SNP detection performance. A, Performance of a single, sense strand probe: The ability of a single sense stranded probe overlapping a SNP to call the correct allele as a function of distance from the center of the probe to the SNP is shown. At a stringent P-value threshold of 10-4, approximately 65% of SNPs are called correctly using a probe centered exactly on the SNP (see haploid genotyping simulation section in Materials & Methods for a description of P-value calculations). B, Performance of an alternate probe when centered sense probe fails: When the centered probe fails to call the correct allele at a chosen threshold, the ability of one additional probe to rescue the call is shown as a function of strand and distance of the probe relative to the SNP. Probes on the sense strand at close distances to the SNP contribute little, presumably due to the same local constraints that caused the centered sense probe to fail, where as the opposite strand centered probe recovers 60% of missed calls at a threshold of 10-4. Therefore, at a threshold of 10-4, we achieve an 86% success rate.