Table 3 Statistics for glocal alignment of real human optical maps from GM12878 HapMap cell line
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 |