Genome assembly ASM4092330v1
- NCBI RefSeq assembly
- GCF_040923305.1
- Submitted GenBank assembly
- GCA_040923305.1
- Taxon
- Bacteroides fragilis
- Strain
- RTP31084st1_G2_RTP31084_210423
- WGS project
- JBCOOA01
- Submitter
- Icahn School of Medicine at Mount Sinai
- Date
- Jul 27, 2024
Assembly statistics
RefSeq | GenBank | |
---|---|---|
Genome size | 5.2 Mb | 5.2 Mb |
Total ungapped length | 5.2 Mb | 5.2 Mb |
Number of scaffolds | 118 | 118 |
Scaffold N50 | 79.3 kb | 79.3 kb |
Scaffold L50 | 22 | 22 |
Number of contigs | 131 | 131 |
Contig N50 | 71.3 kb | 71.3 kb |
Contig L50 | 23 | 23 |
GC percent | 43 | 43 |
Genome coverage | 23.7x | 23.7x |
Assembly level | Scaffold | Scaffold |
View sequences | view RefSeq sequences |
Sample details
- BioSample ID
- SAMN41030507
- Description
- MIGS Cultured Bacterial/Archaeal sample from Bacteroides fragilis
- Comment
- Keywords: GSC:MIxS;MIGS:6.0
- Submitter
- Icahn School of Medicine at Mount Sinai
- Collection date
- Apr 23, 2021
- Broad-scale environmental context
- human gut
- Local-scale environmental context
- human feces
- Environmental medium
- rich broth
- Geographic location
- USA: New York
- Host
- Homo sapiens
- Isolation source
- feces
- Isolation and growth condition
- 37C rich media
- Latitude and longitude
- 40.7128 N 74.0060 W
- Number of replicons
- na
- Reference for biomaterial
- 10.1101/2022.11.01.514782
- Strain
- RTP31084st1_G2_RTP31084_210423
- Note
- RTP31084st1
- Isolate name alias
- Bacteroides_fragilis_RTP31084st1_G2_RTP31084_210423
- Sample name
- Bacteroides_fragilis_RTP31084st1_G2_RTP31084_210423
- Models
- MIGS.ba, MIGS/MIMS/MIMARKS.human-gut
- Package
- MIGS.ba.human-gut.6.0
- Submission date
- 2024-04-21T11:48:07.776
- Publication date
- 2024-04-21T00:00:00.000
- Last updated
- 2024-04-22T14:56:45.588
Assembly methods
- Sequencing technology
- Illumina
- Assembly method
- SPAdes v. v3.14.1
Additional genomes
Browse all Bacteroides fragilis genomes (1602)BioProject
PRJNA1093465human gut bacterial isolate genomes Genome sequencing and assembly
Annotation details
RefSeq | |
---|---|
Provider | NCBI RefSeq |
Name | GCF_040923305.1-RS_2024_07_28 |
Date | Jul 28, 2024 |
Genes | 4,350 |
Protein-coding | 4,172 |
Software version | 6.7 |
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: 98.46% (39th Percentile)
Contamination: 1.47%
Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Bacteroides fragilis 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
- Bacteroides fragilis
- Submitted species name
- Bacteroides fragilis
Average Nucleotide Identity (ANI) match details
Best match type-strain for submitted organism | Best match type-strain | |
---|---|---|
Type assembly | GCA_000025985.1 | GCA_000025985.1 |
Organism name | Bacteroides fragilis NCTC 9343 | Bacteroides fragilis |
Type category | type | type |
ANI | 99.46% | 99.46% |
Assembly coverage | 89.51% | 89.51% |
Type assembly coverage | 89.21% | 89.21% |
Chromosomes
Note: This scaffold-level genome assembly includes 118 scaffolds and no assembled chromosomes.
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_040923305.1 | GCF_040923305.1 | ASM4092330v1 | Scaffold | Jul 27, 2024 |