Genome assembly ASM432948v1
- 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
RefSeq | GenBank | |
---|---|---|
Genome size | 2.8 Mb | 2.8 Mb |
Total ungapped length | 2.8 Mb | 2.8 Mb |
Number of contigs | 510 | 510 |
Contig N50 | 444.1 kb | 444.1 kb |
Contig L50 | 3 | 3 |
GC percent | 33.5 | 33.5 |
Genome coverage | 99.0x | 99.0x |
Assembly level | Contig | Contig |
View sequences | view RefSeq sequences | view 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
PRJNA514867Quorum sensing between bacterial species on the skin protects against epidermal injury in atopic dermatitis
Annotation details
RefSeq | GenBank | |
---|---|---|
Provider | NCBI RefSeq | NCBI |
Name | GCF_004329485.1-RS_2024_04_02 | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | Apr 2, 2024 | Jan 16, 2019 |
Genes | 2,984 | 3,000 |
Protein-coding | 2,660 | 2,835 |
Software version | 6.7 | 4.7 |
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 readingQuality 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 organism | Best match type-strain | |
---|---|---|
Type assembly | GCA_900478255.1 | GCA_900478255.1 |
Organism name | Staphylococcus lugdunensis | Staphylococcus lugdunensis |
Type category | type | type |
ANI | 99.44% | 99.44% |
Assembly coverage | 89.13% | 89.13% |
Type assembly coverage | 97.19% | 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_004329485.1 | GCF_004329485.1 | ASM432948v1 | Contig | Mar 6, 2019 |