Fig. 7

Whole-genome PacBio Sequel reads aligned to hg38. Whole-genome reads generated using the PacBio Sequel were aligned to human reference genome hg38 using graphmap. We attained 7× genome-wide median coverage and 8× across the C9orf72 repeat locus. Four reads were from the individual’s wild-type allele of eight repeats, while the other four, were expanded. Three of the four reads capturing an expanded allele did not bridge the entire repeat region, where one captured 178 nucleotides in the repeat region (approximately 30 repeats; red), another captured 419 nucleotides (approximately 69 repeats; blue), and the third captured 5471 nucleotides (approximately 912 repeats; green). The read capturing 419 nucleotides may have bridged the repeat because the end of the read closely matches the sequence adjacent to the repeat region, but was ambiguous (Additional file 1: Figure S3d). The final read spanned the entire repeat with 7941 nucleotides (approximately 1324 repeats; brown), which falls easily within the Southern blot’s range (Fig. 5f). Soft-clipped nucleotides—nucleotides at the end of a read that did not align to the reference—are shown for all reads, and are outlined in green for the read capturing 912 repeats. The approximate location for the repeat expansion is marked by the light-blue lines. A histogram showing read depth per nucleotide is included near the top of the figure. Alignments were visualized using the Integrative Genomics Viewer (IGV)