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ASM208355v1

Organism name:
Nitrospira sp. ST-bin5 (bacteria)
Taxonomy check:
Inconclusive
Isolate:
ST-bin5
BioSample:
SAMN06189318
BioProject:
PRJNA315256
Submitter:
The University Hong Kong
Date:
2017/04/10
Assembly type:
na
Assembly level:
Scaffold
Genome representation:
full
Excluded from RefSeq:
  • derived from metagenome
GenBank assembly accession:
GCA_002083555.1 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
MSXN01
Assembly method:
CLC NGS Cell v. 6.04
Expected final version:
no
Genome coverage:
22.0x
Sequencing technology:
Illumina HiSeq

IDs: 1064701 [UID] 4349018 [GenBank]

See Genome Information for Nitrospira sp. ST-bin5

Pathogen Detection Resources

History (Show revision history)

Comment

Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/genome/annotation_prok/

Organism name changed from Nitrospira defluvii isolate ST-bin5 to Nitrospira sp. ST-bin5 in April 2017

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI
Annotation Date::01/05/2017 16:47:57
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline
Annotation Method::Best-placed reference protein set; GeneMarkS+
Annotation Software revision::4.0
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total)::3,975
CDS (total)::3,927
Genes (coding)::3,845
CDS (coding)::3,845
Genes (RNA)::48
rRNAs::1, 1 (5S, 23S)
complete rRNAs::1 (5S)
partial rRNAs::1 (23S)
tRNAs::42
ncRNAs::4
Pseudo Genes (total)::82
Pseudo Genes (ambiguous residues)::14 of 82
Pseudo Genes (frameshifted)::28 of 82
Pseudo Genes (incomplete)::36 of 82
Pseudo Genes (internal stop)::15 of 82
Pseudo Genes (multiple problems)::11 of 82
##Genome-Annotation-Data-END##

Global statistics

Total sequence length4,009,378
Total ungapped length4,007,813
Gaps between scaffolds0
Number of scaffolds29
Scaffold N50219,543
Scaffold L507
Number of contigs57
Contig N50134,955
Contig L5010
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)29

Supplemental Content

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Assembly Information

Related Information

PubMed articles for this assembly

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
The primary assembly unit does not have any assembled chromosomes or linkage groups.
Please download the full sequence report for information on the scaffolds.

Assembly statistics

MoleculeTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
unplaced4,009,378294,007,813219,543280

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Nitrospira sp. ST-bin5Nitrospira sp. ST-bin5

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
no-typeno-type

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_003012745.1Mesorhizobium ephedraetype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared typenanana
Best-match type87.530.010.01

ANI result

Taxonomy check statusBest match statusComment
Inconclusivelow-coveragena