Multiple alignments of the paired-end reads that display the expected switch in VP patterns. These were at the breakpoint of a duplication on chromosome 1 with breakpoints 155,184,704 and 155,205,331 for Yoruban individual NA19129. The called NAHR duplication was mediated by LCR A (red) with coordinates [155180173,155190755] and LCR B (blue) with coordinates [155200767,155213257]. At the top is a schematic representation of the reference genome (not to scale) in the region chr 1:[155180173,155213257]. For presentation, we collected all paired-end reads that display the expected switch in VPs. This same collection of paired-end reads (mates connected by dots) are shown in three multiple alignments: against the predicted hybrid LCR; against LCR A; and against LCR B. VPs are colored according to which reference LCR’s VP pattern they agree with. Positions in the reads that disagree with the reference/hybrid LCR are colored yellow, while those that agree are colored appropriately. When aligning the reads to LCR A, notice that the reads perfectly agree at the VPs on the right-hand side of the alignment, but completely disagree with the VPs of the left-hand side of the alignment. But when aligning the reads to LCR B, the situation is reversed. Finally, when aligning to the hybrid LCR, all disagreements between the reads and the reference are resolved. The log-odds ratio of the probability of the reads given that there was no NAHR event (that is the hybrid does not exist) versus the probability of the reads given that the two-copy duplication indeed occurred (that is the hybrid LCR does exist) is −13; strong support for the two-copy duplication and the specific hybrid LCR. LCR, low-copy repeat; NAHR, non-allelic homologous recombination; VP, variational position.