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Table 3 SNP content of the major nodes identified in the phylogenetic tree (cladogram)

From: Whole genome single nucleotide polymorphism based phylogeny of Francisella tularensis and its application to the development of a strain typing assay

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
  1. * contains all the type B strains with the exception of FRAN024, Japanese holarctica strain.
  2. 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.