Genome assembly ASM2245469v1

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NCBI RefSeq assembly
GCF_022454695.1
Submitted GenBank assembly
GCA_022454695.1
Taxon
Lactobacillus crispatus
Strain
DZD_CM_03_S771-bin_1
WGS project
JAKXCD01
Submitter
Massachusetts General Hospital
Date
Mar 3, 2022

Assembly statistics

RefSeqGenBank
Genome size1.8 Mb1.8 Mb
Total ungapped length1.8 Mb1.8 Mb
Number of scaffolds140140
Scaffold N5020.5 kb20.5 kb
Scaffold L502525
Number of contigs141141
Contig N5020.5 kb20.5 kb
Contig L502525
GC percent3737
Genome coverage60.0x60.0x
Assembly levelScaffoldScaffold
View sequencesview RefSeq sequences

Sample details

BioSample ID
SAMN25207460
Description
MIGS Cultured Bacterial/Archaeal sample from Lactobacillus crispatus
Comment
Keywords: GSC:MIxS;MIGS:6.0
Submitter
Massachusetts General Hospital
Strain
DZD_CM_03_S771-bin_1
Broad-scale environmental context
ENVO:01001055
Local-scale environmental context
UBERON:0004983
Environmental medium
ENVO:02000040
Geographic location
USA
Host
Homo sapiens
Latitude and longitude
not applicable
Number of replicons
unknown
Reference for biomaterial
unpublished
Isolation source
ectocervical mucosa
Study Source Edited
Vaginal_Health_Project
Sample name
DZD_CM_03_S771-bin_1
Models
MIGS.ba, MIGS/MIMS/MIMARKS.human-vaginal
Package
MIGS.ba.human-vaginal.6.0
Submission date
2022-01-23T10:52:09.143
Publication date
2022-03-02T00:00:00.000
Last updated
2022-03-02T14:21:02.613

Assembly methods

Sequencing technology
Illumina HiSeq
Comment
DNA was extracted from a pure culture and then Nexterra libraries were prepared. To remove possible contamination, resulting sequences were binned using MetBAT2
Assembly method
SPAdes v. 3.13.032

Additional genomes

Browse all Lactobacillus crispatus genomes (791)

BioProject

PRJNA799737

Bactieral isolations derived from Vaginal Health Project samples

Annotation details

RefSeq
ProviderNCBI RefSeq
NameGCF_022454695.1-RS_2024_09_03
DateSep 3, 2024
Genes1,891
Protein-coding1,740
Software version6.8

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.

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Quality analysis

CheckM analysis (v1.2.3)

Completeness: 86.73% (8th Percentile)

Contamination: 0.09%

Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Lactobacillus crispatus 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
Lactobacillus crispatus
Submitted species name
Lactobacillus crispatus

Average Nucleotide Identity (ANI) match details

Best match type-strain for submitted organismBest match type-strain
Type assemblyGCA_001434005.1GCA_001434005.1
Organism nameLactobacillus crispatus DSM 20584 = JCM 1185 = ATCC 33820Lactobacillus crispatus
Type categorysuspected_typesuspected_type
ANI97.72%97.72%
Assembly coverage83.36%83.36%
Type assembly coverage73.39%73.39%

Chromosomes

Note: This scaffold-level genome assembly includes 140 scaffolds and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_022454695.1GCF_022454695.1ASM2245469v1ScaffoldMar 3, 2022