Fig. 3

Structural variant involving the region spanning intron 2 of GBA1LP and intron 5 of MTX1. A The read depth ratios of the short reads aligned to GBA1, GBA1LP, MTX1. and MTX1LP of Case 4 were calculated as the ratio to the average read depth of the five control subjects, and plotted with chromosomal positions. The depth ratio in the GBA1 region was increased to about 1.5, while that in the GBA1LP region was decreased to about 0.5, raising the possibility that the copy numbers of GBA1 and GBA1LP are three and one, respectively. B Physical maps of the GBA1–GBA1LP locus in the reference genome and the structural variant derived from gene conversion involving the GBA1LP–MTX1 locus in Case 4 are shown. The region spanning intron 2 of GBA1LP (ENST00000689630.1) and intron 5 of MTX1 was replaced by the region spanning intron 2 of GBA1 and intron 5 of MTX1LP with a deletion of CAC (c.937_939del) in this region (NC_00001.11:g.155237400_155237404), which was clearly demonstrated by the four long-reads 1–4. C Across the breakpoint of GBA1 and GBA1LP of the complex structural variant, there are several sets of paired-end reads that were preferentially aligned to GBA1 because one of the paired-end reads contains an increased number of bases specific to the GBA1 reference sequence than those specific to GBA1LP. Consequently, c.115+1G>A was miscalled at GBA1 by the short-read sequence analysis. The regions with nucleotide sequences identical between GBA1 and GBA1LP are shown in gray. The regions with nucleotide sequences specific to GBA1 are shown in blue, whereas those specific to GBA1LP are shown in red