TABLE 3.

TaqMan real-time PCR genotyping SNP assay primers and probes

Phylogroup	Gene locus taga	SNP positionb	Forward primer	Reverse primer	Reference probe (FAM)c	Target probe (VIC)
B1	b1756	156	CCGTCTGGCTGTGGAAAATC	GCATGTCAATCCGTTGCTCATT	AAGAAAACTGTCCGGCCAG	CAAGAAAACTGTCCAGCCAG
B1	b3251	342	GCCCGCGCGTTCTG	TGCGCGGCGTTCAAC	AACCGGCACACAAA	CCAACCGGTACACAAA
B2	b0722	60	CCTCCGCATTAGGACGCAAT	GTAGAGCGTCAGGACGATAGC	CTCGTTCGCGCTACC	CCTCGTTCGTGCTACC
D	b1288	504	CGTTATGGGTCTGGCAAAAGC	GCGTTAACACGCACACCTT	TCTGGAAGCAAACGTG	TCTGGAAGCGAACGTG
E	b0405	57	ATGCGCGTTACCGATTTCTC	CAGCGACAGTAAACGACAGCTA	CGTTCAGGCATGGGAT	CGTTCAGGCATCGGAT

^aGene locus tag corresponds to E. coli K-12 MG1655.

^bSNP position indicates the SNP location in the nucleotide sequence of the indicated gene.

^cFAM, 6-carboxyfluorescein.