Table 1 SNPs markers, primers and probes used in RT-PCR

Rv004c-0619n (MTB L4-U)

Forward:5-ATT GCT CGA TGG CAG A-3

^a62 °C

68 °C

57 °C

160

Reverse: 5-AAA CCA GGT ACT TGT CGG-3

LC Red 640-TGA TGA CGG AAA GCC GT GAA A-Pho-3

5-GTT TTC GCG GTA GGT GCC CTC GAT G-Fluo-3

Rv2962c-0711 s (MTB L4-NU)

Forward: 5-GAA CGC CCT TTG CTC TTC-3

56 °C

^a64 °C

51 °C

181

Reverse:5-CAA GGT ACT CGT GGT TGG-3

LC Red 610- CCC GAG CTG ATG CCC ACC T-Pho-3

5-CAC ACC CTG TAT GC GAC G-Fluo-3

Rv0129c-0472n (MTB L3)

Forward:5-CGA CTG GTA TCA GCC CTC-3

^a58 °C

68 °C

53 ° C

191

Reverse:5-GGA ACT GCT GCG GGT AGT A-3

LC Red 610-GAC ACG CC TTG TTG GCC-Pho-3

5-CGC CGC GTT GCC TGT CG –Fluo-3