Genome assembly ASM183720v1

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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

RefSeqGenBank
Genome size2.1 Mb2.1 Mb
Total ungapped length2.1 Mb2.1 Mb
Number of scaffolds7171
Scaffold N50131.7 kb131.7 kb
Scaffold L5066
Number of contigs120120
Contig N5063.2 kb63.2 kb
Contig L501212
GC percent4040
Genome coverage189.0x189.0x
Assembly levelScaffoldScaffold
View sequencesview RefSeq sequencesview 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

PRJNA296304

HMP reference genome

Publications

Showing 1 of 1

View in PubMed

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqNCBI
NameGCF_001837205.1-RS_2024_09_10NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateSep 10, 2024Mar 3, 2016
Genes2,0341,996
Protein-coding1,9301,864
Software version6.83.1

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.

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Quality 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 organismBest 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_001837205.1GCF_001837205.1ASM183720v1ScaffoldOct 25, 2016