Fig. 7
From: Dark and camouflaged genomic regions remain challenging in CHM13
Inversions cause decreased coverage in long read alignments. (a) Chromosome 8 contains a region of 887 bp that is consistently dark-by-depth in all PacBio and ONT samples where minimap2 soft-clipped the reads and Cactus alignments show an inversion between HG38 and CHM13. (b) In CHM13, short-read alignments clearly identify the inversion, while primary long-read alignments (removing supplementary alignments) soft-clip large segments of reads. (c) In contrast to the CHM13 alignments, this region is not inverted in HG38 and is completely covered in all alignments. (d) Supplementary reads resolve dark region caused by only considering primary reads in the inverted region.
