| broad-scale environmental context | human digestive system |
|---|
| collection date | 2012 |
|---|
| environmental medium | subgingival plaque |
|---|
| geographic location | USA |
|---|
| investigation type | metagenome-assembled genome |
|---|
| isolation source | oral metagenome |
|---|
| project name | The samples within this Bioproject represents the oral metagenome (whole genome shotgun (WGS) sequencing) collected from the Native American Indian tribes of South Dakota. The samples were collected from the dental plaque of children aged 5-18 years old. The samples are collected from 5 different conditions: healthy, light caries, moderate caries, severe caries, and periodontal caries. The project goal is to identify the species level characterization of the bacterial community present in the oral metagenome. |
|---|
| sample name | SRR11085305_bin.15_MetaWRAP_v1.3_MAG |
|---|
| ENA-CHECKLIST | ERC000047 |
|---|
| INSDC center name | EMG |
|---|
| Submitter Id | SRR11085305_bin.15_MetaWRAP_v1.3_MAG |
|---|
| assembly quality | Many fragments with little to no review of assembly other than reporting of standard assembly statistics |
|---|
| assembly software | metaSPAdes v3.15.3 |
|---|
| binning parameters | MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters. |
|---|
| binning software | MetaWRAP v1.3 |
|---|
| broker name | EBI-EMG |
|---|
| completeness score | 63.79 |
|---|
| completeness software | CheckM |
|---|
| contamination score | 0.0 |
|---|
| geographic location (latitude) | not provided |
|---|
| geographic location (longitude) | not provided |
|---|
| local environmental context | oral cavity |
|---|
| metagenomic source | oral metagenome |
|---|
| sample derived from | SAMN13714823 |
|---|
| scientific_name | Neisseria sicca |
|---|
| sequencing method | Illumina MiSeq |
|---|
| taxonomic classification | The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Neisseriales;f__Neisseriaceae;g__Neisseria;s__Neisseria sicca |
|---|
| taxonomic identity marker | multi-marker approach |
|---|