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ASM1480408v1

Organism name:
Treponema sp. (spirochetes)
Taxonomy check:
Inconclusive
Isolate:
Mgla_MAG_ref_134
BioSample:
SAMN14407116
BioProject:
PRJNA613381
Submitter:
University of Jyvaskyla
Date:
2020/09/29
Assembly type:
na
Assembly level:
Contig
Genome representation:
full
Excluded from RefSeq:
  • derived from metagenome
GenBank assembly accession:
GCA_014804085.1 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
JAAVAM01
Assembly method:
Megahit v. v.1.1.1-2
Expected final version:
no
Genome coverage:
41.1279900208657x
Sequencing technology:
Illumina

IDs: 8203031 [UID] 22386738 [GenBank]

See Genome Information for Treponema sp.

There are 621 assemblies for this organism

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History (Show revision history)

Comment

The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI
Annotation Date::03/31/2020 14:11:52
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Software revision::4.11
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total)::2,530
CDSs (total)::2,480
Genes (coding)::2,394
CDSs (with protein)::2,394
Genes (RNA)::50
rRNAs::1 (16S)
partial rRNAs::1 (16S)
tRNAs::46
ncRNAs::3
Pseudo Genes (total)::86
CDSs (without protein)::86
Pseudo Genes (ambiguous residues)::52 of 86
Pseudo Genes (frameshifted)::15 of 86
Pseudo Genes (incomplete)::27 of 86
Pseudo Genes (internal stop)::1 of 86
Pseudo Genes (multiple problems)::9 of 86
##Genome-Annotation-Data-END##

Global statistics

Total sequence length2,706,277
Total ungapped length2,706,277
Number of contigs75
Contig N5064,596
Contig L5013
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)75

Supplemental Content

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
Contig
Count
Ungapped
Length
Contig
N50
Spanned
Gaps
Unspanned
Gaps
unplaced2,706,277752,706,27764,59600

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Treponema sp.Treponema sp.

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
no-typeno-type

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_000255555.2Treponema saccharophilumtype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared typenanana
Best-match type78.840.950.75

ANI result

Taxonomy check statusBest match statusComment
Inconclusivelow-coveragena