title: IHE3034F Chromosome
design: We used Escherichia coli IHE3034 as our reference gnome, which was downloaded from ncbi ftp (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/025/745/GCF_000025745.1_ASM2574v1). The reads were directly mapped to the reference genome by using BWA mem (version: 0.7.17) with the default parameters. The variants were called by using GATK HaplotypeCaller (version 4.0.2.1) (-stand-call-conf 30 -ploidy 1, other parameters are default). Filtering for low quality calls was done with GATK VariantFiltration for SNPs and indels separately (SNPs filtering criteria: QD < 2.0 || FS > 60.0 || MQ < 40.0; Indel filtering criteria: QD < 2.0 || FS > 200.0)