Table 1.
Hybrid data assembly
| Organism | Sequencing gaps | Hard stop gaps | Average sequence gap size | Missing sequence | Base pairs in 1× or 0× coverage | Q20 BP in Scaff | Percent Q20 in scaffold | Physical gaps | N50 contig | Coverage | Genome size | Cost difference, % |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MIT9211 5.3× | 11 | 0 | 366 | 4,026 | 8,378 | 1,746,693 | 99.20 | 0 | 277,174 | 6 | 1,760,746 | −37.00 |
| MIT9211 5.3×–one 454 | 0 | 0 | 0 | 0 | 222 | 1,763,720 | 97.66 | 0 | 1,847,284 | 24 | 1,806,060 | 19.13 |
| MIT9211 5.3×–two 454 | 0 | 0 | 0 | 0 | 133 | 1,765,790 | 97.65 | 0 | 1,688,962 | 42 | 1,808,271 | 52.00 |
| MIT9211 two 454 only | 9 | 0 | 394 | 3,546 | 1,499 | 1,707,409 | 99.62 | 0 | 427,124 | 36 | 1,713,978 | 6.55 |
| MIT9211 8×–0 454 | 1 | 0 | 20 | 20 | 31 | 1,854,846 | 97.92 | 0 | 1,228,306 | 10 | 1,894,186 | 0.00 |
| HTCC2594 5.3× | 50 | 0 | 600 | 30,000 | 47,037 | 3,030,260 | 98.80 | 0 | 78,081 | 5 | 3,066,971 | −26.00 |
| HTCC2594 5.3×–one 454 | 11 | 0 | 746 | 8,206 | 5,161 | 3,048,942 | 99.61 | 0 | 265,562 | 15 | 3,060,803 | 9.42 |
| HTCC2594 5.3×–two 454 | 0 | 0 | 0 | 0 | 1,273 | 3,053,801 | 99.93 | 0 | 3,053,801 | 34 | 3,055,839 | 24.28 |
| HTCC2594 8×–one 454 | 1 | 0 | 156 | 156 | 386 | 3,053,178 | 99.98 | 0 | 1,655,186 | 18 | 3,053,827 | 26.50 |
| HTCC2594 8×–two 454 | 0 | 0 | 0 | 0 | 150 | 3,053,677 | 100.00 | 0 | 3,053,801 | 37 | 3,053,801 | 36.60 |
| HTCC2594 two 454 only | 50 | 0 | 4,863 | 243,150 | 6,019 | 3,029,260 | 92.34 | 0 | 125,688 | 29 | 3,280,646 | −14.00 |
| HTCC2594 8×–0 454 | 4 | 0 | 158 | 632 | 4,817 | 3,051,930 | 99.93 | 0 | 865,987 | 9 | 3,054,012 | 0.00 |
| HTCC2649 5.3× | 156 | 28 | 646 | 100,776 | 60,499 | 4,165,998 | 97.37 | 0 | 44,457 | 5 | 4,278,365 | −3.00 |
| HTCC2649 5.3×–1 454 | 61 | 11 | 235 | 14,335 | 29,059 | 4,216,813 | 99.40 | 0 | 121,019 | 12 | 4,242,346 | 2.00 |
| HTCC2649 5.3×–two 454 | 15 | 4 | 1,177 | 17,655 | 19,626 | 4,235,057 | 99.21 | 0 | 489,600 | 21 | 4,268,677 | 13.35 |
| HTCC2649 8×–one 454 | 38 | 11 | 248 | 9,424 | 14,016 | 4,233,589 | 99.64 | 0 | 200,552 | 15 | 4,249,087 | 22.12 |
| HTCC2649 8×–two 454 | 3 | 3 | 13 | 40 | 15,259 | 4,233,767 | 99.97 | 0 | 1,221,599 | 25 | 4,235,038 | 31.26 |
| HTCC2649 two 454 only | 114 | 20 | 6,757 | 770,298 | 12,073 | 4,117,973 | 83.57 | 1 | 54,348 | 16 | 4,927,326 | −33.00 |
| HTCC2649 8×–0 454 | 107 | 76 | 58 | 6,206 | 19,320 | 4,223,352 | 99.72 | 68,491 | 9 | 4,235,057 | 0.00 | |
| S14 5.3× | 266 | 0 | 983 | 261,478 | 149,819 | 5,072,226 | 94.76 | 10 | 29,979 | 5 | 5,352,635 | −24.00 |
