FIG. 1.

Alleles screened in this study. The ORF of each gene is shown as a thick line. Intergenic regions are indicated by thin lines. The position of each allele examined in this study is indicated to the left of the lines. Alleles tested inside an ORF are indicated by their codon positions; alleles tested within an intergenic region are indicated by their nucleotide positions relative to the start of the following ORF, except for ahpC, which is shown relative to the transcription start. The specific mutations examined in the HP assays are indicated in capital letters to the right of each gene. Several mutations are indicated when more than one mutant allele was tested at the same codon or nucleotide position. Deletions are indicated with the symbol “Δ,” and insertions are indicated with colons. Question marks (?) indicate the presence of a mutation detected and confirmed by a molecular beacon assay, but the exact nucleotide change was not identified because the sequencing results are inconclusive at that position. The total sequence examined by each molecular beacon is indicated by a line labeled with the name of that molecular beacon, starting with an MB prefix. Sequence accession numbers for katG, ahpC, kasA, ndh, and inhA are Z97193, Z79701, Z70692, BX842577, and Z79701, respectively. Genes and upstream regions are not drawn to scale. The sequences of the primers, molecular beacons, and sequencing primers used to detect or confirm these alleles are shown in Tables S1 to S3 in the supplemental material.