Fig. 1

Genomic regions may be “dark” by depth or mapping quality, many of which are “camouflaged”. Large, complex genomes are known to contain “dark” regions where standard high-throughput short-read sequencing technologies cannot be adequately assembled or aligned. We split these dark regions into two types: (1) dark because of low depth and (2) dark because of low mapping quality (MAPQ), which are mostly “camouflaged”. a HLA-DRB5 encodes a Major Histocompatibility Complex protein that plays an important role in immune response and has been associated with several diseases, including Alzheimer’s disease. It is well known to be dark (low depth); specifically, when performing whole-genome sequencing using standard short-read sequencing technologies, an insufficient number of reads align, preventing variant callers from assessing mutations. We calculated sequencing depth across HLA-DRB5 for ten male samples from the Alzheimer’s Disease Sequencing Project (ADSP) that were sequenced using standard Illumina whole-genome sequencing with 100-nucleotide read lengths. Approximately 63.5% (49.6% of coding sequence) of HLA-DRB5 is dark by depth (≤ 5 aligned reads; indicated by red lines). b HSPA1A is a heat-shock protein from the 70-kilodalton (kDa) heat-shock protein family and plays an important role in stabilizing proteins against aggregation. HSPA1A is dark because of low mapping quality (MAPQ < 10 for ≥ 90% of reads at a given position). Approximately 41.1% (53.0% coding sequence) of HSPA1A is dark by mapping quality (indicated by red line). Dark gray bars indicate sequencing reads with a relatively high mapping quality, whereas white bars indicate reads with a low mapping quality (MAPQ = 0). c Many genomic regions that are dark because of mapping quality arise because they have been duplicated in the genome, which we term “camouflaged” (or “camo genes”). When confronted with a read that aligns equally well to more than one location, standard sequence aligners randomly assign the read to one location and give it a low mapping quality. Thus, it is unclear from which gene any of the reads indicated by white bars originated from. HSPA1A and HSPA1B are clear examples of camouflaged genes arising from a tandem duplication. The two genes are approximately 14 kb apart and approximately 50% of the genes are identical