Representation of the three haploSNP categories consisting of SNP-SNP (A), Indel-SNP (B), and SNP-in-Insertion (C). A) In the SNP-SNP (A) and indel-SNP (B) strategies the “critical form” of the destabilizing site, to which the probe is targeted, must be coupled to the SNP marker allele. Due to its asymmetric nature, a SNP-SNP or indel-SNP site can be probed only on one strand. A single probe is employed if the marker polymorphism is not A/T or G/C, while two probes are required if it is A/T or G/C. In the SNP-SNP strategy, the destabilizing SNP site must be present within 6 bp of the marker SNP site, while in the indel-SNP strategy, the destabilizing indel site must be present within 14 bp of the marker SNP site. In relation to the background alleles, the critical form of an indel destabilization site (B) can be either an insertion or a deletion. In the SNP-in-Insertion (C) strategy, the probe is expected to anneal only to the insertional form of an indel, and to interrogate a SNP polymorphism that resides within the insertion in one subgenome. A SNP-in-Insertion site can be probed on either or both strands.