Fig. 4: Allelic frequency at variable loci over successive transmission steps.
From: Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data
a Density distribution of mean allelic frequency across different transmission steps. b Linear plot of average of mean allelic frequency changes, grouped by number of transmission steps. c Receiver operating characteristic (ROC) curves showing the performance of mean change in allelic frequency, total change in allelic frequency, and the transmission likelihood as a predictor of transmission with area under the curve (AUC). d–f Violin plots comparing the distribution of each metric in transmission pairs vs non transmission pairs; boxplots are overlayed showing the quantiles with 95% confidence intervals error bars, and dots on the graph indicate individual comparisons. g Distribution of transmission likelihoods between the same chain and in different chains considering donors in preceding transmission steps. h Distribution of transmission likelihoods considering donors at maximum three precedent transmission steps. i Skewness of the distribution based on incremental time/transmission steps (days). Source data are provided as a Source Data file.
