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Table 3 Statistics for glocal alignment of real human optical maps from GM12878 HapMap 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
21157LB (r) 73,365 (7.2X) Avg. quality 0.50; 295 kbp, 18 f; AFS 16.5 kbp 25 % 9 % 3X 2X 21 f | 324 kbp 66 % 0.74 –0.69
  (s) 38,483 (4.7X) Avg. quality 0.53; size 368 kbp, 22 f; AFS 17 kbp 36 % 14 % 2.6X 1.7X 23 f | 361 kbp 65 % 0.73 –0.58
21159LB (r) 75,761 (7.6X) Avg. quality 0.47; size 300 kbp, 17 f; AFS 17.4 kbp 19 % 5 % 4X 1.6X 19 f | 325 kbp 63 % 0.72 –1.07
  (s) 41,236 (5.1X) Avg. quality 0.50; size 370 kbp, 21 f; AFS 17.8 kbp 27 % 8 % 3.4X 1.3X 21 f | 359 kbp 62 % 0.72 –0.97
21431LB (r) 93,896 (8.6X) Avg. quality 0.52; size 274 kbp, 17 f; AFS 15.8 kbp 20 % 8 % 2.6X 1.9X 21 f | 305 kbp 68 % 0.77 –0.42
  (s) 43,667 (5.1X) Avg. quality 0.54; size 348 kbp, 21 f; AFS 16.3 kbp 30 % 13 % 2.4X 1.5X 23 f | 343 kbp 67 % 0.77 –0.29
21443LB (r) 66,857 (6X) Avg. quality 0.51; size 271 kbp, 17 f; AFS 15.8 kbp 19 % 7 % 2.7X 1.3X 20 f | 299 kbp 67 % 0.77 –0.50
  (s) 29,991 (3.5X) Avg. quality 0.53; size 346 kbp, 21 f; AFS 16.3 kbp 29 % 12 % 2.5X 1X 23 f | 340 kbp 66 % 0.77 –0.35
TOTAL (r) 309,879 (29.4X) Avg. quality 0.50; size 285 kbp, 17 f; AFS 16.4 kbp 21 % 7 % 2.9X 6.8X 21 f | 314 kbp 66 % 0.75 –0.66
  (s) 153,377 (18.3X) Avg. quality 0.52; size 359 kbp, 21 f; AFS 16.9 kbp 31 % 11 % 2.7X 5.5X 23 f | 352 kbp 65 % 0.75 –0.55
  1. Statistics are reported independently for each map card of GM12878 cell line, using: (r) relaxed filtering: ≥ 10 fragments and 150kbp; and (s) stringent filtering: ≥ 12 fragments and 250kbp (as shown in column F). From left to right are reported: the total number of input maps and their coverage in bases of the human genome; further details such as average map quality (provided by the Argus machine), average map size in bases and length in fragments, and average fragment size (AFS); aligned maps by OPTIMA and Gentig v.2; OPTIMA alignment rate increase with respect to Gentig v.2; other OPTIMA alignment statistics
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