Overall, our analyses indicate that, on average, single base insertion probes show substantially lower reproducibility across experiments than base substitution, one base deletion and two base deletion probes. The increased inter-and intrasample variability in hybridization specificity of single base insertion and deletion probes relative to single base substitution and two base deletion probes should be considered when designing and interpreting microarray-based screens for genetic variation. For a given microarray design, substantially more control hybridization experiments may be needed to determine baseline fluctuations in the hybridization specificities of insertion and deletion probes relative to those of substitution probes.