(A) An example of three samples identified as potential mixtures. The consensus lineage is given first and coloured blue, while the potentially co-infecting lineage is given second and coloured red. Minority variants that do not match the co-infecting lineage are coloured grey. (B) The mean number of shared iSNVs shared by each pair of samples binned by the probability they were the result of a direct transmission according to the model of Stimson et al., 2019. Results, with a minimum minor allele frequency of 0.01, 0.02, 0.05, and 0.1 are shown in each of the facets. Within-host variants observed in more than 2% of samples were excluded. (C) The same plot as Figure 3B but having removed all samples that were inferred to be mixed infections. (D) A diagram demonstrating the four scenarios that can lead to shared within-host variants. (i) Superinfection of a common strain. (ii) Superinfection followed by co-transmission (iii) Transmission of the within-host variants through a large bottleneck. (iv) Independent de novo acquisitions of the same within-host variants. Shared within-host variants in scenarios (ii, iii) are concordant with the transmission tree, while (i, iv) are discordant, potentially confounding transmission inference efforts.