Genome assembly ASM4605282v1

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NCBI RefSeq assembly
GCF_046052825.1
Submitted GenBank assembly
GCA_046052825.1
Taxon
Limnohabitans sp.
Isolate
L_335
WGS project
JAVLFP01
Submitter
McGill University - Macdonald Campus
Date
Dec 12, 2024

Genome notes

NCBI has noted the following for this genome assembly. View definitions

  • derived from metagenome

Assembly statistics

RefSeqGenBank
Genome size3.6 Mb3.6 Mb
Total ungapped length3.6 Mb3.6 Mb
Number of contigs109109
Contig N5058.3 kb58.3 kb
Contig L502020
GC percent58.558.5
Genome coverage10.0x10.0x
Assembly levelContigContig
View sequencesview RefSeq sequences

Sample details

BioSample ID
SAMN35725285
Description
MIMAG Metagenome-assembled Genome sample from Limnohabitans sp.
Comment
Keywords: GSC:MIxS;MIMAG:6.0
Submitter
McGill University - Macdonald Campus
Isolate
L_335
Collection date
Jun 1, 2021
Depth
0
Broad-scale environmental context
Freshwater lake
Local-scale environmental context
shoreline
Environmental medium
freshwater water
Geographic location
Canada:IISD-ELA,Lake 260
Isolation source
naphthalene degrading culture inoculated with crude oil contaminated freshwater lake water
Latitude and longitude
restricted access
Metagenomic
1
Environmental-sample
1
Sample type
metagenomic assembly
Metagenome source
freshwater metagenome
Derived from
SAMN35999591
Sample name
L_335
Models
MIMAG.water
Package
MIMAG.water.6.0
Submission date
2023-06-13T17:13:03.337
Publication date
2024-09-30T00:51:43.063
Last updated
2024-09-30T00:51:43.063

Assembly methods

Sequencing technology
Illumina HiSeq
Assembly method
metaBAT v. 2

Additional genomes

Browse all Limnohabitans sp. genomes (189)

BioProject

PRJNA983395

MAGs generated from freshwater PAH or alkane degrading cultures

Annotation details

RefSeq
ProviderNCBI RefSeq
NameGCF_046052825.1-RS_2024_12_16
DateDec 16, 2024
Genes3,546
Protein-coding3,449
Software version6.9

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: 96.25% (93rd Percentile)

Contamination: 3.78%

Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Comamonadaceae CheckM marker set. For more information on CheckM, see Parks, et al. Genome Res (2015).

Taxonomy check

Taxonomy check status
OK
Best match status
genus_match
Submitted organism name
Limnohabitans sp.
Submitted species name
Limnohabitans sp.

Average Nucleotide Identity (ANI) match details

Best match type-strain for submitted organismBest match type-strain
Type assembly

n/a

GCA_003063475.1
Organism name

n/a

Limnohabitans curvus
Type category

n/a

type
ANI

n/a

81.93%
Assembly coverage

n/a

22.54%
Type assembly coverage

n/a

26.81%

Chromosomes

Note: This contig-level genome assembly includes 109 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_046052825.1GCF_046052825.1ASM4605282v1ContigDec 12, 2024