Marker frequency analysis samples were prepared from bacterial cultures collected in exponential growth phases. Exponential-phase cultures were obtained by inoculating 0.1 mL of overnight culture into 100 mL fresh medium and growing with shaking to OD450 0.20.4. Cells were collected by centrifugation and pellets were immediately stored at -20C to arrest replication. Genomic DNA was extracted from cell pellets using the GeneMATRIX Bacterial & Yeast Genomic DNA Purification Kit (EurX). Sequencing libraries were prepared using the TruSeq DNA PCR-Free Library Preparation protocol (Illumina) and sequenced on Illumina HiSeq 2500 (paired-end 100 bp) or NextSeq 500 (paired-end 150 bp) platforms.