| Organism Summary | |
|---|---|
| Catalog Number | ATCC® TSD-290™ |
| Isolation | Human oral cavity |
| Tags | Methylation DataType Strain |
| Biosafety Level | 2 |
| Type Strain | Yes |
| Assembly Summary | |
|---|---|
| Date Published | June 3, 2024 |
| Length | 3,045,103 nt |
| Sequencing Technology | Illumina + Oxford Nanopore Hybrid Assembly |
| Number of Contigs | 6 (0 Circularized) |
| N50 | 2,335,839 nt |
| %GC | 60.91% |
| Annotations Summary | |
|---|---|
| Number of CDS | 2673 |
| Number of Hypothetical Proteins | 437 |
| Number of tRNA | 93 |
| Number of 5s rRNA | 4 |
| Number of 16s rRNA | 4 |
| Number of 23s rRNA | 4 |
| Input Reads Summary | |
|---|---|
| Oxford Nanopore Read Count | 17,482 |
| Oxford Nanopore Median Q Score | 24 |
| Illumina Read Count | 11,762,246 |
| Illumina Mean Coverage Depth | 570.427× |
| Illumina Median Q Score | 34 |
| Contig | Start | End | Name | Protein Product | EC Number | Type | RefSeq ID | Jump |
|---|
Most similar genomes
The following genomes have the greatest genomic similarity to this one (≥95% average nucleotide identity):
| Taxonomic Name | ATCC Product Page | Strain Alias | Tags | Date Published | Length | Download |
|---|
| Sequencing Quality Control | |
|---|---|
| Number of trimmed reads | 11,762,246 |
| Median Q score, all bases | 34 |
| Percent of median Q scores per cycle greater than 25 | 1% |
| Ambiguous content (% N bases) | 0% |
| Assembly Quality Control | |
|---|---|
| Estimated genome completeness | 100% |
| Estimated genome contamination | 86.21% |
| Average depth of coverage | 570.427× |
Notes
The assembly here is deposited as a co-culture of two organisms as is received in the stock vial. Due to the episymbiotic lifestyle of ATCC TSD-290, it was deposited as a co-culture with its host bacterium, Schaalia odontolytica ATCC BAA-3209. Contig 1 of this assembly belongs to Schaalia odontolytica ATCC BAA-3209 (genomeID - 6b4f165d2f45467e); contigs (2, 3, 4, 5, 6) belong to Nanosynbacter lyticus ATCC TSD-290. Due to these contraints, CheckM contamination QC thresholds have been ignored for this co-culture assembly. This bacterium was assembled, annotated, and curated using Oatmeal v1.2. See our technical documentation for further details: https://docs.onecodex.com/en/articles/5357065-assembly-qc-and-annotation-pipeline-versions