Genome assembly ASM4008189v1
- NCBI RefSeq assembly
- GCF_040081895.1
- Submitted GenBank assembly
- GCA_040081895.1
- Taxon
- Xenorhabdus nematophila
- Strain
- Duz-14
- WGS project
- JBEBLX01
- Submitter
- Ordu University
- Date
- Jun 5, 2024
Assembly statistics
RefSeq | GenBank | |
---|---|---|
Genome size | 4.8 Mb | 4.8 Mb |
Total ungapped length | 4.8 Mb | 4.8 Mb |
Number of contigs | 330 | 330 |
Contig N50 | 32.1 kb | 32.1 kb |
Contig L50 | 45 | 45 |
GC percent | 44 | 44 |
Genome coverage | 205.0x | 205.0x |
Assembly level | Contig | Contig |
View sequences | view RefSeq sequences |
Sample details
- BioSample ID
- SAMN41580818
- Description
- Microbe sample from Xenorhabdus nematophila
- Submitter
- Ordu University
- Strain
- Duz-14
- Host
- Steinernema carpocapsae
- Collection date
- 2014
- Geographic location
- Turkey: Duzce
- Sample type
- whole organism
- Collected by
- Not applicable
- Culture collection
- Not applicable
- Depth
- Not applicable
- Genotype
- Not applicable
- Identified by
- Not applicable
- Lab host
- Not applicable
- Mating type
- Not applicable
- Passage history
- Not applicable
- Sample size
- Not applicable
- Sample name
- Xenorhabdus nematophila
- Models
- Microbe, viral or environmental
- Package
- Microbe.1.0
- Submission date
- 2024-05-29T11:01:04.047
- Publication date
- 2024-05-29T00:00:00.000
- Last updated
- 2024-05-29T12:01:04.770
Assembly methods
- Sequencing technology
- Illumina NovaSeq
- Comment
Bacteria and source DNA available from Selcuk Hazir
The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
- Assembly method
- CLC NGS Cell v. 22.0.1
Additional genomes
Browse all Xenorhabdus nematophila genomes (17)BioProject
PRJNA1117817Xenorhabdus nematophila strain:Duz-14 Genome sequencing
Publications
RefSeq microbial genomes database: new representation and annotation strategy
T Tatusova, et al.
Annotation details
RefSeq | GenBank | |
---|---|---|
Provider | NCBI RefSeq | NCBI |
Name | GCF_040081895.1-RS_2024_06_06 | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | Jun 6, 2024 | May 31, 2024 |
Genes | 4,664 | 4,663 |
Protein-coding | 4,309 | 4,364 |
Software version | 6.7 | 6.7 |
View RefSeq annotation | View GenBank annotation |
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: 94.42% (73rd Percentile)
Contamination: 5.94%
Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Xenorhabdus 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
- Xenorhabdus nematophila
- Submitted species name
- Xenorhabdus nematophila
Average Nucleotide Identity (ANI) match details
Best match type-strain for submitted organism | Best match type-strain | |
---|---|---|
Type assembly | GCA_000252955.1 | GCA_000252955.1 |
Organism name | Xenorhabdus nematophila ATCC 19061 | Xenorhabdus nematophila |
Type category | type | type |
ANI | 99.09% | 99.09% |
Assembly coverage | 78.83% | 78.83% |
Type assembly coverage | 81.96% | 81.96% |
Chromosomes
Note: This contig-level genome assembly includes 330 contigs and no assembled chromosomes.
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_040081895.1 | GCF_040081895.1 | ASM4008189v1 | Contig | Jun 5, 2024 |