| collection date | not collected |
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| broad-scale environmental context | Bos taurus |
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| local-scale environmental context | stomach |
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| environmental medium | bodily fluid |
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| geographic location | United Kingdom |
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| investigation type | metagenome |
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| isolation source | cattle rumen |
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| project name | Metagenomic sequencing of the rumen of 240 cattle from Scotland |
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| 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. |
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| sample name | RUG14135 |
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| ENA-CHECKLIST | ERC000047 |
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| ENA-FIRST-PUBLIC | 2019-11-14T04:04:37Z |
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| ENA-LAST-UPDATE | 2019-11-01T20:36:19Z |
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| External Id | SAMEA6152273 |
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| INSDC center name | THE ROSLIN INSTITUTE |
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| INSDC first public | 2019-11-14T04:04:37Z |
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| INSDC last update | 2019-11-01T20:36:19Z |
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| INSDC status | public |
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| Submitter Id | RUG14135 |
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| assembly quality | Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs |
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| assembly software | MEGAHIT; v1.1.1; --kmin-1pass, -m 60e+10, --k-list 27,37,47,57,67,77,87, --min-contig-len 1000, -t 16 |
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| binning parameters | tetra-nucleotide frequencies and abundance |
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| binning software | MetaBAT2 |
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| completeness score | 92.72 |
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| completeness software | CheckM |
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| contamination score | 0.89 |
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| geographic location (latitude) | 55.861398 |
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| geographic location (longitude) | -3.206493 |
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| metagenomic source | bovine gut metagenome |
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| sample derived from | ERS3623224 |
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| scientific_name | Ruminococcus flavefaciens |
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| sequencing method | Illumina HiSeq 4000 |
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| 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 |
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