Fig. 2. Schematic of JAG1 inversion identified in proband 12.

The reference genome (upper structure) depicts the 679-kb inverted region, encompassing JAG1 exons 1–3, bounded by dashed lines. The breakpoints extend from intron 3 to a gene desert upstream of the JAG1 promoter. The rearranged structure is shown below. Paired-end reads with abnormal insert size and orientation were used to infer the approximate boundaries of the inversion and soft-clipped reads at the ends of the inversion were used to precisely map the breakpoints at nucleotide-level resolution.