To test the accuracy of CGS, E. coli strains W3110 Kohara and MG1655 were obtained from the E. Coli Genetic Stock Collection (CGSC). DNA was extracted and submitted to Nimblegen Systems Inc. for CGS, using MG1655 as the reference. Nimblegen reported 25 SNPs in strain W3110, 4 of which corresponded to known sequence differences. Regions surrounding the other SNPs were PCR amplified and subjected to Sanger sequencing. In this way, 19 of the remaining putative SNPs were refuted, though 2 were confirmed. These two mutations are not present in the W3110 genome sequence, and must have been introduced into the strain after Kohara et al. [14] made the lambda phage library that was sequenced. In sum, there were 19 false positive SNPs out of 25 reported, or one false positive per 244 kb ( Table 2 ). Figure 1 shows a sample of hybridization signals surrounding three different sequence differences. It can be seen that the ratio of signal intensities near the mutations were distinctly elevated. When these regions were resequenced at single bp resolution, the sequence differences in ycdT and acnA were correctly determined. The intensity of hybridization signals in other areas where there were no sequence differences varied considerably.