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Table 2 Number of total single nucleotide polymorphisms (SNPs) identified by Parsnp as well as number of informative SNPs after pruning variants with a LD r2 = 1 on the chromosome, pO157 plasmid, and in some cases clade specific plasmids

From: Rates of evolutionary change of resident Escherichia coli O157:H7 differ within the same ecological niche

Clade

Percentage of Similarity in clade

Number of Samples in clade

Number of Variants Identified

After pruning number in Chromosome

After Pruning number in pO157

Other (plasmids specific to clade)

Total of Informative SNPs

Overall

88.3%

181

2386

186

23

N/A

209

1: stx2c

90.5%

59

347

118

2

1 (6.1 kb)

121

2: stx1a stx2c

90.8%

47

351

74

6

4 (40 kb)

84

3: mixed

90.0%

32

343

48

5

N/A

53

4: stx1a stx2a

90.3%

37

671

74

5

N/A

79