Most species are dominated by a single strain in the human gut. (A) Distribution of dominant allele frequency for all nucleotide positions in concatenated species-specific markers across all analyzed samples (>482 million total nucleotides). (B) Distribution of the dominant allele frequency for polymorphic positions. We report the median frequencies for each species/sample pair. (C) Distribution of nonpolymorphic site prevalence in samples for the 10 most prevalent gut bacterial species (for the full set of species, see Supplemental Fig. S9). The fraction of nonpolymorphic sites varies from sample to sample and from species to species. In parentheses, we quantify the percentage of strains with >99.9% of nonpolymorphic sites.
