Figure 1. A schematic of sites used for different types of analyses in this paper.

A mock linearized S. aureus genome is shown, with codons on the strand from which they are transcribed shown in boxes. Note coding content is over-represented on the leading strand. Only first codon positions are considered for the sake of simplicity. The results presented in Figure 2, Figure 3, and Figure 5 consider coding sites underlined with a thick line, meaning the identities of the nucleotides are all taken from the published strand in dedicated coding sites, regardless of the sense direction of the gene. Thus Figure 2 and Figure 3 do not explicitly distinguish between leading and lagging AT skews, but give an averaged picture of skews along both strands of the genome. All other analyses of AT skew in coding sites in this paper consider the sites underlined with a thin line. The identities of these nucleotides are all in the sense direction of the gene, i.e. that nucleotide which appears within the transcript, and may be easily divided into groups according to whether they are encoded on the leading or lagging strand. The analysis of intergenic regions is simpler in concept as intergenic sites clearly divide into either leading or lagging.