Fig. 1

Universal gene frequency distribution in bacteria and the single-reference problem. A Frequency distribution of genes in 10 genomes of 6 bacterial species (Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, Salmonella enterica, and Streptococcus pneumoniae) showing the characteristic U-shaped curve—most genes are rare or common. B Illustrative depiction of the single-reference problem, a consequence of the U-shaped distribution. Each vertical column is a bacterial genome, and each colored bar is a gene. Numbers are identifiers for SNPs—there are 36 in total. For example the dark blue gene has 4 SNPs numbered 1–4. This figure does not detail which genome has which allele. Below each column is the proportion of SNPs that are discoverable when that genome is used as a reference genome. Because no single reference contains all the genes in the population, it can only access a fraction of the SNPs