Small variable segments constitute a major type of diversity of bacterial genomes at the species level

Table 1 Characteristics of the four whole-genome alignments, involving five strains each

	*E. coli*	*E. coli*B2	*S. aureus*	*S. pyogenes*
Median genome size (Mb)	5.2	5.2	2.8	1.8
Maximal MUMi distance	0.3	0.156	0.197	0.175
Coverage^a	72.7%	83.5%	84.5%	83.5%
Percent identity of backbone	98.05%	99.43%	98.73%	99.18%
Total number of loci^b	1,037	539	768	344
Number of microdiversity loci	640	370	556	250
Median size of VS (bp)^c	93	68	78	61

^aProportion of the genome included in the backbone (average). ^bPositions in the alignment where the backbone is interrupted by at least one variable segment (VS).

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