Table 3. High quality SNPs in L.monocytogenes 4b H7858 and L.monocytogenes 1/2a F6854 when compared with L.monocytogenes 4b F2365.

	L.monocytogenes 4b H7858	L.monocytogenes 1/2a F6854
Total high quality SNPs	8605	105 050
Intergenic SNPs	653	6780
Synonymous SNPs	5968	81 459
Codon position 1	233	3736
Codon position 2	3a	17a
Codon position 3	5732	77 706
Non-synonymous SNPs	1984	16 811
Codon position 1	915	7328
Codon position 2	687	5121
Codon position 3	732	4362
Transition rate	70.1%	68.3
Transversion rate	39.9%	31.7%

^aSynonymous SNPs at the second position of a stop codon TGA→TAA or synonymous SNPs at both the first and second position of a serine codon.