In addition to SNPs, Nimblegen also provided the location of probes that showed hybridization differences, yet could not be resolved as SNPs ("non-called Regions Of Interest" or ROIs). These probes may indicate the presence of mutations other than SNPs, such as insertions or deletions. Nimblegen reported 1094 ROI probes located in 36 clusters, a cluster being a group of probes that are within 500 bp of each other. One of these clusters corresponded to the known 6.6 kb deletion of intZ thru yffS (b2442-2450) ( Table 1) . Three other clusters corresponded to known sequence differences that were not reported as SNPs -the substitutions in rpoS and crp and the 2 bp insertion in dcuA. Nine clusters corresponded to known IS-element insertions in W3110. Most of the IS-element insertions were evident as clusters consisting of multiple ROI probes, though three were only evident as singleprobe clusters. There were three IS element insertions that were not detected as either SNPs or ROIs. The large inversion in W3110 of all genes between ribosomal RNA genes rrlD and rrlE was not detected as either SNPs or ROIs.