Skip to main content

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