whole genome resequencing of E. coli: Sample Escherichia coli
 Genomes were paired-end re-sequenced using the Illumina HiSeq 2000/2500 instrument (Illumina inc., San Diego, CA, USA) with around 20× coverage for each genome. The initial strains in this experiments were genomes sequenced. Genomic DNA from different isolates were all genomes sequenced independently. Reads were 100/125 bp long, sequenced in pairs with a mean insert size of 500 bp. For E. coli between 405 and 1,260 Mb clean data (793 Mb on average) were obtained for each individual.
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