Determination of <i>in vivo</i> fitness factors.

<p>(A) Transposon insertion sites (filled arrow heads) that map to a specific location in the <i>sap</i> gene cluster in the <i>E. coli</i> CFT073 genome are depicted along with the number of normalized reads. Fitness factors were calculated as the ratio of number of reads that map to a specific insertion site in the inoculum (input) to the number of reads that map to the same insertion site in the splenic cultures (output). (B) To better visualize the coverage of transposon mutagenesis, a 30 Kbp window with 25 mapped Tn-insertion sites that exhibit a range of fitness factors is illustrated. Dotted line indicates the threshold (mean+2 standard deviations) used to delineate fitness genes. Fitness factors corresponding to the insertion sites within <i>sapF</i> (red), <i>sapC</i> (blue) and <i>sapA</i> (purple) genes are denoted.