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.测序读段计数表首先进行预处理：由于本次比对采用双端配对比对模式（即正向读段与反向读段的配对比对），需将所有计数值除以2，处理后的数据表称为原始计数表（详见条目A）。随后，原始计数表将按照每种微生物的基因组大小进行归一化，再经总求和缩放法处理，最终得到的计数表详见条目B与C。数据表中收录的微生物已被聚合至属分类水平。针对抗菌耐药组分析，所有基因的原始读段计数均除以2（详见条目D），并按照每个样本的总细菌读段数（比对至bacteria、bacteria_draft及HumanMicrobiome数据库）进行归一化，转换为每百万细菌片段对应每千碱基参考序列的片段数（FPKM, Fragments Per Kilobase of reference per Million bacterial Fragments）（详见条目E）。FPKM数据表还被聚合至抗菌药物类别抗性层级（详见条目F），且每个抗菌耐药基因（AMR-genes, Antimicrobial Resistance Genes）的类别层级信息详见条目G。