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Overview
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Quality Control
| Organism Summary | |
|---|---|
| Catalog Number | ATCC® 700893™ |
| Strain Alias | JCM 9820 [DSM 11879, K1, Nomura K1] |
| Isolation | Hot sediment and venting water at a coastal solfataric vent |
| Tags | Type Strain |
| Biosafety Level | 1 |
| Type Strain | Yes |
| Assembly Summary | |
|---|---|
| Date Published | September 16, 2025 |
| Length | 1,669,695 nt |
| Sequencing Technology | Illumina + Oxford Nanopore Hybrid Assembly |
| Number of Contigs | 1 (All Circularized) |
| N50 | 1,669,695 nt |
| %GC | 56.31% |
| Annotations Summary | |
|---|---|
| Number of CDS | 1718 |
| Number of Hypothetical Proteins | 411 |
| Number of tRNA | 46 |
| Number of 5s rRNA | 1 |
| Number of 16s rRNA | 1 |
| Number of 23s rRNA | 1 |
| Input Reads Summary | |
|---|---|
| Oxford Nanopore Read Count | 43,990 |
| Oxford Nanopore Median Q Score | 37 |
| Illumina Read Count | 2,969,480 |
| Illumina Mean Coverage Depth | 442.289× |
| Illumina Median Q Score | 40 |
| 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):
All Genomes
| Taxonomic Name | ATCC Product Page | Strain Alias | Tags | Date Published | Length | Download |
|---|
Displaying Genome
| Sequencing Quality Control | |
|---|---|
| Number of trimmed reads | 2,969,480 |
| Median Q score, all bases | 40 |
| Percent of median Q scores per cycle greater than 25 | 1% |
| Ambiguous content (% N bases) | 0% |
| Assembly Quality Control | |
|---|---|
| Estimated genome completeness | 93.82% |
| Estimated genome contamination | 2.09% |
| Average depth of coverage | 442.289× |
Notes
This bacterium was assembled, annotated, and curated using Oatmeal v3.0. See our technical documentation for further details: https://docs.onecodex.com/en/articles/5357065-assembly-qc-and-annotation-pipeline-versions. This item has been approved for publication to the AGP, despite not meeting ATCC's CheckM minimum completion or maximum contamination score requirements. This item has been manually compared to the available public reference genomes for this organism and the completion and contamination statistics are comparable or surpass those of the identified public genomes.
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