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Table 4 Statistics for glocal alignment of real human optical maps from HCT116 colorectal cancer cell line

From: OPTIMA: sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis

Map card F Input maps Details OPTIMA Gentig v.2 Increase w.r.t. Gentig v.2 Yield (genome coverage) Avg. length and size Avg. digestion rate Avg. false/extra cut rate Avg. WHT chi square sizing error
17182LA (r) 10,911 (0.9X) Avg. quality 0.33; size 257 kbp, 16 f; AFS 15.7 kbp 4 % 0.5 % 8.1X 0.04X 19 f | 245 kbp 66 % 1.29 –1.15
  (s) 3,744 (0.4X) Avg. quality 0.33; size 351 kbp, 20 f; AFS 17.7 kbp 4 % 0.9 % 4.5X 0.02X 22 f | 326 kbp 63 % 1.23 –0.83
17184LA-2 (r) 55,719 (5.7X) Avg. quality 0.43; size 305 kbp, 19 f; AFS 16.3 kbp 18 % 9 % 1.9X 1.1X 23 f | 332 kbp 68 % 0.76 –0.65
  (s) 28,658 (3.7X) Avg. quality 0.45; size 390 kbp, 23 f; AFS 17.2 kbp 25 % 15 % 1.6X 0.9X 25 f | 378 kbp 67 % 0.74 –0.51
17185LA (r) 56,879 (5.4X) Avg. quality 0.55; size 285 kbp, 19 f; AFS 14.7 kbp 24 % 18 % 1.4X 1.5X 23 f | 325 kbp 70 % 0.76 –0.17
  (s) 28,003 (3.4X) Avg. quality 0.59; size 365 kbp, 24 f; AFS 15.1 kbp 35 % 28 % 1.2X 1.2X 26 f | 367 kbp 70 % 0.74 –0.04
17186LA-3 (r) 52,984 (5.8X) Avg. quality 0.54; size 328 kbp, 20 f; AFS 16.0 kbp 33 % 19 % 1.7X 2X 24 f | 342 kbp 70 % 0.68 –0.35
  (s) 31,588 (4.3X) Avg. quality 0.56; size 404 kbp, 25 f; AFS 16.4 kbp 42 % 28 % 1.5X 1.7X 26 f | 380 kbp 69 % 0.67 –0.26
17187LA (r) 88,730 (7.8X) Avg. quality 0.45; size 264 kbp, 18 f; AFS 14.8 kbp 12 % 7 % 1.7X 1X 21 f | 285 kbp 69 % 0.94 –0.56
  (s) 36,018 (4.2X) Avg. quality 0.46; size 349 kbp, 22 f; AFS 15.8 kbp 17 % 11 % 1.6X 0.7X 24 f | 338 kbp 68 % 0.92 –0.35
14593LB (r) 30,994 (2.7X) Avg. quality 0.39; size 261 kbp, 14 f; AFS 18.9 kbp 6 % 0.6 % 9.9X 0.2X 16 f | 269 kbp 63 % 0.85 –1.23
  (s) 10,944 (1.2X) Avg. quality 0.39; size 337 kbp, 17 f; AFS 20.2 kbp 9 % 0.7 % 12.3X 0.1X 18 f | 320 kbp 60 % 0.87 –0.97
TOTAL (r) 296,217 (28.3X) Avg. quality 0.47; size 287 kbp, 18 f; AFS 15.7 kbp 18 % 11 % 1.7X 5.7X 23 f | 322 kbp 69 % 0.77 –0.44
  (s) 138,955 (17.2X) Avg. quality 0.50; size 372 kbp, 23 f; AFS 16.5 kbp 27 % 18 % 1.5X 4.6X 25 f | 368 kbp 68 % 0.75 –0.28
  1. Statistics are reported for each map card of HCT116 cell line using the relaxed filtering (r) and the stringent filtering (s), similarly as in Table 3 These results further suggest a mean yield of 1.25 × and 1 × for (r) and (s), respectively, in terms of aligned coverage of the human genome per map card using OPTIMA
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