Body sites and samples included in study (Table S1); supervised learning using P. acnes pangenome presence/absence features (Table S2) and nucleotide diversity of shared clade-specific markers (Table S3); comparison of 1-nearest-neightbor classification accuracies (Fig. S1); selected features from all body sites using correlation-based feature selection (Table S4); conditional logistic regression odds ratios (Table S5).
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