Additional file 4 of A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

Additional file 4: Table S4. Overview and characteristics of the 2114 MAGs, the 74 Hungate and the 102 RefSeq genomes used to reconstruct phylogenies in our study. From left to right: the internal code (a derivative of the accession number the data came from and the autometa id); the alternative name, which we either generated by identifying the closest match following BLAST comparisons with RefSeq or the assigned strain name (for reference genomes downloaded from databases); the accession number the MAG came from (when relevant); country where the sample was collected; author; dRep clustering and checkm (estimated completeness and contamination) and mean contig coverage (estimated by mapping filtered reads to contigs using Bowtie2). The overall mean and median are presented as well. The MAGs with the same drep clustering id are >99% identical. The last column indicates the 1232 MAGs that were selected for the dereplicated dataset. The sequences of the 2114 MAGs are available here: doi.org/10.15454/UIJTJA . B: Mapping of filtered reads to contigs and the core MAGs. From left to right: Sample names, the total number of reads for each sample and the number of reads successfully mapped to contigs, the percentage of the number of reads mapped to contigs, the number of reads mapped to MAGs, and the percentage of reads mapped to MAGs. The smaller subtable to the right presents: the average percentage of reads successful mapping to contigs and to MAGs (top); the average percentage of reads mapped only to bacterial contigs (based on the classification from Autometa; NR database); the percentage of bacterial reads (based on the bacterial contig estimate) mapped to MAGs.