Instead of clone-by-clone assemblies, the Rat genome assembly is pieced together from Bactig assemblies, which are reassemblies of the reads from sets of overlapping skimmed BAC clones, including mapped whole genome shotgun (WGS) reads. The assembly process reworks the contigs (splitting some) and selects them under more stringent criteria than used for the BAC submissions.
Thanks to Paul Havlak at the Baylor College of Medicine Human Genome Sequencing Center for providing the data.