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.

首先对读取计数表进行处理：由于测序比对采用成对末端正确比对模式（即正向reads与反向reads的配对比对），将所有计数值除以2，处理后的数据表称为原始计数表（见条目A）。随后针对每种微生物，依据其基因组大小对原始计数表进行归一化处理，再执行总和缩放（total sum scaling）。最终得到的数据表称为计数表（见条目B与C）。表中所列的微生物已被聚合至属分类水平。针对抗菌抗性组（antimicrobial resistome）分析，我们提供了所有基因的原始读取计数（已将计数除以2，见条目D）；该计数将依据每个样本的总细菌读取数（比对至数据库：bacteria、bacteria_draft及HumanMicrobiome），以每百万细菌片段的每千碱基参考片段数（FPKM）进行归一化（见条目E）。该FPKM表还被聚合至抗菌药物类别抗性层面（见条目F），每种AMR基因（Antimicrobial Resistance Genes）的类别层级信息可参见条目G。