Fig. 4: Recovery of somatic SVs using the Sniffles2 mosaic mode.

a,b, Benchmark of mixtures of HG002 with HG00733. We spiked HG002 in various concentrations and measured the precision (a) and recall (b) of Sniffles2 default (blue) and mosaic (yellow) modes, alongside cuteSV (in red). For the recall, we added an adjusted recall (in green) as Sniffles2 mosaic mode calls SVs only in the range of 0.05 to 0.20 VAF, and, thus, everything outside that range will not be analyzed. c, Overview of the number of SV types identified as germline (blue) and mosaic (red) in the cingulate cortex brain region of an MSA patient brain sample sequenced with 55× ONT long reads. A zoom is shown for duplication and inversion SVs. d,e, Validated mosaic SVs detected by Sniffles2. Each PCR was done once (d)—mosaic deletion close to a germline Alu insertion. The IGV screenshot shows bulk WGS: top panel 55× ONT, bottom panel 85× Illumina. PCR validation shows both products from the MSA brain (column b, insertion in top and deletion in bottom) compared to a control (column c) and the ladder (column a). The PCR products highlighted in squares were Sanger sequenced, and the alignment is shown below the gel (colors matching), with the INS position marked with a purple triangle. e, Mosaic deletion within RBFOX3. The IGV screenshot shows bulk WGS: top panel 55× ONT, bottom panel 85× Illumina. PCR demonstrates the mosaic deletion (column b, wild-type in top and deletion in bottom) compared to two controls (column c, brain control) and the ladder (column a). The PCR products highlighted in squares were Sanger sequenced, and the alignment is shown below the gel (colors matching). Supplementary Fig. 6 shows the complete unannotated gels, and Supplementary Fig. 7 shows a different view of the same Illumina results for e. Supplementary Table 14 shows the complete list of candidate SVs, and Supplementary Fig. 8a–h shows all IGV screenshots for the same candidates.