Genome assembly ASM4092330v1

FTP
Actions
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

RefSeqGenBank
Genome size5.2 Mb5.2 Mb
Total ungapped length5.2 Mb5.2 Mb
Number of scaffolds118118
Scaffold N5079.3 kb79.3 kb
Scaffold L502222
Number of contigs131131
Contig N5071.3 kb71.3 kb
Contig L502323
GC percent4343
Genome coverage23.7x23.7x
Assembly levelScaffoldScaffold
View sequencesview 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

PRJNA1093465

human gut bacterial isolate genomes Genome sequencing and assembly

Annotation details

RefSeq
ProviderNCBI RefSeq
NameGCF_040923305.1-RS_2024_07_28
DateJul 28, 2024
Genes4,350
Protein-coding4,172
Software version6.7

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 reading

Quality 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 organismBest match type-strain
Type assemblyGCA_000025985.1GCA_000025985.1
Organism nameBacteroides fragilis NCTC 9343Bacteroides fragilis
Type categorytypetype
ANI99.46%99.46%
Assembly coverage89.51%89.51%
Type assembly coverage89.21%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_040923305.1GCF_040923305.1ASM4092330v1ScaffoldJul 27, 2024