Fig. 2
From: Dark and camouflaged genomic regions remain challenging in CHM13
Dark-by-MAPQ dark bases predominate. (a) As the genome becomes more complete, short-read data exhibits increasing dark-by-MAPQ nucleotides while long reads plateau. (b) While millions of bases are obscured by dark-by-depth regions, they pale in comparison to dark-by-MAPQ (c) ONT has the least number of dark bases within genes in all types of dark regions (i), dark-by-depth (ii), dark-by-MAPQ (iii), and camouflaged regions (iv) across all references. HG38 with alternates has the highest amount of dark bases. (d) ONT has the least number of dark bases within protein coding genes in all types of dark regions (i), dark-by-depth (ii), dark-by-MAPQ (iii), and camouflaged regions (iv) across all references. HG38 with alternates has the worst amount of dark bases.
