Genome assembly ASM523504v1
- Taxon
- Enterococcus faecium
- Strain
- ARL08-484
- WGS project
- QPRN01
- Submitter
- University of Otago
- Date
- May 8, 2019
Assembly statistics
RefSeq | GenBank | |
---|---|---|
Genome size | 2.9 Mb | 2.9 Mb |
Total ungapped length | 2.9 Mb | 2.9 Mb |
Number of scaffolds | 185 | 185 |
Scaffold N50 | 48.4 kb | 48.4 kb |
Scaffold L50 | 17 | 17 |
Number of contigs | 187 | 187 |
Contig N50 | 48.4 kb | 48.4 kb |
Contig L50 | 17 | 17 |
GC percent | 38 | 38 |
Genome coverage | 119.0x | 119.0x |
Assembly level | Scaffold | Scaffold |
Sample details
- BioSample ID
- SAMN09435321
- Description
- Pathogen: clinical or host-associated sample from Enterococcus faecium
- Submitter
- University of Otago
- MLST type
- 375
- Strain
- ARL08-484
- Collected by
- Institute of Environmental Science and Research (ESR)
- Collection date
- 2008
- Geographic location
- New Zealand
- Isolation source
- feces swab
- Latitude and longitude
- not collected
- Host
- Homo sapiens
- Sample type
- pure culture
- Sample name
- ARL08-484
- Models
- Pathogen.cl
- Package
- Pathogen.cl.1.0
- Submission date
- 2018-06-17T18:32:13.676
- Publication date
- 2019-05-06T00:00:00.000
- Last updated
- 2019-05-06T13:51:43.817
Assembly methods
- Sequencing technology
- Illumina NextSeq
- 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. 3.7.1
Additional genomes
Browse all Enterococcus faecium genomes (31128)BioProject
PRJNA476469Agricultural origins of a highly-persistent clone of vancomycin-resistant Enterococcus faecalis in New Zealand
Pathogen Detection Resource
Annotation details
RefSeq | GenBank | |
---|---|---|
Provider | NCBI RefSeq | NCBI |
Name | GCF_005235045.1-RS_2024_11_27 | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | Nov 27, 2024 | Jul 23, 2018 |
Genes | 2,926 | 3,070 |
Protein-coding | 2,728 | 2,830 |
Software version | 6.9 | 4.6 |
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 (v1.2.3)
Completeness: 99.19% (67th Percentile)
Contamination: 0.31%
Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Enterococcus faecium 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
- Enterococcus faecium
- Submitted species name
- Enterococcus faecium
Average Nucleotide Identity (ANI) match details
Best match type-strain for submitted organism | Best match type-strain | |
---|---|---|
Type assembly | GCA_001544255.1 | GCA_001544255.1 |
Organism name | Enterococcus faecium NBRC 100486 | Enterococcus faecium |
Type category | type | type |
ANI | 99.62% | 99.62% |
Assembly coverage | 79.84% | 79.84% |
Type assembly coverage | 94.18% | 94.18% |
Chromosomes
Note: This scaffold-level genome assembly includes 185 scaffolds and no assembled chromosomes.
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_005235045.1 | GCF_005235045.1 | ASM523504v1 | Scaffold | May 8, 2019 |