We evolved populations of E. coli under strict genetic drift effects by transferring a single colony daily to a fresh plate. The E. coli is the strain K12 substrain MG1655 with a mutS deletion. Two evolved populations were sequenced at two time points of the evolution experiment, including one at 85 passages and another at 180 passages. The ancestral parental genome was sequenced by 454 and representative colonies of each of the two populations were sequenced at the two isolation time points.