Additional file 2: of Efficacy of a workplace osteoporosis prevention intervention: a cluster randomized trial

Result description and Sensitivity analysis report. (PDF 221 kb

Coverage across virulence genes detected in the assemblies of the seven <i>S</i>. Typhi isolates when screened against VFDB.

Coverage across virulence genes detected in the assemblies of the seven S. Typhi isolates when screened against VFDB.</p

Proportion of the classified bacteria reads from the kitome.

Classification was performed against Centrifuge’s prebuild p+h+v index (12/06/2016 version). Image was generated using Krona version 2.8. (TIF)</p

Inferred insertion site of IS<i>10R</i> based on analogous positions in 129-0238-M.

Inferred insertion site of IS10R based on analogous positions in 129-0238-M.</p

Multiple genomic comparison of the genomes in this study.

The reference genome, as demarcated in the figure, is presented in the centre of the ring. Each coloured rings represents a different query genome and coloured regions represent BLASTN matches to the reference. Query genomes along with percent BLASTN identity are colour coded in the figure key. The outermost ring in alternating red and blue represent the contigs of the reference genome, separated by black lines. Image was generated using BRIG version 0.95-dev.0004. (TIF)</p

Separation of the seven isolates into three subpopulations.

(A) ML tree based on core SNP alignments of the seven isolates along with contextual sequences. Number of detected homoplasic SNPs are labelled on the branches. Number of nucleotide substitutions per site is represented in the scale bar. (B) Comparison of 41 SNPs between the seven S. Typhi pseudomolecules and the reference genome. Discriminatory SNP positions are marked in the figure and expanded upon in Table 2. S. Typhi populations of the source genomes are represented next to the isolate name and colour-coded according to the Figure Key. Image was generated using snipit (https://github.com/aineniamh/snipit).</p

Additional file 1: Table S1. of Whole genome sequencing of Salmonella Typhimurium illuminates distinct outbreaks caused by an endemic multi-locus variable number tandem repeat analysis type in Australia, 2014

Genomic features of SNPs identified. (XLS 33 kb