| S14 5.3×–one 454 | 120 | 0 | 1,278 | 153,360 | 54,485 | 4,965,321 | 96.50 | 11 | 61,684 | 10 | 5,145,225 | 4.61 |
| S14 5.3×–two 454 | 30 | 0 | 4,500 | 135,000 | 15,594 | 5,044,842 | 97.20 | 5 | 351,723 | 17 | 5,190,011 | 17.97 |
| S14 8×–one 454 | 26 | 0 | 2,878 | 74,828 | 15,130 | 5,027,642 | 98.39 | 6 | 313,097 | 12 | 5,109,753 | 22.11 |
| S14 8×–two 454 | 18 | 0 | 4,000 | 72,000 | 8,493 | 5,095,940 | 98.35 | 5 | 404,679 | 21 | 5,181,460 | 31.25 |
| S14 two 454 only | 125 | 0 | 9,529 | 1,191,125 | 18,500 | 4,768,229 | 78.54 | 95 | 22,966 | 13 | 6,070,860 | −33.00 |
| S14 8×–0 454 | 59 | 0 | 1,979 | 116,761 | 57,071 | 5,047,120 | 98.94 | 6 | 139,234 | 8 | 5,101,447 | 0.00 |
| CNPT3 5.3× | 297 | 0 | 1,009 | 299,673 | 105,754 | 2,698,477 | 89.27 | 8 | 14,163 | 4 | 3,022,992 | −18.00 |
| CNPT3 5.3×–one 454 | 107 | 0 | 1,232 | 131,824 | 40,304 | 2,973,045 | 94.84 | 5 | 67,811 | 11 | 3,134,706 | 20.83 |
| CNPT3 5.3×–two 454 | 12 | 0 | 3,400 | 40,800 | 8,884 | 3,038,758 | 97.62 | 0 | 286,979 | 23 | 3,112,910 | 34.73 |
| CNPT3 8×–one 454 | 42 | 0 | 2,316 | 97,272 | 20,524 | 3,038,403 | 96.74 | 1 | 127,506 | 13 | 3,140,913 | 30.90 |
| CNPT3 8×–two 454 | 12 | 0 | 3,387 | 40,644 | 9,610 | 3,070,512 | 98.38 | 0 | 286,979 | 24 | 3,121,209 | 41.73 |
| CNPT3 two 454 only | 88 | 0 | 2,977 | 261,976 | 7,480 | 2,918,009 | 90.91 | 18 | 44,842 | 19 | 3,209,644 | 5.72 |
| CNPT3 8×–0 454 | 136 | 0 | 1,305 | 177,480 | 58,925 | 2,932,134 | 95.31 | 3 | 47,074 | 6 | 3,076,427 | 0.00 |
| D2 5.3× | 437 | 0 | 417 | 182,303 | 196,439 | 4,808,623 | 98.47 | 28 | 14,970 | 4 | 4,883,418 | −42.00 |
| D2 5.3×–one 454 | 254 | 0 | 380 | 96,523 | 118,977 | 4,895,192 | 99.05 | 27 | 26,468 | 8 | 4,942,189 | −16.00 |
| D2 5.3×–two 454 | 37 | 0 | 614 | 22,733 | 39,971 | 4,934,010 | 99.31 | 12 | 155,774 | 15 | 4,968,469 | −1.00 |
| D2 8×–one 454 | 16 | 0 | 1,161 | 18,570 | 40,346 | 4,944,178 | 99.46 | 12 | 269,204 | 13 | 4,971,208 | 20.56 |
| D2 8×–two 454 | 5 | 0 | 2,430 | 12,148 | 28,912 | 4,975,666 | 99.62 | 10 | 660,254 | 20 | 4,994,573 | 29.29 |
| D2 two 454 only | 77 | 0 | 9,320 | 717,640 | 16,195 | 4,593,629 | 84.54 | 130 | 21,045 | 12 | 5,433,827 | −62.94 |
| D2 8×–0 454 | 23 | 0 | 986 | 22,685 | 42,629 | 4,921,016 | 98.77 | 14 | 253,418 | 9 | 4,982,425 | 0.00 |
Comparison of gaps (type and size), base pairs in low-coverage areas and high-quality areas, as well as coverage, N50 numbers, and cost differentials. The assembly quality score is a rough indication of assembly quality, with a higher number being an assembly of lower quality based on the equation in the table.