The single SNP not detected is a substitution in the gene rrlE, which is duplicated 6 other times in the E. coli genome. In previous work, we noted the failure of CGS to detect a 9 bp duplication, a 1 bp deletion and a 28 bp deletion near a transcriptional terminator [8] . It appears that CGS has trouble in regions of high local secondary a. This number only includes those differences reported in reference 13, and not the new ones discovered in this study. b. The number of non-called ROI's that did not contain mutations was taken as the number of false positives for both IS-element insertions and indels.