Pseudomonas aeruginosa
Sputum metagenomic reads alligned to PAO1 (GenBank accession NC_002516.2; genome size of 6.4 Mb) with Bowtie 2 V2.0.2 and The Genome Analysis Toolkit (GATK) V1.0.5083 for realignment around indels. Removing all non-P. aeruginosa reads from the metagenomic reads. The pileups of read alignments were performed with SAM tools V0.1.7 (r50), and the uploded data is the .bam files.