Diagnostic SNPs. Subspecific-origin assignments with diagnostic SNPs overlaid within a fine-scale window. Diagnostic SNPs are similarly indicated by color. Diagnostic SNPs were determined by  based upon whether each SNP variant was unique to a particular subspecies, and categorized as either fully informative (common to all members of the subspecies) or partially informative (occurring within some members of the subspecies). The SNPs with diagnostic alleles are displayed as individual bars with the height representing the confidence with which that allele indicates the particular subspecies. The subspecific origin intervals are computed using an HMM over the set of diagnostic SNPs for each strain, as described in .