Mapping of RNA-Seq reads onto the H. somni genome sequence resulted in more than 94% coverage with at least one read per base. This observation is consistent with the reported 94% genome expression in Bacillus anthracis, 89.5% in Sulfolobus solfataricus, and 95% in Burkholderia cenocepacia, studied under one or more experimental growth conditions using RNA-Seq [32, 33, 34] . These results indicate that most of the bacterial genome sequence is expressed at some basal level. To identify significantly expressed regions above this baseline, we used two alternative methods (discussed in Results section) to estimate the background expression. Both methods yielded similar results (6-7 reads per base). We selected the higher stringency cutoff of 7 reads per base to minimize the number of false positives.