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Overview
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Quality Control
| Organism Summary | |
|---|---|
| Catalog Number | ATCC® 700867™ |
| Strain Alias | 1D1609 |
| Isolation | Crown gall tumor on field-grown alfalfa plant, Medicago sativa, in Imperial Valley, southern California |
| Biosafety Level | 1 |
| Type Strain | No |
| Assembly Summary | |
|---|---|
| Date Published | June 10, 2025 |
| Length | 5,962,693 nt |
| Sequencing Technology | Illumina + Oxford Nanopore Hybrid Assembly |
| Number of Contigs | 10 (4 Circularized) |
| N50 | 1,189,134 nt |
| %GC | 59.5% |
| Annotations Summary | |
|---|---|
| Number of CDS | 5614 |
| Number of Hypothetical Proteins | 631 |
| Number of tRNA | 50 |
| Number of 5s rRNA | 3 |
| Number of 16s rRNA | 3 |
| Number of 23s rRNA | 3 |
| Input Reads Summary | |
|---|---|
| Oxford Nanopore Read Count | 168,254 |
| Oxford Nanopore Median Q Score | 32 |
| Illumina Read Count | 9,913,274 |
| Illumina Mean Coverage Depth | 243.487× |
| 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):
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| Taxonomic Name | ATCC Product Page | Strain Alias | Tags | Date Published | Length | Download |
|---|
Displaying Genome
| Sequencing Quality Control | |
|---|---|
| Number of trimmed reads | 9,913,274 |
| 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 | 0.42% |
| Average depth of coverage | 243.487× |
Notes
This bacterium was assembled, annotated, and curated using Oatmeal v2.0. See our technical documentation for further details: https://docs.onecodex.com/en/articles/5357065-assembly-qc-and-annotation-pipeline-versions
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