Genome assembly ASM432948v1

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NCBI RefSeq assembly
GCF_004329485.1
Submitted GenBank assembly
GCA_004329485.1
Taxon
Staphylococcus lugdunensis
Strain
E7
WGS project
SCHB01
Submitter
University of California San Diego
Date
Mar 6, 2019

Assembly statistics

RefSeqGenBank
Genome size2.8 Mb2.8 Mb
Total ungapped length2.8 Mb2.8 Mb
Number of contigs510510
Contig N50444.1 kb444.1 kb
Contig L5033
GC percent33.533.5
Genome coverage99.0x99.0x
Assembly levelContigContig
View sequencesview RefSeq sequencesview GenBank sequences

Sample details

BioSample ID
SAMN10735326
Description
MIGS Cultured Bacterial/Archaeal sample from Staphylococcus lugdunensis
Comment
Keywords: GSC:MIxS;MIGS:6.0
Submitter
University of California San Diego
Strain
E7
Collection date
2017-07
Broad-scale environmental context
Human skin
Local-scale environmental context
Swabs
Environmental medium
Trizol|Ethanol
Geographic location
USA: California
Host
Homo sapiens
Latitude and longitude
32.71 N 117.16 W
Number of replicons
not applicable
Reference for biomaterial
not applicable
Isolation source
skin
Sample name
Isolate8
Models
MIGS.ba, MIGS/MIMS/MIMARKS.human-skin
Package
MIGS.ba.human-skin.6.0
Submission date
2019-01-12T15:52:05.830
Publication date
2019-03-09T00:00:00.000
Last updated
2021-02-28T06:48:03.726

Assembly methods

Sequencing technology
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/
Assembly method
SPAdes v. 3.10.0

Additional genomes

Browse all Staphylococcus lugdunensis genomes (143)

BioProject

PRJNA514867

Quorum sensing between bacterial species on the skin protects against epidermal injury in atopic dermatitis

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqNCBI
NameGCF_004329485.1-RS_2024_04_02NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateApr 2, 2024Jan 16, 2019
Genes2,9843,000
Protein-coding2,6602,835
Software version6.74.7

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: 97.88% (73rd Percentile)

Contamination: 6.47%

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

Average Nucleotide Identity (ANI) match details

Best match type-strain for submitted organismBest match type-strain
Type assemblyGCA_900478255.1GCA_900478255.1
Organism nameStaphylococcus lugdunensisStaphylococcus lugdunensis
Type categorytypetype
ANI99.44%99.44%
Assembly coverage89.13%89.13%
Type assembly coverage97.19%97.19%

Chromosomes

Note: This contig-level genome assembly includes 510 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_004329485.1GCF_004329485.1ASM432948v1ContigMar 6, 2019