Genome assembly Stap_aure_VET0417R_V1

FTP
Actions
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

RefSeqGenBank
Genome size2.8 Mb2.8 Mb
Total ungapped length2.8 Mb2.8 Mb
Number of scaffolds3535
Scaffold N50395.6 kb395.6 kb
Scaffold L5033
Number of contigs3636
Contig N50395.6 kb395.6 kb
Contig L5033
GC percent3333
Genome coverage89.0x89.0x
Assembly levelScaffoldScaffold
View sequencesview RefSeq sequencesview 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

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqBroad Institute
NameNCBI Prokaryotic Genome Annotation Pipeline (PGAP)Annotation submitted by Broad Institute
DateNov 6, 2023Apr 23, 2014
Genes2,7672,641
Protein-coding2,5952,579
Software version6.6

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.

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Quality 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 organismBest match type-strain
Type assemblyGCA_022869625.1GCA_022869625.1
Organism nameStaphylococcus aureusStaphylococcus aureus
Type categorytypetype
ANI97.55%97.55%
Assembly coverage90.38%90.38%
Type assembly coverage90.36%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_000644555.1GCF_000644555.1Stap_aure_VET0417R_V1ScaffoldApr 23, 2014