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Overview
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Quality Control
| Organism Summary | |
|---|---|
| Catalog Number | ATCC® TSD-454™ |
| Strain Alias | V4C-8 |
| Isolation | Nitrogen-fixing, hydrogen-oxidizing chemolithoautotrophic community enrichment from a root and sediment sample from the Muddy River. |
| Tags | Methylation DataType Strain |
| Biosafety Level | 1 |
| Type Strain | Yes |
| Assembly Summary | |
|---|---|
| Date Published | June 10, 2025 |
| Length | 4,576,106 nt |
| Sequencing Technology | Illumina + Oxford Nanopore Hybrid Assembly |
| Number of Contigs | 2 (0 Circularized) |
| N50 | 4,420,121 nt |
| %GC | 67.17% |
| Annotations Summary | |
|---|---|
| Number of CDS | 3878 |
| Number of Hypothetical Proteins | 384 |
| Number of tRNA | 53 |
| Number of 5s rRNA | 4 |
| Number of 16s rRNA | 4 |
| Number of 23s rRNA | 4 |
| Input Reads Summary | |
|---|---|
| Oxford Nanopore Read Count | 5,814 |
| Oxford Nanopore Median Q Score | 35 |
| Illumina Read Count | 5,904,150 |
| Illumina Mean Coverage Depth | 340.442× |
| 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):
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| Taxonomic Name | ATCC Product Page | Strain Alias | Tags | Date Published | Length |
|---|
Displaying Genome
| Sequencing Quality Control | |
|---|---|
| Number of trimmed reads | 5,904,150 |
| 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 | 82.05% |
| Estimated genome contamination | 5.92% |
| Illumina depth of coverage | 340.442× |
| ONT depth of coverage | 11.497× |
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. CheckM contamination metric has been omitted from publication QC criteria for this item due to its rarity in the CheckM database as a type strain deposit.
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