Table 1.

Oligonucleotides primers and labeled probes used for detection of three synonymous SNPs specific of the Beijing 1071-32-cluster.

Gene, codon	Position in gene	Position in genome	Primer, probe, and sequence
Rv0144 74GCC/GCT	222 C>T	170505 C>T	170505F 5′-CCAACGGTAGGTACCAAGC 170505R 5′-GCTTCCGAGTCTCATCTGCT 170505C wt 5′-[HEX]GTTCAATGTCGCTCACGGC[C-LNA]G[BHQ1] 170505 T mut 5′-[FAM]GTTCAATGTCGCTCACGGC[T-LNA]G[BHQ1]
Rv0373c 98CCG/CCA	294 G>A	451510 C>T	451510F 5′-CGCATCGATGTGACTGCC 451510R 5′-CACGGCTTGTACGTCGTTG 451510G wt 5′-[HEX]GCCTGGCTTGGATGCC[G-LNA]ACA[BHQ1] 451510A mut 5′-[FAM]GCCTGGCTTGGATGCC[A-LNA]ACA[BHQ1]
Rv0334 87GCG/GCA	261 G>A	398918 G>A	398918F 5′-GAGTGAACATCAGCTACGC 398918R 5′-GGCCGTAGAAGATGTTGTC 398918G wt 5′-[HEX]TCAGCCTGACGGTCTGGC[G-LNA]CA[BHQ1] 398918A mut 5′-[FAM]TCAGCCTGACGGTCTGGC[A-LNA]CA[BHQ1]

wt, wild type; mut, mutant; LNA, locked nucleic acid.