Candidates with predicted in vitro fitness defects and/or lower than expected gene insertion indices by tradis_essentiality testing.

Calculations for determining a fitness defect were made by tradis_essentiality.R analysis of library 1 and 2 passage samples. Repetitive transposable elements were removed from this data set, as multi-mapped reads were ignored during the insertion quantification step, giving these open reading frames an insertion index of 0. Gene insertion index distribution changepoints were calculated at 0.0149 for passage 1 and 0.0087 for passage 2 samples. Only genes failing to pass the calculated thresholds in both samples were included in the putative housekeeping gene pool. A description of analysis methods can be found in the Materials and Methods section. Pathway and COG prediction was performed by eggNOGmapper-V2 analysis and comparisons to the KEGG database using the N. musculi reference genome. Transposon insertions for each ORF are listed for each sample output. Gene insertion indices (Tn5 insertions normalized to gene length) are listed for passage 1 and 2 samples. Insertion counts are listed for all samples. (XLSX)