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ASM4017054v1

Organism name:
Sphingobium sp. MK2 (a-proteobacteria)
Taxonomy check:
OK
Infraspecific name:
Strain: MK2
BioSample:
SAMN39584109
BioProject:
PRJNA1060937
Submitter:
Helmholtz Centre for Environmental Research - UFZ
Date:
2024/06/13
Assembly type:
na
Assembly level:
Scaffold
Genome representation:
full
GenBank assembly accession:
GCA_040170545.1 (latest)
RefSeq assembly accession:
GCF_040170545.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
JAZDXA01
Assembly method:
SPAdes v. 13.5.2
Expected final version:
yes
Genome coverage:
123.0x
Sequencing technology:
Illumina MiSeq

IDs: 22872191 [UID] 59605098 [GenBank] 59640478 [RefSeq]

History (Show revision history)

Comment

Bacteria and source DNA available from Lukas Wick, Helmholtz Centre for Environmental Research, Leipzig, Germany
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::01/29/2024 13:26:59
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Software revision::6.6
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA
Genes (total)::4,112
CDSs (total)::4,041
Genes (coding)::3,968
CDSs (with protein)::3,968
Genes (RNA)::71
tRNAs::67
ncRNAs::4
Pseudo Genes (total)::73
CDSs (without protein)::73
Pseudo Genes (ambiguous residues)::0 of 73
Pseudo Genes (frameshifted)::22 of 73
Pseudo Genes (incomplete)::63 of 73
Pseudo Genes (internal stop)::11 of 73
Pseudo Genes (multiple problems)::19 of 73
CRISPR Arrays::2
##Genome-Annotation-Data-END##

Global statistics

Total sequence length4,140,971
Total ungapped length4,140,485
Gaps between scaffolds0
Number of scaffolds118
Scaffold N5088,159
Scaffold L5015
Number of contigs123
Contig N5083,506
Contig L5015
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)118

Supplemental Content

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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
unplaced4,140,9711184,140,48588,15950

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Sphingobium sp. MK2Sphingobium sp. MK2

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
no-typeno-type

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_012927105.1Sphingobium psychrophilumtype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared typenanana
Best-match type85.6246.7937.53

ANI result

Taxonomy check statusBest match statusComment
OKgenus-matchna