Genome assembly ASM4605282v1
- 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
RefSeq | GenBank | |
---|---|---|
Genome size | 3.6 Mb | 3.6 Mb |
Total ungapped length | 3.6 Mb | 3.6 Mb |
Number of contigs | 109 | 109 |
Contig N50 | 58.3 kb | 58.3 kb |
Contig L50 | 20 | 20 |
GC percent | 58.5 | 58.5 |
Genome coverage | 10.0x | 10.0x |
Assembly level | Contig | Contig |
View sequences | view 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
PRJNA983395MAGs generated from freshwater PAH or alkane degrading cultures
Annotation details
RefSeq | |
---|---|
Provider | NCBI RefSeq |
Name | GCF_046052825.1-RS_2024_12_16 |
Date | Dec 16, 2024 |
Genes | 3,546 |
Protein-coding | 3,449 |
Software version | 6.9 |
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 readingQuality 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 organism | Best 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_046052825.1 | GCF_046052825.1 | ASM4605282v1 | Contig | Dec 12, 2024 |