Extended Data Fig. 6: Impact of SNP thresholding strategies on transmission inference.

The inferred number of transmission pairs, inferred by each algorithm, between samples taken as part of a study investigating the impact of Faecal Microbiota Transplants (FMTs) (Ianiro et al., 2022). Transmission between samples from unrelated participants (shown in red) are highly likely to be false positives. In contrast, samples from the same participant following FMT (shown in black) are more likely to be true positives, with an error rate proportional to that observed in the unrelated participant results. Species specific SNP thresholds for identifying recent transmission were inferred using the mixture distribution approach (solid colour). Additional transmission pairs identified using the Youden cut-off method proposed in Valles-Collomer et al., 2023, are shown in a lighter colour with a dotted outline. This indicates that the Youden approach is substantially more relaxed and is likely to result in a high rate of false positives.