144 Chapter 7 Figure S2. Distribution of the log10 Consistency Indexes of all genomic position based on the E. coli ampC_0069 reference genome, compared to the log10 Consistency Indexes of the promoter and attenuator region. attenuator promoter −1.5 −1.0 −0.5 0.0 ConsistencyIndex (log10) density 0.19% FIG S2 Distribution of the log10 Consistency Indexes of all genomic SNP positions based on the E. coli ampC_0069 reference chromosome, compared to the log10 Consistency Indexes of the promoter and attenuator region. Figure S3. Recombination events inferred from all 172 E. coli isolates by Gubbins displayed along the approximately maximum-likelihood phylogenetic tree based on the coreSNP alignment. Phylogroups are depicted as in FIG 2. Gubbins blocks are coloured red if they are ancestral, and blue if they only affect one isolate. The line graph represents the recombination prevalence along the sequence. The 24 positions with a significant association with cefotaxime resistance (FDR ≤0.05) and a consistency index ≤0.05882353 are indicated on the top of the figure. The two missense mutations and ampC promoter region are displayed in blue Phylogroup 44 88 132 1Mb 2Mb 3Mb 4Mb 5Mb 0bp 176 gspL thiM ampC promoter CladeIV Phylogroup FIG S3 Recombination events inferred from all 172 E. coli isolates by Gubbins displayed along the approximately maximum-likelihood phylogenetic tree based on the coreSNP alignment. Phylogroups are depicted as in FIG 2. Gubbins blocks are coloured red if they are ancestral, and blue if they only affect one isolate. The line graph represents the recombination prevalence along the sequence. The 24 positions with a significant association with cefotaxime resistance (FDR ≤0.05) and a consistency index ≤ 0.05882353 are indicated on the top of the figure. The two missense mutations and ampC promoter region are displayed in blue.
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