Genome assembly ASM1977872v1

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NCBI RefSeq assembly
GCF_019778725.1
Submitted GenBank assembly
GCA_019778725.1
Taxon
Rhizobium laguerreae
Strain
KalkanB
WGS project
JABCNS01
Submitter
UNIVERSITY OF CALIFORNIA DAVIS
Date
Aug 26, 2021

Assembly statistics

RefSeqGenBank
Genome size7.5 Mb7.5 Mb
Total ungapped length7.5 Mb7.5 Mb
Number of contigs4343
Contig N50354.9 kb354.9 kb
Contig L5099
GC percent6161
Genome coverage102.3x102.3x
Assembly levelContigContig
View sequencesview RefSeq sequences

Sample details

BioSample ID
SAMN14539367
Description
Genome sequencing and assembly of Rhizobium leguminosarum KalkanB
Submitter
UNIVERSITY OF CALIFORNIA DAVIS
Strain
KalkanB
Host
Lens culinaris
Isolation source
nodule
Geographic location
Turkey
Sample type
cell culture
Biomaterial provider
Cook Lab of UC Davis
Sample name
KalkanB
Models
Microbe, viral or environmental
Package
Microbe.1.0
Submission date
2020-04-04T15:25:07.870
Publication date
2021-05-01T00:50:53.810
Last updated
2021-05-01T00:50:53.810

Assembly methods

Sequencing technology
Illumina HiSeq
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/
Assembly method
SPAdes v. 3.13.1

Additional genomes

Browse all Rhizobium laguerreae genomes (105)

BioProject

PRJNA623125

Rhizobium leguminosarum GsC GsD GsE GsF GsG Genome sequencing and assembly

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqNCBI
NameGCF_019778725.1-RS_2024_10_12NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateOct 12, 2024Apr 29, 2020
Genes7,3037,296
Protein-coding6,9946,948
Software version6.84.11

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.

Continue reading

Quality analysis

CheckM analysis (v1.2.3)

Completeness: 99.94% (100th Percentile)

Contamination: 0.42%

Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Rhizobium 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
Rhizobium laguerreae
Submitted species name
Rhizobium laguerreae

Average Nucleotide Identity (ANI) match details

Best match type-strain for submitted organismBest match type-strain
Type assemblyGCA_002008165.1GCA_002008165.1
Organism nameRhizobium laguerreaeRhizobium laguerreae
Type categorytypetype
ANI96.63%96.63%
Assembly coverage83.88%83.88%
Type assembly coverage85.58%85.58%

Chromosomes

Note: This contig-level genome assembly includes 43 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_019778725.1GCF_019778725.1ASM1977872v1ContigAug 26, 2021