Nucleotide alignment of concatenated SNPs. The consensus sequence is shown above the alignment, with a threshold of 75 %. Mean pairwise identity over all pairs in the column is also shown below the consensus. Green: 100 % identity, khaki: at least 30 % identity but less than 100 % identity, Red: less than 30 % identity. Differences from the consensus are highlighted with Clustal colors. (TIF 2136 kb
Figure S7. Correlation between genome size, pan-genome size, and effective population sizes as compu...
Results of polymerase chain reaction (PCR) amplification using specific primers of significant singl...
Alignments from Analyses. All alignments and topologies of one-to-one orthologs used for analyses of...
Functional analysis of genes carrying non-synonymous and synonymous SNPs. a nsSNPs. b sSNPs. Genes c...
Mapping of G6 reads to the reference GR4 pSymB. a Region spanning 48 kb (800,349 to 848,330) and dis...
Dendrograms based on GR4-type isolate DNA fingerprints constructed by the UPGMA method. a Based on t...
<p>The genomes were aligned by BioEdit and edited using Base-by-Base software. A consensus sequence ...
(A) Dinucleotide mutation bias among TE copies belonging to different TE orders. Mutation rates were...
<p>This fileset contains all the alignments used in the above manuscript. These sequences were colle...
Additional file 4: Fig. S3. Selected multiple alignments for 34 families with high fraction of conse...
Multilocus linkage disequilibrium (index of association IA). These analyses were based on 249 SNPs s...
<p>Non-identical nucleotides for genotypes A, D, F1b and F4 are shown. Nucleotides shared between ge...
This collection of data files contains, for each bacterial species: All raw genome sequence files...
(A) Phylogenetic inconsistency between individual single nucleotide variants (SNVs) and core-genome-...
Figure S8. Precision and recall statistics for scaffolding adjacencies on three artificially fragmen...
Figure S7. Correlation between genome size, pan-genome size, and effective population sizes as compu...
Results of polymerase chain reaction (PCR) amplification using specific primers of significant singl...
Alignments from Analyses. All alignments and topologies of one-to-one orthologs used for analyses of...
Functional analysis of genes carrying non-synonymous and synonymous SNPs. a nsSNPs. b sSNPs. Genes c...
Mapping of G6 reads to the reference GR4 pSymB. a Region spanning 48 kb (800,349 to 848,330) and dis...
Dendrograms based on GR4-type isolate DNA fingerprints constructed by the UPGMA method. a Based on t...
<p>The genomes were aligned by BioEdit and edited using Base-by-Base software. A consensus sequence ...
(A) Dinucleotide mutation bias among TE copies belonging to different TE orders. Mutation rates were...
<p>This fileset contains all the alignments used in the above manuscript. These sequences were colle...
Additional file 4: Fig. S3. Selected multiple alignments for 34 families with high fraction of conse...
Multilocus linkage disequilibrium (index of association IA). These analyses were based on 249 SNPs s...
<p>Non-identical nucleotides for genotypes A, D, F1b and F4 are shown. Nucleotides shared between ge...
This collection of data files contains, for each bacterial species: All raw genome sequence files...
(A) Phylogenetic inconsistency between individual single nucleotide variants (SNVs) and core-genome-...
Figure S8. Precision and recall statistics for scaffolding adjacencies on three artificially fragmen...
Figure S7. Correlation between genome size, pan-genome size, and effective population sizes as compu...
Results of polymerase chain reaction (PCR) amplification using specific primers of significant singl...
Alignments from Analyses. All alignments and topologies of one-to-one orthologs used for analyses of...