Figure 1.

Reproducibility and distribution of Himar1 transposon insertions in V. cholerae. (A) The total reads from transposon insertions in each intergenic and genic region (∼6000 loci) were summed for each library. Pairwise comparisons of read abundance for each locus were plotted for the three libraries and used to determine the coefficient of determination (R² value) between each pair. (B) The fraction of TA sites containing a transposon insertion was calculated for every gene in the pooled transposon-insertion sequencing data set, and the number of genes associated with each fraction is plotted. Using the distribution for presumed neutral genes (right peak), the 1% significance cutoff was calculated as 0.34 (dotted line). Genes to the left of this line have significantly fewer transposon insertions than expected for neutral insertion events (P < 0.01). (C) After positional correction, the total reads for all transposon insertions within each gene in the data set were averaged to the total TA sites in the gene. The number of genes associated with each average frequency is plotted.