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Genome assembly ASM523504v1

Actions
Taxon
Enterococcus faecium
Strain
ARL08-484
WGS project
QPRN01
Submitter
University of Otago
Date
May 8, 2019

Assembly statistics

RefSeqGenBank
Genome size2.9 Mb2.9 Mb
Total ungapped length2.9 Mb2.9 Mb
Number of scaffolds185185
Scaffold N5048.4 kb48.4 kb
Scaffold L501717
Number of contigs187187
Contig N5048.4 kb48.4 kb
Contig L501717
GC percent3838
Genome coverage119.0x119.0x
Assembly levelScaffoldScaffold

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

PRJNA476469

Agricultural origins of a highly-persistent clone of vancomycin-resistant Enterococcus faecalis in New Zealand

Pathogen Detection Resource

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqNCBI
NameGCF_005235045.1-RS_2024_11_27NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateNov 27, 2024Jul 23, 2018
Genes2,9263,070
Protein-coding2,7282,830
Software version6.94.6

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 reading

Quality 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 organismBest match type-strain
Type assemblyGCA_001544255.1GCA_001544255.1
Organism nameEnterococcus faecium NBRC 100486Enterococcus faecium
Type categorytypetype
ANI99.62%99.62%
Assembly coverage79.84%79.84%
Type assembly coverage94.18%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_005235045.1GCF_005235045.1ASM523504v1ScaffoldMay 8, 2019