Phylogeny of C. pneumoniae reference isolates based on different SNP types (see table 2). Distance calculated as number of SNPs. Analysis revealed a phylogenetic proximity between CWL-029 and TW-183, and AR-39 and J-138, respectively. The topology of the tree was not significantly altered when sSNP, nsSNP or SNP of intergenic regions were analysed separately. Only sSNPs were not able to resolve the common branch of CWL-029 and TW-183.