Fig. 7

Long-read technologies resolve many camouflaged regions, with variable success. We found that ONT’s long-read technology appeared to resolve all camouflaged regions well with the high sequencing depth. PacBio performed similarly well, and 10x Genomics performs well under certain circumstances. a SMN1 and SMN2 were 94.6% and 88.0% camouflaged CDS, respectively, based on standard Illumina sequencing with 100-nucleotide read lengths (illuminaRL100). Both genes were 0% camouflaged CDS for 10x Genomics, PacBio, and ONT data. 10x Genomics and ONT perform particularly well in these genes, with consistently high mapping coverage. b HSPA1A and HSPA1B were 53.0% and 51.5% camouflaged CDS, respectively, based on illuminaRL100 data. Both genes were 0% camouflaged CDS based on ONT and PacBio data and were 45.8% and 51.8% camouflaged CDS based on 10x Genomics data. In contrast to the results for SMN1 and SMN2, 10x Genomics was unable to resolve the HSPA1A and HSPA1B camouflaged regions. c CR1 was 26.0% camouflaged CDS based on illuminaRL100. 10x Genomics did not improve coverage for CR1; the region remained 26.4% camouflaged CDS. Both ONT and PacBio were 0% camouflaged CDS. While both PacBio and ONT were able to fill the camouflaged region, coverage dropped throughout the region, particularly for PacBio. The duplicated region is indicated by blue bars, where white lines indicate regions that have diverged sufficiently for short-reads to align uniquely. Regions were visualized with IGV. Reads with a MAPQ < 10 were filtered, and insertions, deletions, and mismatches are not shown