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. (XLSX)

本研究中的变异以NCBI PAO1参考基因组（RefSeq登录号NC_002516.2）为参照进行调用，并通过snpEff完成注释。各注释字段说明如下：LINEAGE：首位为基础基因型（1=MPAO1野生型；2=MPAO1突变STn），后续为谱系分级（A至D）；POSITION：核苷酸位点；REFERENCE：参考等位基因；ALTERNATE：替代等位基因；EFFECT：变异分类类型，涵盖基因间区、错义、移码或同义变异；FEATURE：变异所属区域，为编码区或基因间区；FEATUREID：若为编码区变异则为受影响编码序列（CDS）的基因座标签，若为基因间区变异则为邻近编码序列（CDS）的基因座标签；IMPACT：snpEff预测的变异影响程度；GENE NAME：若有可用信息则为对应基因名称；BASE CHANGE：核苷酸变化情况；AMINO ACID CHANGE：氨基酸变化情况。（数据格式：XLSX）