Comparison of the three assemblies for the subset of the 21 BACs from the Rat genome.

The “original Atlas with UMD Plausible” and “original Atlas with UMD reliable” assembly results obtained by substituting Phrap for PhrapUMD with UMD plausible and reliable overlaps respectively. The best assembly (the bottom line) uses PhrapUMD and UMD reliable overlaps utilizing the 2-pass approach described in the “Methods” section. It has almost 3% more sequence matching finished sequence than original Atlas with Phrap at less than 1/4 the original base error rate.