Table 3.
Varying Coverage
| Cov | Gap | Clones | Bury (%)a | Largest (order)b | F+ clonesc |
|---|---|---|---|---|---|
| 10× | 18 | 6676 | 62 | 506 (4, 2, 0) | 13 (3), 11 (2) |
| 20× | 3 | 13353 | 74 | 3529 (17, 2, 0) | 33 (9), 18 (2) |
| 30× | 0 | 20030 | 79 | 5306 (15, 2, 0) | 54 (9), 32 (2) |
| 40× | 0 | 26707 | 83 | 7110 (15, 2, 0) | 72 (9), 44 (2) |
| 50× | 0 | 33384 | 85 | 9534 (37, 4, 0) | 93 (9), 57 (2) |
| Cov | 1e-08 | 1e-10 | 1e-10, CpMd | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Ctgs | F− | F+ | Qs | Ctgs | F− | F+ | Qs | Ctgs | F− | Qs | |
| 10× | 135 | 144 | 29 | 30 (1) | 193 | 216 | 28 | 2 (1) | 92 | 80 | 4 (1) |
| 20× | 48 | 60 | 76 | 190 (3)e | 95 | 106 | 65 | 2 (1) | 24 | 25 | 18 (1) |
| 30× | 22 | 28 | 262 | 1229 (4) | 51 | 59 | 228 | 45 (1) | 9 | 11 | 81 (1) |
| 40× | 15 | 19 | 524 | 674 (3) | 34 | 38 | 465 | 62 (1) | 5 | 7 | 365 (1) |
| 50× | 12 | 15 | 941 | 1086 (3) | 27 | 28 | 778 | 204 (1) | 4 | 3 | 724 (1) |
(Cov) coverage; (CpM) cutoff plus marker; (Ctgs) contigs; (F−) false-negative; (F+) false-positive; (Qs) questionable.
The data set has perfect data, 145–185 kb clone lengths, a marker every 20 kb, and a tolerance of 7.
Percentage buried in which a buried clone has 90% or more shared bands with the parent clone.
The largest contig with no Q clones and its order triple.
The number of clones that have an F+ overlap for the 1e-08 and 1e-10 cutoff, respectively. In parentheses is the number of regions that have F+ overlaps. The number of F+ overlaps is the same for 1e-10 with or without markers.
The CpM rules are (1 1e-08) (2 1e-07) (3 1e-06).
There are four chimeric contigs, but the fourth does not have Q clones. The three F+'s occur at the end of two contigs and bridge the contigs with little difficulty, i.e., F+'s at the ends of contigs causing an incorrect merge may result in a number of extra bands and gaps that looks the same as error in the data.