A high false discovery rate is generally not a problem with resequencing projects. The cost of PCR amplifying and Sanger sequencing up to 100 candidate regions is small compared to the cost of resequencing itself. The false negative rate on the other hand is very important. In order to associate genotypic change to phenotypic change it is critical to know with some certainty that all of the important mutations were detected. Nimblegen estimates that the false negative rate for SNPs is less than 5% (Tom Albert, personal communication). We found that only half of the small sequence differences actually present were reported as SNPs. If we consider detection in ROI probes as well, then 7 out of 8 small sequence differences were detected, yielding a false negative rate of 12.5%. Given the small sample size, this rate may be consistent with Nimblegen's claims. CGS is meant for the detection of SNPs, but ROI data also reveals deletions and IS-element insertions. The false negative rate for detection of IS element insertions was double the rate for small sequence differences, possibly because CGS has not been optimized for detection of insertions. Conceptually, insertions and inversions could result in a more pronounced hybridization difference at the insertion site. If the insertion site/inversion breakpoint occurs in the middle of the region covered by a probe, then genomic DNA will only match one half of the probe or the other. Detection of insertions might be improved by manipulation of the hybridization/wash conditions or changes to the algorithm to specifically identify probe series indicative of insertions.