Variant annotation in isolates serially passaged on media without antibiotic.

Variants were called against the NCBI PAO1 reference (RefSeq accession NC_002516.2) and annotated with snpEff. Annotation fields are as follows: LINEAGE = underlying genotype in first position (1 = MPAO1-WT; 2 = MPAO1-mutSTn) followed by the lineage (A–D); POSITION = Nucleotide position; REFERENCE = reference allele; ALTERNATE = alternate allele; EFFECT = variant classification (intergenic, missense, frameshift or synonymous); FEATURE = coding or intergenic variant; FEATUREID = locus tag of affected CDS or neighboring CDS when intergenic; IMPACT = variant impact as predicted by snpEff; GENE NAME = gene name when available; BASE CHANGE = nucleotide change; AMINO ACID CHANGE = amino acid change.
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