Different Random Sets
| Set | Ctgs | F− | F+ | Qs | Order | Order/no Qs[iii] |
| 1 | 42 + 1 | 102 − 59 | 59 | 112 (13) | (2770, 3400, 9) | (186, 220, 0) |
| 2 | 43 + 2 | 95 − 50 | 108 | 48 (12) | (2861, 3414, 1) | (395, 475, 0) |
| 3 | 38 + 1 | 88 − 49 | 91 | 145 (14) | (3024, 3634, 25) | (414, 458, 1) |
| 4 | 44 + 4 | 92 − 44 | 123 | 243 (16) | (2871, 3416, 10) | (391, 458, 1) |
| 4[iv] | 27 + 0 | 35 − 9 | 236 | 8 (1) | (111, 16, 0) | (84, 11, 0) |
| 4[v] | 6 + 0 | 7 − 2 | 312 | 22 (1) | (508, 422, 1) | (4, 1, 0) |
[i] (Ctgs) contigs; (F−) false-negative; (F+) false-positive; (Qs) questionable.
[ii] Each of the first four sets is a different random selection of 16,692 clones from the same pool, a 25× coverage with clone lengths of 130–190 kb, and one marker per 45 kb, and there is one chimeric contig. The error includes end fragments, 4% F+, 4% F, and the tolerance distribution of (16, 20, 18, 15, 12, 9, 6, 4). All the data sets were assembled with a 7 tolerance, 1e-10 cutoff with cutoff plus marker table (1 1e-08, 2, 1e-07, 3 1e-06). On the average, 17% of the clones are buried. The data sets assembled without markers resulted in 143, 155, 137, and 138 contigs, respectively.
[iii] The second order triplet is for the contigs with no Q clones.
[iv] The data set is the same as the previous one but without error. The set with error has 28 F+ clones with an average of 7 F+ overlaps per clone, whereas the set without error has 32 F+ clones with an average of 13 F+ overlaps per clone.
[v] The data set is the same as the previous one that has no error but is assembled with a tolerance of 0 and a cutoff of 1e-12. The largest contig with no F+'s has 4738 clones and two out-of-order pairs.