Genome assembly ASM183720v1
- NCBI RefSeq assembly
- GCF_001837205.1
- Submitted GenBank assembly
- GCA_001837205.1
- Taxon
- Streptococcus sp. HMSC064D12
- Strain
- HMSC064D12
- WGS project
- LTPP01
- Submitter
- The Genome Institute at Washington University
- Date
- Oct 25, 2016
Assembly statistics
RefSeq | GenBank | |
---|---|---|
Genome size | 2.1 Mb | 2.1 Mb |
Total ungapped length | 2.1 Mb | 2.1 Mb |
Number of scaffolds | 71 | 71 |
Scaffold N50 | 131.7 kb | 131.7 kb |
Scaffold L50 | 6 | 6 |
Number of contigs | 120 | 120 |
Contig N50 | 63.2 kb | 63.2 kb |
Contig L50 | 12 | 12 |
GC percent | 40 | 40 |
Genome coverage | 189.0x | 189.0x |
Assembly level | Scaffold | Scaffold |
View sequences | view RefSeq sequences | view GenBank sequences |
Sample details
- BioSample ID
- SAMN04498650
- Description
- Sample from Streptococcus sp. HMSC064D12
- Submitter
- The Genome Center at Washington University School of Medicine in St. Louis
- Host
- Homo sapiens
- Strain
- HMSC064D12
- Isolation source
- sputum
- Sample name
- 615290
- SRA
- SRS1300360
- Models
- Generic
- Package
- Generic.1.0
- Submission date
- 2016-02-18T16:05:22.110
- Publication date
- 2016-02-19T11:05:23.297
- Last updated
- 2016-02-26T17:14:53.857
Assembly methods
- Sequencing technology
- Illumina
- Comment
Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
The WUSC is a large strain collection isolated from clinical samples. Each sample is associated with metadata, including source, isolation site, 16s rRNA, metabolic, and other phenotypic information. The goal is to sample an adequate number of important, yet minor species, further adding to the catelogue of sequenced bacterial genomes and improving the diversity of the genomes available to the public. WGS will be preformed on approximely 550 isolates. Samples were selected based on RDP analysis at the genus level. This is a reference genomes for the Human Microbiome Project and the work was funded by the National Institutes of Health (NIH) grant U54 HG004968.
- Assembly method
- Velvet v. 1.1.06
Additional genomes
Browse all Streptococcus sp. HMSC064D12 genomes (1)BioProject
PRJNA296304HMP reference genome
Publications
RefSeq microbial genomes database: new representation and annotation strategy
T Tatusova, et al.
Annotation details
RefSeq | GenBank | |
---|---|---|
Provider | NCBI RefSeq | NCBI |
Name | GCF_001837205.1-RS_2024_09_10 | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | Sep 10, 2024 | Mar 3, 2016 |
Genes | 2,034 | 1,996 |
Protein-coding | 1,930 | 1,864 |
Software version | 6.8 | 3.1 |
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: 99.69% (100th Percentile)
Contamination: 0.06%
Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Streptococcus 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
- Streptococcus sp. HMSC064D12
- Submitted species name
- Streptococcus sp. HMSC064D12
Average Nucleotide Identity (ANI) match details
Best match type-strain for submitted organism | Best match type-strain | |
---|---|---|
Type assembly | n/a | GCA_000785515.1 |
Organism name | n/a | Streptococcus salivarius |
Type category | n/a | type |
ANI | n/a | 95.88% |
Assembly coverage | n/a | 84.56% |
Type assembly coverage | n/a | 81.37% |
Chromosomes
Note: This scaffold-level genome assembly includes 71 scaffolds and no assembled chromosomes.
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_001837205.1 | GCF_001837205.1 | ASM183720v1 | Scaffold | Oct 25, 2016 |