The one large deletion present in the genome sequence was easily detected, though the chromosomal inversion was not. We conclude that the accuracy of CGS is sufficient for effective resequencing studies, but with some precautionary notes. All clusters of non-called ROI probes should be PCR amplified and Sanger sequenced to detect IS-element insertions and small indels. Also, multiple replicates and/or site-directed mutagenesis should be used in cases where rare false negatives may affect the scientific interpretation.