Differentially expressed transcript when comparing the rpoS mutant to wild-type.

The included transcript met the criteria of >1 log2 fold-change and an adjusted p-value (padj) when comparing the rpoS mutant to wild-type. One transcript was impacted, not including the mutated gene, by the mutation. The first column contains the CDS/custom transcript ID which is the transcript ID for all coding sequences obtained from the NCBI Gene file format file or the transcript ID given to ncRNAs. RefSeq entries are further separated by the character “_”. The first portion gives the genetic element from which it is derived, the second describes the type of element (CDS), the third provides RefSeq ID, and the fourth provides a number indicating the particular entries ordered number in the RefSeq entry. The second column is the gene information, for the ncRNAs it contains the location relative to other genes and for predicted or known genes it contains gene name. The remaining columns describe the various metrics of expression of each impacted transcript including, base mean (average library size normalized counts across all samples), log2FC (Fold change estimate), lfcSE (uncertainty of the log fold change estimate), stat (Wald statistic), pvalue, padj (pvalue following Benjamini-Hochberg adjustment). The ncRNA is listed according to the nomenclature the previous analyses of the strain B31 ncRNA transcriptome [30].