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Table 3 SNP location, primers and PCR designed for pyrosequencing analysis

From: Single nucleotide polymorphism (SNP) analysis used for the phylogeny of the Mycobacterium tuberculosis complex based on a pyrosequencing assay

PCR primer sequence (5′ → 3′)

Geneª

SNP locationª

PCRb

Amplicon (bp)b

Forwardb

Reverseb

dnaA:dnaN

1977

Multiplex 1

131

[M13] - TGAGAAGCTCTACGGTTGTTGTTCG

TTTCACCTCACGATGAGTTCGATCC

(Rv0001:Rv0002)

Rv0260c

311613

114

CACCACTGTTGCCACGATGTTCTT

[M13] - GGCGACTTGCTACGCGTCCTAC

icd2 (Rv0066c)

74092

Multiplex 2

88

[M13] - GACGGTCCGAATTGCCTTGG

GACCAGGAGAAGGCCATCAAAGAG

phoT (Rv0820)

913274

141

GCAATCGCCGTGCAACC

[M13] - CTGCATGTTATGGGTGACGATGAC

Rv0095c

105139

Multiplex 3

94

ATAACGTCGGGCACTGACAAAGAG

[M13]-TCCCGTATCAACTCGTAGGATCTGG

Rv0197

232574

81

CCACGGCGGGGACAAGAT

[M13] -AGAAAGGCGCCGCTGTAGG

qcrB (Rv2196)

2460626

Multiplex 4

120

[M13] - GGGCTCGCAGCCAGACTTC

ATGATCACGGCGACCCAGAC

leuB (Rv2995c)

3352929

108

[M13] - TCGACGTCCGGGTAGCATTC

GCGTCGCAAGCATCTGACATT

gyrA (Rv0006)

codon 95

Simplex

320

CAGCTACATCGACTATGCGA

[M13] - GGGCTTCGGTGTACCTCAT

    

Universal primer

 
    

[M13]: CGCCAGGGTTTTCCCAGTCACGAC

 
  1. aGene name and SNP location in M. tuberculosis H37Rv genome map (http://tuberculist.epfl.ch/). One gene is listed when SNP location is situated in that gene and two genes are listed when SNP is intergenic.
  2. bPCR name, amplicon expected size, and primers used.