Fig. 2

Whole-genome LoMA analysis. A. The workflow of the whole-genome analysis. Unclear regions were first defined based on the alignment status (indels and clips) of ONT reads. Reads mapped to the regions were separately collected. For each region, LoMA attempted a localized assembly to obtain CSs. CAMPHOR collectively detected structural variants from the CSs for NA18943 and NA19240. B. The relative density of unclear regions of NA18943 and NA19240 are shown in red- and blue-colored heatmaps, respectively. The light-colored regions are dense with unclear regions. The white arrows indicate the autosomal centromeres except chromosome 6. The arrows on chromosome 6 represent the HLA region. C. The precision of indels to the standard SV set was assessed for NA19240. The left vertical axis (bar graphs) shows the number of indels found in each bin (the number of constitutive reads). The right (line graphs) shows the precision of indels in each bin. Both graphs were binned per 2 reads