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ASM1332185v1

Organism name:
Rhizobium rhizogenes (a-proteobacteria)
Taxonomy check:
OK
Infraspecific name:
Strain: C16/80
BioSample:
SAMN14165495
BioProject:
PRJNA607555
Submitter:
Oregon State University
Date:
2020/06/10
Assembly type:
na
Assembly level:
Scaffold
Genome representation:
full
GenBank assembly accession:
GCA_013321855.1 (latest)
RefSeq assembly accession:
GCF_013321855.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
JAAMEJ01
Assembly method:
SPAdes v. 3.13.1
Expected final version:
yes
Genome coverage:
55x
Sequencing technology:
Illumina HiSeq

IDs: 7259991 [UID] 20002758 [GenBank] 20066978 [RefSeq]

See Genome Information for Rhizobium rhizogenes

There are 97 assemblies for this organism

See more

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::02/29/2020 01:55:11
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)::6,924
CDSs (total)::6,860
Genes (coding)::6,744
CDSs (with protein)::6,744
Genes (RNA)::64
rRNAs::2, 1, 2 (5S, 16S, 23S)
complete rRNAs::2, 1, 2 (5S, 16S, 23S)
tRNAs::55
ncRNAs::4
Pseudo Genes (total)::116
CDSs (without protein)::116
Pseudo Genes (ambiguous residues)::0 of 116
Pseudo Genes (frameshifted)::57 of 116
Pseudo Genes (incomplete)::61 of 116
Pseudo Genes (internal stop)::21 of 116
Pseudo Genes (multiple problems)::22 of 116
##Genome-Annotation-Data-END##

Global statistics

Total sequence length7,319,985
Total ungapped length7,319,149
Gaps between scaffolds0
Number of scaffolds77
Scaffold N50892,609
Scaffold L504
Number of contigs79
Contig N50892,609
Contig L504
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)77

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
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
unplaced7,319,985777,319,149892,60920

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Rhizobium rhizogenesRhizobium rhizogenes

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_007002985.1Rhizobium rhizogenestype

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_007002985.1Rhizobium rhizogenestype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type99.4291.4294.86
Best-match type99.4291.4294.86

ANI result

Taxonomy check statusBest match statusComment
OKspecies-matchna