| collection date | not collected |
|---|
| broad-scale environmental context | Bos taurus |
|---|
| local-scale environmental context | stomach |
|---|
| environmental medium | bodily fluid |
|---|
| geographic location | United Kingdom |
|---|
| investigation type | metagenome |
|---|
| isolation source | cattle rumen |
|---|
| project name | Metagenomic sequencing of the rumen of 240 cattle from Scotland |
|---|
| reference for biomaterial | Stewart RD, Auffret MD, Warr A, Walker AW, Roehe R, Watson M. Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery. (2019) Nat Biotechnol. 37(8):953-961. doi: 10.1038/s41587-019-0202-3. |
|---|
| sample name | RUG13435 |
|---|
| ENA-CHECKLIST | ERC000047 |
|---|
| ENA-FIRST-PUBLIC | 2019-11-14T04:04:37Z |
|---|
| ENA-LAST-UPDATE | 2019-11-01T20:35:38Z |
|---|
| External Id | SAMEA6151572 |
|---|
| INSDC center name | THE ROSLIN INSTITUTE |
|---|
| INSDC first public | 2019-11-14T04:04:37Z |
|---|
| INSDC last update | 2019-11-01T20:35:38Z |
|---|
| INSDC status | public |
|---|
| Submitter Id | RUG13435 |
|---|
| assembly quality | Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs |
|---|
| assembly software | IDBA-UD; v1.1.3; --num_threads 16 --pre_correction --min_contig 300 |
|---|
| binning parameters | tetra-nucleotide frequencies and abundance |
|---|
| binning software | MetaBAT2 |
|---|
| completeness score | 84.66 |
|---|
| completeness software | CheckM |
|---|
| contamination score | 5.49 |
|---|
| geographic location (latitude) | 55.861398 |
|---|
| geographic location (longitude) | -3.206493 |
|---|
| metagenomic source | bovine gut metagenome |
|---|
| sample derived from | ERS3613956 |
|---|
| scientific_name | Fibrobacter succinogenes |
|---|
| sequencing method | Illumina HiSeq 4000 |
|---|
| taxonomic identity marker | multi-marker approach - MAGpy - Stewart RD, Auffret MD, Snelling TJ, Roehe R, Watson M. (2019) MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs). Bioinformatics. 35(12):2150-2152. doi: 10.1093/bioinformatics/bty905 |
|---|