Fig. 2

Genome graph, copy-number and haplotype frequency of insertions. A Graph representation of the genome generated using large-scale (> 100 kbp breakpoint distance or translocation) SVs. Segments are colored according to alignments to the reference genome chromosome. Connections between segments are established from large-scale SVs and are indicated with black lines. Haplotype structure can be reconstructed by graph traversal, where forks in the graph reflect different haplotypes. B Distribution in percent (Y-axis) of copy number in 50 bp genomic bins per chromosome (X-axis). C The chromosomal haplotype frequency (X-axis) and the abundance in percent (Y-axis) of inserted repetitive sequences (breakpoints < 1 kbp) in tetraploid regions. Rearrangement haplotype frequency were determined by counting read support. Black bars represent the distribution of all insertions and gray bars represent the distribution of insertions absent in the source fly stock (based on short-read analysis of insertions in S1, S2-DRSC, and S3)