Fig. 3
Recombination and accessory genome analysis of S. pneumoniae serotype 1 isolates. a Recombination using Gubbins: The tree was built from non-recombinant regions in the core genome alignment. The colored strip highlights the BAPS clusters. Red blocks indicate recombinant regions along the core genome. Blue blocks indicate recombination event that have occurred in a single isolate. b Linear regression analysis of genomic fluidity (accessory genome) against synonym diversity (core genome). Plotting the values are in ln-ln. c Same as b but done by sublineage; Sublineage 1:R2 = 0.01047, p-value = 0.01066, Sublineage 2: R2 = 0.1448, p-value = 7.31e− 7, Sublineage 3: R2 = 0.2698, p-value = 2.2 e− 17. Sublineage 4 and 5 were not plotted because they have a limited value due to the small number of isolates