Annotation of variants present in MPAO1-WT relative to PAO1 (sheet “Variants in MPAO1-WT vs. PAO1”) and variants present in MPAO1-<i>mutS</i>^<i>Tn</i> relative to MPAO1-WT, separated into (1) those variants present in the starting stock (sheet “Muts-Tn starting stock variants”), and (2) those additional variants present at the end of the first passage (sheet “MutS-Tn first passage variants”, see Methods).

Variants were called against the NCBI PAO1 reference (RefSeq accession NC_002516.2) and annotated with snpEff. Annotation fields are as follows: POS = Nucleotide coordinate position in PAO1 reference; REF = reference allele; ALT = alternate allele; EFFECT = variant classification (intergenic, missense, frameshift or synonymous); GENE = gene name when available, LOCUS_TAG = feature or neighboring features locus tag; DNA_MUT = nucleotide variant annotation; AA_MUT = amino acid change annotation when applicable. (XLSX)