Genome assembly ASM2245469v1
- 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
RefSeq | GenBank | |
---|---|---|
Genome size | 1.8 Mb | 1.8 Mb |
Total ungapped length | 1.8 Mb | 1.8 Mb |
Number of scaffolds | 140 | 140 |
Scaffold N50 | 20.5 kb | 20.5 kb |
Scaffold L50 | 25 | 25 |
Number of contigs | 141 | 141 |
Contig N50 | 20.5 kb | 20.5 kb |
Contig L50 | 25 | 25 |
GC percent | 37 | 37 |
Genome coverage | 60.0x | 60.0x |
Assembly level | Scaffold | Scaffold |
View sequences | view 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- unpublished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
PRJNA799737Bactieral isolations derived from Vaginal Health Project samples
Annotation details
RefSeq | |
---|---|
Provider | NCBI RefSeq |
Name | GCF_022454695.1-RS_2024_09_03 |
Date | Sep 3, 2024 |
Genes | 1,891 |
Protein-coding | 1,740 |
Software version | 6.8 |
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.
Continue readingQuality 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 organism | Best match type-strain | |
---|---|---|
Type assembly | GCA_001434005.1 | GCA_001434005.1 |
Organism name | Lactobacillus crispatus DSM 20584 = JCM 1185 = ATCC 33820 | Lactobacillus crispatus |
Type category | suspected_type | suspected_type |
ANI | 97.72% | 97.72% |
Assembly coverage | 83.36% | 83.36% |
Type assembly coverage | 73.39% | 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_022454695.1 | GCF_022454695.1 | ASM2245469v1 | Scaffold | Mar 3, 2022 |