As another measure for estimating background expression level, we analyzed the coverage in the intergenic regions of the genome. We assumed that at least half of the intergenic region is not expressed (considering the presence of known expressed regions, such as 39 and 59 UTR of genes, intergenic region of the operons, and sRNAs) and calculated the coverage, which corresponded to #6 reads per base, lower than our first cutoff estimate. We retained the most conservative cutoff for expression, i.e., 7 reads per base for describing the expression map of H. somni. Nucleotides in the genome sequence with coverage depth above our threshold value were considered to be expressed. This resulted in the generation of a whole genome transcriptome profile of H. somni 2336 at a single nucleotide resolution. Figure 1 show the steps involved in the analysis of expressed intergenic regions.