Fig. 2.

Pangenome counts for 413 Mycobacterium tuberculosis genomes from an outbreak in London [27]. The maximum pairwise SNP distance between these isolates was 9, suggesting extremely limited variation. Consequently, we would expect a very limited accessory genome and a core genome of approximately 4000 genes. All tools with the exception of Panaroo found in excess of 2500 accessory genes, which can be attributed to annotation errors