129 Genome-wide analysis in E. coli unravels homoplasy associated with cefotaxime resistance Figure 2. Approximately maximum-likelihood phylogenetic tree of all 172 E. coli isolates based on the coreSNP alignment with the resistance for CTX, pampC gene presence, MLST STs, phylogroups, and the alignments of the promoter and the attenuator region. Positions with a SH-like (Shimodaira–Hasegawa like) branch support ≤60% are indicated as red dots. Scale bar indicates branch length calculated by FastTree. Genomic homoplastic mutations We calculated the consistency index for all SNP positions on the E. coli reference chromosome. A low consistency index value for a position indicates a high degree of inconsistency with the chromosomal phylogeny and can be calculated by HomoplasyFinder as described in earlier studies (Crispell, Balaz, and Gordon 2019; Crispell et al. 2019; Van Dorp et al. 2020). As can be observed in Fig. 3, results clearly 7
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