Genome assembly ASM393602v1

Actions
NCBI RefSeq assembly
GCF_003936025.1
Submitted GenBank assembly
GCA_003936025.1
Taxon
Stutzerimonas stutzeri
Strain
PS_138
WGS project
RHRE01
Submitter
Washington University in St. Louis School of Medicine
Date
Dec 11, 2018

Assembly statistics

RefSeqGenBank
Genome size4.4 Mb4.4 Mb
Total ungapped length4.4 Mb4.4 Mb
Number of scaffolds5252
Scaffold N50168.6 kb168.6 kb
Scaffold L5088
Number of contigs5656
Contig N50157.5 kb157.5 kb
Contig L5099
GC percent6464
Genome coverage28.0x28.0x
Assembly levelScaffoldScaffold

Sample details

BioSample ID
SAMN10249100
Description
Microbe sample from Stutzerimonas stutzeri
Submitter
Washington University in St. Louis School of Medicine
Strain
PS_138
Isolation source
nursing call button in hospital intensive care unit
Collection date
2016-04
Geographic location
Pakistan
Sample type
whole organism
Relative week
12
Collection room
PAK-2
Sample name
PS_138
SRA
SRS5369388
Models
Microbe, viral or environmental
Package
Microbe.1.0
Submission date
2018-10-16T18:54:07.316
Publication date
2018-12-08T00:00:00.000
Last updated
2022-07-29T21:06:01.098

Assembly methods

Sequencing technology
Illumina NextSeq
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. 3.11.0

Additional genomes

Browse all Stutzerimonas stutzeri genomes (726)

BioProject

PRJNA497126

Pakistan and United States ICU transmission dynamics

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqNCBI
NameGCF_003936025.1-RS_2024_03_12NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateMar 12, 2024Nov 9, 2018
Genes4,1004,099
Protein-coding3,9853,962
Software version6.74.6

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.

Continue reading

Quality analysis

CheckM analysis (v1.2.3)

Completeness: 99.4% (39th Percentile)

Contamination: 0.02%

Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Pseudomonas stutzeri 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
Stutzerimonas stutzeri
Submitted species name
Stutzerimonas stutzeri

Average Nucleotide Identity (ANI) match details

Best match type-strain for submitted organismBest match type-strain
Type assemblyGCA_000219605.1GCA_000219605.1
Organism nameStutzerimonas stutzeriStutzerimonas stutzeri
Type categorytypetype
ANI97.56%97.56%
Assembly coverage89.73%89.73%
Type assembly coverage85.98%85.98%

Chromosomes

Note: This scaffold-level genome assembly includes 52 scaffolds and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_003936025.1GCF_003936025.1ASM393602v1ScaffoldDec 11, 2018