Auxillary Table S6

A table containing statistics, accession numbers and other contextual data about the 12682 Metagenome Assembled Genomes of moderate and high-quality submitted to ENA (e.g. completeness estimated higher then 40% and redundancy lower then 5%). A table with the whole ~500.000 bins generated in this study can be found at the scilifelab-figshare doi:10.17044/scilifelab.13005311. Contains the fields: • bin_id: the unique identifier of a MAG • GC: GC-content of MAG • coding_density: coding-density estimate, e.g. sum of the length of all predicted amino-acid sequences times 3 divided by the length of the genome (in bases) • completeness: estimated completeness computed by CheckM • contamination: estimated redundancy computed by CheckM • strain_heterogeneity: computed by CheckM • length: length in bases of the MAG • nb_contigs: number of contigs in the MAG • nb_proteins: number of predicted proteins encoded in the bin (for the predicted amino-acid sequences in the easy-access repository) • gtdbtk_classification: classification by GTDBtk r89 • sourmash_classification: classification by sourmash using 2 databases, the GTDB (r89), and a database based on our GTDBtk classification • taxonomy: conclusion of the two previous • mOTU: membership to a metagenomic Operational Taxonomic Unit (mOTU), e.g. species level clustering of bins • path: relative path a tar-ball containing nucleotide, CDS- and amino-acid sequences, GFF, eggNOGmapper, and sourmash-signature files. Relative to https://export.uppmax.uu.se/uppstore2018116/stratfreshdb/ • accession: SRA/ENA sample ID of the assembly • genbank_accession: genbank accession number

本数据集为一张统计表，涵盖提交至欧洲核苷酸档案库（European Nucleotide Archive, ENA）的12682条中高品质宏基因组组装基因组（Metagenome Assembled Genomes, MAG）的统计数据、收录编号及其他关联信息，其筛选标准为估计完整度高于40%、冗余度低于5%。本研究中生成的全部约50万个宏基因组分箱（bins）对应的完整表格，可于scilifelab-figshare平台的doi:10.17044/scilifelab.13005311处获取。
该统计表包含以下字段：
• bin_id：MAG的唯一标识符
• GC：MAG的GC含量（GC-content）
• coding_density：编码密度估算值，计算公式为所有预测氨基酸序列的总长度乘以3后，除以基因组的碱基总长度
• completeness：由CheckM计算得到的估计完整度
• contamination：由CheckM计算得到的估计冗余度
• strain_heterogeneity：由CheckM计算得到的菌株异质性
• length：MAG的碱基总长度
• nb_contigs：MAG所包含的重叠群（contigs）数量
• nb_proteins：该分箱中预测得到的蛋白质编码基因数量（对应易获取仓库中的预测氨基酸序列）
• gtdbtk_classification：基于GTDBtk r89的分类结果
• sourmash_classification：sourmash基于两类数据库完成的分类结果，分别为GTDB（r89版本）以及基于本研究GTDBtk分类结果构建的数据库
• taxonomy：上述两种分类结果的综合结论
• mOTU：宏基因组操作分类单元（metagenomic Operational Taxonomic Unit, mOTU）归属，即分箱的物种级聚类结果
• path：包含核苷酸序列、编码序列（CDS）、氨基酸序列、通用特征格式（GFF）、eggNOGmapper注释结果及sourmash特征文件的tar打包文件相对路径，该路径的基准目录为https://export.uppmax.uu.se/uppstore2018116/stratfreshdb/
• accession：对应组装实验的序列读取档案（Sequence Read Archive, SRA）/ENA样本编号
• genbank_accession：GenBank收录编号