Nested SVs called by Sniffles in LC-2/ad. The thin black lines are repeat annotations. The brown and purple lines are gene annotations. The red and orange lines are an end of an inversion called by Sniffles. There are two possibilities for the genome structure: one is that MUC3A and its flanking region are a duplication, and the internal region of MUC12 is an inverted duplication. The other is that MUC3A and its flanking region are an inverted duplication, and the internal region of MUC12 is a duplication. Several read alignments support the former interpretation. Although SVs called from the Illumina reads did not include any of the SVs shown here, the alignment coverage by the Illumina reads is consistent with both duplications. Note that the y-axis of the blue thin line on the chromosome showing the alignment coverage is logarithmic.