Jee, J. et al. Nature 534, 693–696 (2016).

Spontaneous mutations underlie the diversity of bacteria, but because the per-generation mutation rate is several orders of magnitude lower than the error rates of high-throughput sequencers, it is challenging to detect these mutations accurately. To find such rare mutations in a genomic region of interest, Jee et al. designed maximum-depth sequencing (MDS), a strategy that involves the use of a barcoded primer for linear amplification of the target region followed by the addition of a second barcode during subsequent exponential PCR. The researchers profiled the mutation rate of Escherichia coli at six target regions and found that it differs by at least an order of magnitude. Their data allowed them to investigate the relationships among transcription, translation and mutation rate and to characterize the types of mutations induced by antibiotics.