Genome assembly ASM233233v1

FTP
Actions
NCBI RefSeq assembly
GCF_002332335.1
Submitted GenBank assembly
GCA_002332335.1
Taxon
Brevibacterium aurantiacum
Strain
900_6
WGS project
NRGO01
Submitter
Dutton Lab, UCSD
Date
Sep 21, 2017

Assembly statistics

RefSeqGenBank
Genome size4 Mb4 Mb
Total ungapped length4 Mb4 Mb
Number of scaffolds5858
Scaffold N50246 kb246 kb
Scaffold L5055
Number of contigs6565
Contig N50232.5 kb232.5 kb
Contig L5055
GC percent6363
Genome coverage50.0x50.0x
Assembly levelScaffoldScaffold
View sequencesview RefSeq sequencesview GenBank sequences

Sample details

BioSample ID
SAMN07141153
Description
Microbe sample from Brevibacterium aurantiacum
Submitter
Dutton Lab, UCSD
Strain
900_6
Geographic location
France
Collection date
2011-09
Isolation source
Cheese rind
Sample type
whole organism
Note
Originally submitted as Brevibacterium linens but changed in October 2018 because of ANI results to Brevibacterium aurantiacum
Sample name
Brevibacterium linens 900_6
Models
Microbe, viral or environmental
Package
Microbe.1.0
Submission date
2017-05-18T14:24:06.836
Publication date
2017-05-18T00:00:00.000
Last updated
2021-02-28T04:22:05.775

Assembly methods

Sequencing technology
Pacbio; 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/

The organism was changed from "Brevibacterium linens" to "Brevibacterium aurantiacum" in October 2018.

Assembly method
Canu v. 1.5

Additional genomes

Browse all Brevibacterium aurantiacum genomes (38)

BioProject

PRJNA387187

Cheese rind isolates Genome sequencing and assembly

Publications

Showing 3 of 3

View in PubMed

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqNCBI
NameGCF_002332335.1-RS_2024_03_31NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateMar 31, 2024Aug 22, 2017
Genes3,6883,684
Protein-coding3,5863,551
Software version6.74.2

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 (v1.2.2)

Completeness: 97.27% (30th Percentile, dark blue bar)

Contamination: 3.61%

Completeness of Brevibacterium aurantiacum RefSeq assemblies

Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Brevibacterium 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
Brevibacterium aurantiacum
Submitted species name
Brevibacterium aurantiacum

Average Nucleotide Identity (ANI) match details

Best match type-strain for submitted organismBest match type-strain
Type assemblyGCA_006539005.1GCA_006539005.1
Organism nameBrevibacterium aurantiacumBrevibacterium aurantiacum
Type categorytypetype
ANI97.41%97.41%
Assembly coverage82.47%82.47%
Type assembly coverage80.64%80.64%

Chromosomes

Note: This scaffold-level genome assembly includes 58 scaffolds and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_002332335.1GCF_002332335.1ASM233233v1ScaffoldSep 21, 2017