U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Download Assembly



ASM1332221v1

  • Anomalous assembly.
Organism name:
Rhizobium rhizogenes (a-proteobacteria)
Taxonomy check:
Inconclusive
Infraspecific name:
Strain: 17-2069-2c
BioSample:
SAMN14165591
BioProject:
PRJNA607555
Submitter:
Oregon State University
Date:
2020/06/10
Assembly type:
na
Assembly level:
Contig
Genome representation:
full
Assembly anomaly:
contaminated
Excluded from RefSeq:
  • contaminated
GenBank assembly accession:
GCA_013322215.1 (latest)
RefSeq assembly accession:
GCF_013322215.1 (suppressed)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
JAAMEZ01
Assembly method:
SPAdes v. 3.13.1
Expected final version:
yes
Genome coverage:
26x
Sequencing technology:
Illumina HiSeq

IDs: 7260161 [UID] 20003088 [GenBank] 20067618 [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 03:58:29
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)::7,725
CDSs (total)::7,671
Genes (coding)::7,530
CDSs (with protein)::7,530
Genes (RNA)::54
rRNAs::1, 1, 1 (5S, 16S, 23S)
complete rRNAs::1, 1, 1 (5S, 16S, 23S)
tRNAs::47
ncRNAs::4
Pseudo Genes (total)::141
CDSs (without protein)::141
Pseudo Genes (ambiguous residues)::0 of 141
Pseudo Genes (frameshifted)::62 of 141
Pseudo Genes (incomplete)::85 of 141
Pseudo Genes (internal stop)::22 of 141
Pseudo Genes (multiple problems)::25 of 141
##Genome-Annotation-Data-END##

Global statistics

Total sequence length8,158,939
Total ungapped length8,158,939
Number of contigs59
Contig N50486,930
Contig L505
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)59

Supplemental Content

PubMed articles for this assembly

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

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
unplaced8,158,939598,158,939486,93000

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_000696095.1Rhizobium rhizogenes NBRC 13257type

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_900094555.1Rhizobium hainanensetype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type84.4541.2447.77
Best-match type91.3775.3484.77

ANI result

Taxonomy check statusBest match statusComment
Inconclusivebelow-threshold-mismatchna