Table 3.

SNP content of the major nodes identified in the phylogenetic tree (cladogram)

Node	Sub-species/clade/sub-clade	Number of strains per node	Total SNPs	Total SNPs in LVS genome	Total SNPs in SchuS4 unique sequence	Common SNPs	Unique SNPs	Differentiating SNPs	Maximum SNP separation
50	B	13	3771	3686	85	5	2837	3656	2833
51	B*	12	1154	1115	39	6	233	1060	602
52	B1	7	779	750	29	385	164	161	76
64	B2	5	705	677	28	7	153	628	549
4	A	26	8653	8559	94	2905	514	3765	2779
39	A2	6	6003	5919	84	3789	358	316	201
5	A1	20	7306	7291	15	4953	323	497	176
8	A1a	9	7001	6993	8	5491	277	129	75
23	A1b	10	7030	7022	8	5537	234	71	38

* contains all the type B strains with the exception of FRAN024, Japanese holarctica strain.

Total SNPs are locations at which a SNP occurs in one or more strains in the node (if the same SNP occurs in more than one strain, that location is counted only once). Common SNPs are locations where all strains in the node share the same base call, which is different from the reference call on the resequencing platform. Unique SNPs are locations where just a single strain in the node has a base call that differs from the reference sequence. Differentiating SNPs are locations at which at least two strains in the node have different base calls. Maximum SNP separation is the number of base calls separating the two most distant members of the node. Differentiating SNPs and maximum SNP separation are both indicators of the degree of diversity within the node. The detection of diversity is limited by the extent to which our sample set is representative of the variability within each clade in nature. Refer to Figure 2 for the details of strain clustering.