Genome assembly ASM400407v1
- NCBI RefSeq assembly
- GCF_004004075.1
- Submitted GenBank assembly
- GCA_004004075.1
- Taxon
- Sinorhizobium meliloti
- Strain
- USDA1031
- WGS project
- RPNJ01
- Submitter
- University of Minneosta
- Date
- Jan 8, 2019
Assembly statistics
RefSeq | GenBank | |
---|---|---|
Genome size | 6.6 Mb | 6.6 Mb |
Total ungapped length | 6.6 Mb | 6.6 Mb |
Number of contigs | 145 | 145 |
Contig N50 | 103.4 kb | 103.4 kb |
Contig L50 | 22 | 22 |
GC percent | 62 | 62 |
Genome coverage | 12.6x | 12.6x |
Assembly level | Contig | Contig |
View sequences | view RefSeq sequences | view GenBank sequences |
Sample details
- BioSample ID
- SAMN07640758
- Description
- Microbe sample from Sinorhizobium meliloti
- Submitter
- University of Minnesota
- Strain
- USDA1031
- Host
- Medicago sativa
- Isolation source
- root nodule
- Collection date
- 1952
- Geographic location
- Turkey
- Sample type
- Single Cell
- Sample name
- USDA1031
- SRA
- SRS2529096
- Models
- Microbe, viral or environmental
- Package
- Microbe.1.0
- Submission date
- 2017-09-13T18:02:06.623
- Publication date
- 2018-08-02T00:00:00.000
- Last updated
- 2018-11-20T10:24:29.802
Assembly methods
- Sequencing technology
- Illumina Miseq
- Comment
- Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
- Assembly method
- SPAdes v. 3.13.0
Additional genomes
Browse all Sinorhizobium meliloti genomes (471)BioProject
PRJNA401434Ensifer spp associated with Medicago whole genome sequencing
Annotation details
RefSeq | GenBank | |
---|---|---|
Provider | NCBI RefSeq | NCBI |
Name | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | Jan 26, 2024 | Nov 22, 2018 |
Genes | 6,414 | 6,688 |
Protein-coding | 6,074 | 6,244 |
Software version | 6.6 | 4.7 |
About PGAP
The NCBI Prokaryotic Genome Annotation Pipeline (PGAP) uses multiple approaches to predict protein-coding and RNA genes and other functional elements directly from sequence.
Continue readingQuality analysis
CheckM analysis (v1.2.2)
Completeness: 98.97% (41st Percentile)
Contamination: 0.96%
Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Ensifer meliloti CheckM marker set. For more information on CheckM, see Parks, et al. Genome Res (2015).
Taxonomy check
- Taxonomy check status
- OK
- Best match status
- species_match
- Submitted organism name
- Sinorhizobium meliloti
- Submitted species name
- Sinorhizobium meliloti
Average Nucleotide Identity (ANI) match details
Best match type-strain for submitted organism | Best match type-strain | |
---|---|---|
Type assembly | GCA_017876815.1 | GCA_017876815.1 |
Organism name | Sinorhizobium meliloti | Sinorhizobium meliloti |
Type category | suspected_type | suspected_type |
ANI | 99.57% | 99.57% |
Assembly coverage | 94.77% | 94.77% |
Type assembly coverage | 85.33% | 85.33% |
Chromosomes
Note: This contig-level genome assembly includes 145 contigs and no assembled chromosomes.
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_004004075.1 | GCF_004004075.1 | ASM400407v1 | Contig | Jan 8, 2019 |