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.