Dataset 2: Read count tables

The read count table was first processed by dividing all counts with two, since mapping was performed as proper pairs (mapping of a forward and reverse read), this is referred to as the raw count table (see item A). The raw count table was normalized according to genome size for each microorganism, followed by total sum scaling. The resulting table is referred to as the count table (see item B and C). The microorganisms listed in the tables were aggregated to genus level. For the antimicrobial resistome analysis, raw read counts are provided for all genes divided by two (see item D) and normalized according to the total bacterial reads per sample (mapping to the databases: bacteria, bacteria_draft and HumanMicrobiome) as fragments per kilo base reference per million bacterial fragments (FPKM) (see item E). The FPKM table was also aggregated to resistance against antimicrobial classes (see item F), and the class-level information for each AMR-genes are available as see item G.