Table 1 Dark region statistics reveal long-read dark regions are fewer in number but span larger regions. For all four sequencing technologies and all four reference genomes, we compared the number of dark bases (excluding missing nucleotides indicated by ‘N’ in the reference genomes), regions (groups of contiguous dark bases), average bases per region, and median number of bases per region for dark-by-depth, dark-by-MAPQ, and the combination of those two. We found that short-read sequencing data has more, smaller dark regions, while long-read sequencing has fewer, larger dark regions.

From: Dark and camouflaged genomic regions remain challenging in CHM13