(A) Variation in the number of simple sequence repeats (SSRs; grey boxes) associated with a gene: (i) if the SSR tract is located in the ORF of a gene, this results in ON-OFF switching of expression of the encoded protein. If the number of SSRs leads to the gene remaining in-frame, the gene is expressed (ON). However, gain or loss of repeat units in the SSR tract results in a frame-shift downstream of the SSR tract, and a premature stop codon means the gene is non-functional (OFF). Therefore, the bacterial population contains variants that express the protein or that do not; (ii) alternatively, if the SSR tract is located in the promoter of gene, this can result in graded protein expression, from high expression to low/no expression, with the resulting bacterial population containing a mixture of variants. (B) Phase-variable loci can shuffle between expressed (red + blue) and silent (white + green) loci, often by recombination between inverted repeats (IRs; yellow and grey boxes). In the example shown, this results in four different gene variants possible in the expressed locus, meaning four protein allelic variants are expressed, with the resulting bacterial population containing all four protein variants. (C) Inversion of a promoter means that the gene it controls is either expressed (promoter in the correct orientation to allow expression; green box), or not expressed, as the promoter is pointing in the opposite orientation (red box). Similar to the ON-OFF switching seen with SSR tracts in an ORF, this results in the bacterial population containing variants expressing the protein, or not.