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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)

From: Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

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