Table 1.
Dark and camouflaged regions vary by genome build. We identified dark and camouflaged regions throughout the genome for three different builds, including GRCh37, GRCh38, and GRCh38+alt, across five different sequencing technologies (or read lengths for Illumina). Specifically, we measured dark regions for Illumina based on 100-nucleotide read lengths, Illumina based on 250-nucleotide read lengths, 10x Genomics, PacBio, and Oxford Nanopore Technologies (ONT). Here, the counts for dark and camouflaged regions are combined. We found that the number of dark regions and nucleotides, both within gene bodies (represented as GB in the table) and outside gene bodies, varies dramatically by build and technology. Overall, each technology has its respective strengths. GRCh38 including alternate contigs has > 3x more dark nucleotides than GRCh37, and more than 2x more dark regions. Results presented throughout the manuscript are based on GRCh38 (in gray)
| Dark regions | GRCh37 | GRCh38 | GRCh38+alt | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| il100 | il250 | 10x | PacBio | ONT | il100 | il250 | 10x | PacBio | ONT | il100 | PacBio | ONT | |
| Non-GB nucs. | 22.4M | 15.7M | 5.4M | 11.1M | 6.7M | 68.7M | 42.5M | 57.0M | 56.8M | 52.1M | 88.4M | 69.5M | 59.1M |
| Non-GB regs. | 38,931 | 16,247 | 17,481 | 10,615 | 13,441 | 84,174 | 54,418 | 20,650 | 20,276 | 23,613 | 91,263 | 35,136 | 25,682 |
| GB nucs. | 16.3M | 11.4M | 4.2M | 6.7M | 3.7M | 15.1M | 12.2M | 4.3M | 6.4M | 3.3M | 41.6M | 26.9M | 16.2M |
| GBs | 5857 | 4424 | 3828 | 2095 | 4454 | 6054 | 4227 | 3993 | 2170 | 4465 | 7396 | 3332 | 4465 |
| Protein-coding | 3792 | 2814 | 2845 | 1251 | 3464 | 3804 | 2437 | 2875 | 1275 | 3406 | 4291 | 1741 | 3041 |
| Pseudogenes | 1134 | 955 | 454 | 483 | 417 | 1232 | 1080 | 518 | 474 | 425 | 1701 | 876 | 668 |
| lincRNAs | 732 | 492 | 398 | 254 | 476 | 753 | 513 | 459 | 284 | 546 | 920 | 417 | 529 |
| Others | 199 | 163 | 131 | 107 | 97 | 265 | 197 | 141 | 137 | 88 | 484 | 298 | 227 |
| GB regions | 37,874 | 20,030 | 15,076 | 9729 | 9757 | 36,794 | 21,052 | 14,878 | 8999 | 8701 | 59,703 | 29,302 | 20,657 |
| Intronic | 28,751 | 13,971 | 11,700 | 6632 | 8000 | 27,982 | 14,405 | 11,322 | 6126 | 7371 | 41,219 | 18,842 | 14,029 |
| ncRNA exons | 4188 | 2799 | 1052 | 1734 | 959 | 4351 | 3396 | 1216 | 1738 | 878 | 6589 | 3573 | 2117 |
| CDS | 2657 | 1836 | 1313 | 731 | 416 | 2855 | 2221 | 1452 | 766 | 222 | 7885 | 4754 | 2952 |
| 5′UTR | 1106 | 613 | 617 | 258 | 132 | 908 | 518 | 580 | 191 | 90 | 2238 | 1221 | 861 |
| 3′UTR | 1135 | 785 | 381 | 369 | 233 | 698 | 512 | 307 | 178 | 140 | 1769 | 910 | 695 |
| Other UTR | 37 | 26 | 13 | 5 | 6 | 0 | 0 | 1 | 0 | 0 | 3 | 2 | 3 |
| Total nucs. | 38.7M | 27.1M | 9.6M | 17.8M | 10.4M | 83.8M | 54.7M | 61.3M | 63.2M | 55.4M | 130.0M | 96.4M | 75.3M |
| Total regs. | 76,805 | 36,277 | 32,557 | 20,344 | 23,198 | 120,968 | 75,470 | 35,528 | 29,275 | 32,314 | 150,966 | 64,438 | 46,339 |