FIG 1.

Changes in variant frequencies during culture. Variants are defined as synonymous or nonsynonymous single nucleotide polymorphisms, insertions, or deletions. Total variant numbers were determined from frozen culture collection stocks of D39N (leftmost points on the graphs) after culture overnight on agar (second points from the left), followed by liquid culture overnight (third points from the left) and, finally, subculture to mid-exponential phase (rightmost points). The experiment was conducted in parallel with three different cultures, all originating from a single frozen stock. Variant calling was performed using Breseq. Blue lines indicate the number of variants present at a frequency of >5% in the total population at each culture step. Green lines show the number of new variants arising, or first detected, at each culture step. Histograms show the number of variants with a >0.5-fold change in the frequency between individual culture steps (right axis).