Genome assembly ASM400407v1

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NCBI RefSeq assembly
GCF_004004075.1
Submitted GenBank assembly
GCA_004004075.1
Taxon
Sinorhizobium meliloti
Strain
USDA1031
WGS project
RPNJ01
Submitter
University of Minneosta
Date
Jan 8, 2019

Assembly statistics

RefSeqGenBank
Genome size6.6 Mb6.6 Mb
Total ungapped length6.6 Mb6.6 Mb
Number of contigs145145
Contig N50103.4 kb103.4 kb
Contig L502222
GC percent6262
Genome coverage12.6x12.6x
Assembly levelContigContig
View sequencesview RefSeq sequencesview GenBank sequences

Sample details

BioSample ID
SAMN07640758
Description
Microbe sample from Sinorhizobium meliloti
Submitter
University of Minnesota
Strain
USDA1031
Host
Medicago sativa
Isolation source
root nodule
Collection date
1952
Geographic location
Turkey
Sample type
Single Cell
Sample name
USDA1031
SRA
SRS2529096
Models
Microbe, viral or environmental
Package
Microbe.1.0
Submission date
2017-09-13T18:02:06.623
Publication date
2018-08-02T00:00:00.000
Last updated
2018-11-20T10:24:29.802

Assembly methods

Sequencing technology
Illumina Miseq
Comment
Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
Assembly method
SPAdes v. 3.13.0

Additional genomes

Browse all Sinorhizobium meliloti genomes (471)

BioProject

PRJNA401434

Ensifer spp associated with Medicago whole genome sequencing

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqNCBI
NameNCBI Prokaryotic Genome Annotation Pipeline (PGAP)NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateJan 26, 2024Nov 22, 2018
Genes6,4146,688
Protein-coding6,0746,244
Software version6.64.7

About PGAP

The NCBI Prokaryotic Genome Annotation Pipeline (PGAP) uses multiple approaches to predict protein-coding and RNA genes and other functional elements directly from sequence.

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Quality analysis

CheckM analysis (v1.2.2)

Completeness: 98.97% (41st Percentile)

Contamination: 0.96%

Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Ensifer meliloti CheckM marker set. For more information on CheckM, see Parks, et al. Genome Res (2015).

Taxonomy check

Taxonomy check status
OK
Best match status
species_match
Submitted organism name
Sinorhizobium meliloti
Submitted species name
Sinorhizobium meliloti

Average Nucleotide Identity (ANI) match details

Best match type-strain for submitted organismBest match type-strain
Type assemblyGCA_017876815.1GCA_017876815.1
Organism nameSinorhizobium melilotiSinorhizobium meliloti
Type categorysuspected_typesuspected_type
ANI99.57%99.57%
Assembly coverage94.77%94.77%
Type assembly coverage85.33%85.33%

Chromosomes

Note: This contig-level genome assembly includes 145 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_004004075.1GCF_004004075.1ASM400407v1ContigJan 8, 2019