Genome assembly ASM4008189v1

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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

RefSeqGenBank
Genome size4.8 Mb4.8 Mb
Total ungapped length4.8 Mb4.8 Mb
Number of contigs330330
Contig N5032.1 kb32.1 kb
Contig L504545
GC percent4444
Genome coverage205.0x205.0x
Assembly levelContigContig
View sequencesview 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

PRJNA1117817

Xenorhabdus nematophila strain:Duz-14 Genome sequencing

Publications

Showing 1 of 1

View in PubMed

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqNCBI
NameGCF_040081895.1-RS_2024_06_06NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateJun 6, 2024May 31, 2024
Genes4,6644,663
Protein-coding4,3094,364
Software version6.76.7
View RefSeq annotationView 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 reading

Quality 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 organismBest match type-strain
Type assemblyGCA_000252955.1GCA_000252955.1
Organism nameXenorhabdus nematophila ATCC 19061Xenorhabdus nematophila
Type categorytypetype
ANI99.09%99.09%
Assembly coverage78.83%78.83%
Type assembly coverage81.96%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_040081895.1GCF_040081895.1ASM4008189v1ContigJun 5, 2024