TABLE 1.
Summary of FPC map, BAC end sequences, and alignments of O. punctata
| Chromosome | Total no. contigs | Total no. of BACs | Total CB length (CB) | Estimated size (kb) (1.27 kb/CB)a | No. of OP BES | BES succ ratio | Genome representationb | % of OP BES (normalized) | No. of aligned OP BES (%) | O. sativa chromosome sizec (kb) | O. sativa pseudomolecules sizec (kb) | Covered length by alignment (kb) | % coverage of OP by the alignment | % coverage of O. sativa pseudomolecule by the aligment | % coverage of O. sativa chromosome by the alignment |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 17 | 3,698 | 36,689 | 46,595 | 6,922 | 94% | 10.5% | 11.5 (8.4) | 3,594 (52) | 45,050 | 43,261 | 42,211 | 91 | 98 | 94 |
| 2 | 11 | 3,121 | 32,965 | 41,866 | 5,872 | 94% | 10.0% | 9.8 (7.9) | 2,880 (49) | 36,780 | 35,954 | 36,392 | 87 | 101 | 99 |
| 3 | 13 | 3,043 | 32,197 | 40,890 | 5,716 | 94% | 9.9% | 9.5 (7.9) | 3,058 (53) | 37,370 | 36,190 | 35,424 | 87 | 98 | 95 |
| 4 | 10 | 2,823 | 27,678 | 35,151 | 5,317 | 94% | 10.7% | 8.8 (8.5) | 2,235 (42) | 36,150 | 35,489 | 35,185 | 100 | 99 | 97 |
| 5 | 18 | 2,456 | 24,014 | 30,498 | 4,606 | 94% | 10.7% | 7.7 (8.5) | 2,039 (44) | 30,000 | 29,733 | 29,723 | 97 | 100 | 99 |
| 6 | 17 | 2,813 | 28,987 | 36,813 | 5,308 | 94% | 10.2% | 8.8 (8.1) | 2,056 (39) | 31,600 | 30,731 | 28,960 | 79 | 94 | 92 |
| 7 | 18 | 2,338 | 24,781 | 31,472 | 4,377 | 94% | 9.9% | 7.3 (7.8) | 1,927 (44) | 30,280 | 29,644 | 29,536 | 94 | 100 | 98 |
| 8 | 12 | 2,324 | 22,838 | 29,004 | 4,360 | 94% | 10.7% | 7.3 (8.5) | 1,768 (41) | 28,570 | 28,435 | 29,205 | 101 | 103 | 102 |
| 9 | 16 | 2,271 | 22,088 | 28,052 | 4,281 | 94% | 10.8% | 7.1 (8.6) | 1,520 (36) | 30,530 | 22,693 | 22,442 | 80 | 99 | 74 |
| 10 | 15 | 2,240 | 21,413 | 27,195 | 4,206 | 94% | 11.0% | 7.0 (8.7) | 1,411 (34) | 23,960 | 22,684 | 20,366 | 75 | 90 | 85 |
| 11 | 14 | 2,582 | 24,798 | 31,493 | 4,814 | 93% | 10.9% | 8.0 (8.6) | 1,726 (36) | 30,760 | 28,358 | 27,401 | 87 | 97 | 89 |
| 12 | 15 | 2,326 | 23,085 | 29,318 | 4,384 | 94% | 10.6% | 7.3 (8.4) | 1,358 (31) | 27,770 | 27,562 | 25,800 | 88 | 94 | 93 |
| No chromosome | 32 | 701 | 7,902 | 10,000 | 1,293 | 92% | — | — | — | — | — | — | — | — | — |
| Singleton | — | 1,488 | — | — | 2,486 | 84% | — | — | — | — | — | — | — | — | — |
| FP failure | — | 3,640 | — | — | 4,442 | 54% | — | — | — | — | — | — | — | — | — |
| Total/average | 208 | 37,864 | 329,435 | 418,347 | 68,384 | 93% | 11.4% | 88.0 | 25,572 (43) | 388,820 | 370,733 | 362,645 | 87 | 98 | 93 |
FP, fingerprinting.
a
1 .27 kb/CB was obtained using the formula [real size of the clone/CB unit of the clone] by sizing 539 O. punctata BAC clones selected randomly.
b
Based on estimated O. punctata chromosome size.