Fig. 5.

Recombination introduces copy-number variation. a Recombination between two haplotypes with translocated regions can lead to copy-number differences in the recombined genomes. b Such differences can be observed by aligning short-read sequencing data from recombinant genomes to the reference genome. c–e Three different tests to assess the existence of the predicted translocations have been applied. These included c testing for the absence of reads in samples with no copy of the translocated DNA, d goodness-of-fit between expected copy number and observed copy number, and e clustering of samples with the same genotypes at the translocation. f In the heatmap, columns correspond to individual translocations and rows correspond to the three different tests, while the color of a cell represents whether a translocation was validated (green), was selected but could not be validated (dark gray), or was filtered out as the test was not applicable (gray)