Genome assembly Stap_aure_VET0417R_V1
- NCBI RefSeq assembly
- GCF_000644555.1
- Submitted GenBank assembly
- GCA_000644555.1
- Taxon
- Staphylococcus aureus VET0417R
- Strain
- VET0417R
- WGS project
- JILY01
- Submitter
- Broad Institute
- Date
- Apr 23, 2014
Assembly statistics
RefSeq | GenBank | |
---|---|---|
Genome size | 2.8 Mb | 2.8 Mb |
Total ungapped length | 2.8 Mb | 2.8 Mb |
Number of scaffolds | 35 | 35 |
Scaffold N50 | 395.6 kb | 395.6 kb |
Scaffold L50 | 3 | 3 |
Number of contigs | 36 | 36 |
Contig N50 | 395.6 kb | 395.6 kb |
Contig L50 | 3 | 3 |
GC percent | 33 | 33 |
Genome coverage | 89.0x | 89.0x |
Assembly level | Scaffold | Scaffold |
View sequences | view RefSeq sequences | view GenBank sequences |
Sample details
- BioSample ID
- SAMN02404226
- Description
- Generic sample from Staphylococcus aureus VET0417R
- Submitter
- Broad Institute
- Strain
- VET0417R
- Collection date
- Aug 18, 2009
- Geographic location
- Netherlands
- Host
- Homo sapiens
- Sample name
- VET0417R
- SRA
- SRS586921
- Models
- Generic
- Package
- Generic.1.0
- Submission date
- 2013-11-15T13:07:25.100
- Publication date
- 2013-11-15T00:00:00.000
- Last updated
- 2019-06-20T16:42:42.457
Assembly methods
- Sequencing technology
- Illumina
- Comment
- Please be aware that the annotation is done automatically with little or no manual curation.
- Assembly method
- allpaths v. R48559
Additional genomes
Browse all Staphylococcus aureus genomes (102389)BioProject
PRJNA228736MRSA ST398
Pathogen Detection Resource
Publications
RefSeq microbial genomes database: new representation and annotation strategy
T Tatusova, et al.
Annotation details
RefSeq | GenBank | |
---|---|---|
Provider | NCBI RefSeq | Broad Institute |
Name | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) | Annotation submitted by Broad Institute |
Date | Nov 6, 2023 | Apr 23, 2014 |
Genes | 2,767 | 2,641 |
Protein-coding | 2,595 | 2,579 |
Software version | 6.6 |
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: 98.47% (59th Percentile, dark blue bar)
Contamination: 0.43%
Completeness of Staphylococcus aureus RefSeq assemblies
Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Staphylococcus aureus 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
- Staphylococcus aureus VET0417R
- Submitted species name
- Staphylococcus aureus
Average Nucleotide Identity (ANI) match details
Best match type-strain for submitted organism | Best match type-strain | |
---|---|---|
Type assembly | GCA_022869625.1 | GCA_022869625.1 |
Organism name | Staphylococcus aureus | Staphylococcus aureus |
Type category | type | type |
ANI | 97.55% | 97.55% |
Assembly coverage | 90.38% | 90.38% |
Type assembly coverage | 90.36% | 90.36% |
Chromosomes
Note: This scaffold-level genome assembly includes 35 scaffolds and no assembled chromosomes.
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_000644555.1 | GCF_000644555.1 | Stap_aure_VET0417R_V1 | Scaffold | Apr 23, 2014 |