned by a read) can be interpreted using the coverage profile. Increased coverage indicates duplication while decreased coverage indicates deletion. Regions annotated as repetitive (e.g., centromere- and telomere-proximal regions) are not analyzed. B The abundance (Y-axis) of insertions > 1 kbp in length with > 90% classification to a single repetitive element (X-axis). Only the four most abundant element classes are shown individually; the rest are pooled into “Other”. C Violin plot showing the insertion length (Y-axis) distribution density (X-axis) per element as individual violins. Thin dashed red lines show insertions comprising 90–110% of a full-length Gypsy element. D Chromosome sequence expansion in percent due to Gypsy insertions