Table 9.

Rich medium replicate 1: All mutations detected above a frequency of 0.2 in rounds 5, 10 and 15 of rich medium selection replicate 1. The first number in each cell denotes the distance in base pairs from ori (location). The second entry (mutation) identifies the mutations with ‘IG’ denoting an intergenic mutation. The third entry (fraction) is the fraction of the population carrying this mutation (as inferred by breseq in polymorphism mode). The fourth entry (coverage) is the number of reads that aligned to this location. In the round 15 strain, the clpX SNP and $\mathrm{\Delta }$1 bp deletion at position 523,086 were confirmed by Sanger sequencing.

DOI: http://dx.doi.org/10.7554/eLife.24669.034

Rich medium replicate 1
Round, (coverage)	5, ($172\times$)	10, ($213\times$)	15, ($180\times$)
Mutation (loc., mut., frac., cov.)	457978, clpX E185${}^{*}$, 75.2%, 179	457978, clpX E185${}^{*}$, 100%, 199	457978, clpX E185${}^{*}$, 100%, 164
	523086, IG $\mathrm{\Delta }$1 bp, 100%, 194	523086, IG $\mathrm{\Delta }$1 bp, 100%, 266	523086, IG $\mathrm{\Delta }$1 bp, 100%, 168
	950518, pflA T188I, 22.2%, 144	990379, IG A${\displaystyle \to }$C, 100%, 201	663115, dacA $\mathrm{\Delta }$1 bp, 100%, 150
	1978458, IG G$\to$T, 21.2%, 156		990379, IG A$\to$C, 100%, 156
	3618863, nikR H92H, 20.7%, 189