Table 5.
Microrearrangements scenarios on applying MGR independently to genes/anchors within synteny blocks
| Gene-based
|
Sequence-based
|
||||||
|---|---|---|---|---|---|---|---|
| Run | gene4 | gene7 | gene10 | gene20 | 100K | 200K | 300K |
| Blocks | 627 | 586 | 567 | 518 | 583 | 474 | 430 |
| Conserved blocks | 0.758 | 0.660 | 0.628 | 0.577 | 0.425 | 0.259 | 0.193 |
| Perfect match | 0.016 | 0.026 | 0.026 | 0.037 | 0.177 | 0.251 | 0.298 |
| Mismatch | 0.002 | 0.007 | 0.009 | 0.010 | 0.003 | 0.006 | 0.016 |
| Inconclusive | 0.982 | 0.967 | 0.965 | 0.953 | 0.820 | 0.743 | 0.686 |
| Microrearrangements | 272 | 383 | 437 | 543 | 1408 | 1941 | 2329 |
| Microrearrangements (force topology) | 273 | 387 | 442 | 548 | 1410 | 1944 | 2336 |
“Blocks” indicates the number of synteny blocks in each run. “Conserved blocks” stands for the fraction of synteny blocks in which gene/anchor order is preserved in human-mouse-rat-chicken. “Perfect match” is the fraction of recovered topologies that agrees with the known topology for these four genomes (this requires the internal edge to have at least one rearrangement). “Mismatch” is the fraction of recovered topologies that do not agree with the known topology. “Inconclusive” is the fraction of recovered topologies with a zero-length internal edge, which cannot be used to verify any topology. “Microrearrangements” indicates the total number of rearrangements within these synteny blocks. “Microrearrangements (force topology)” is similar, but the scenario is computed with the constraint that it must obey the correct topology.