Fig. 4

Simulated reads created from the 10 kb of the ALT assembly immediately outside of each breakpoint, shown a as an overview, and b as a close up (in split screen) at the ends of the Manta inversion calls from the short reads. For both views, 1 is the Manta calls, 2 is the 10 kb simulated reads aligned to the correct sides, 3 is the simulated reads aligned to the opposite sides, and 4 is the short-read sequence with RR- and LL-paired reads shown in turquoise and blue respectively. The green arrow indicates the section that was copied from the AKR1C1 end and pasted over the equivalent site at the other end, making the two simulated reads identical at that point