(A) The GC CNV (BTA 6:88,681,767–88,693,553) is shown in the IGV screen shot. The grey reads are normally mapped reads, whereas green ones are discordantly mapped reads, providing evidence for a tandem duplication. The sequencing coverage of the CNV region is higher than non-CNV region. (B) The left breakpoint is flanked by MIR repeat. (C) The right breakpoint does not overlap with repeats. (D, E) The proximal and distal breakpoints are zoomed in and the soft-clipped reads (positions where nucleotide sequences are written) information revealed the 5-bp microhomology “CACAT” at the breakpoints (marked as yellow). (F-H) A schematic overview demonstrating a tandem configuration of the GC CNV. (F) The start and end of the GC CNV (shown in yellow-to-orange gradient colour) is flanked by non-CNV background, forming two junctions shown as 1–2 and 3–4 (marked with solid vertical lines). Sequencing reads from Wt (CN1) haploid genome can uniquely aligned to the 1–2 junction (blue-yellow reads) and the 3–4 junction (orange-green reads). The microhomology sequence is marked with grey shade. (G) A haploid CN4 genome forms unique junctions spanning over 3–2 formed by tandemly aligned 12-kb segments (marked with dotted vertical lines). Thus, reads from haploid CN4 would have reads spanning over 3–2 junction (orange-yellow reads), in addition to reads aligned to junctions 1–2 and 3–4. (H) Alignment of a heterozygous genome (CN1/CN4) to the reference genome (Wt) is shown. Both CN1 and CN4 have reads spanning over 1–2 and 3–4 junctions that are present in the reference genomes; these reads can be uniquely mapped. Reads spanning over 3–2 junctions cannot be uniquely mapped to the reference genome; these reads will be discordantly mapped either at 1–2 or 3–4 junctions (grey lines). The 3–2 junctions reads can be aligned to the junction 1–2, however orange reads will appear as soft-clipped. Likewise, these reads can be aligned to the 3–4 junction. However, the 4 junction started with the “CACAT” sequence. Hence, the sequences after ...