Fig. 2.

Burden of rare variation between invasive and carriage isolates, based on mapping and calling short variants against a single reference genome. Loss-of-function (LoF) are frameshift or nonsense mutations. a The site frequency spectrum (SFS) stratified by niche and by predicted consequence. Frequency has been normalized with respect to the number of samples in each population. b Histogram of Tajima’s D for all coding sequences in the genome, stratified by niche. c Boxplot of the number of rare variants per sample, stratified by niche and predicted consequence. Damaging mutations are LoF mutations and missense mutations predicted damaging by PROVEAN. Centre line is the median, box spans lower to upper quartiles. Whiskers show the outlier range, defined as being >1.5× the interquartile range above or below the lower and upper quartiles