Fig. 6
From: Dark and camouflaged genomic regions remain challenging in CHM13
Centromeric/pericentromeric satellites cause problems in alignments. (a) The pericentromeric region exhibits major alignment challenges with varying degrees of dark-by-MAPQ and dark-by-depth regions. (b) Using Repeat Masker, we identified multiple types of repetitive elements rather than just the annotated HSATII. (c) When zooming out we see that ONT has more deletions and insertions, combined with a large section with nearly complete sequence variability that still aligns (indicated by high mismatch rate in histogram above the ONT reads). On the other hand, PacBio has large dark-by-depth regions.
