Genome sc|0003622


Database

NCBI Assembly

Accession

GCF_002287885.2

Genomics

Accession
NCBI Assembly:GCF_002287885.2
Cultures
Strain sc|0038985
Type
Isolate Genome
Estimated Quality Metrics
  • Completeness: 91.6%
  • Contamination: 0.0%
  • Quality: 91.6
Ribosomal and transfer RNA genes
  • 1 16S rRNA (up to 100.0%)
  • 1 23S rRNA (up to 100.0%)
  • tRNAs for 20 amino acids
Sequencing depth
800.0 ×
Source
Other features
  • G+C Content: 41.5%
  • Coding Density: 95.21%
  • Codon Table: 11
  • N50: 1,238,108 bp
  • Contigs: 1
  • Largest Contig: 1,238,108 bp
  • Assembly Length: 1,238,108 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
Genome of a culture with growth arrest. DNA was amplified by MDA (REPLI-g single cell kit) prior to sequencing. Sequencing was done with Illuminia MiSeq (PE250), assembly was done with SPAdes-3.7.0. The genome was manually curated to a circular chromosome in Geneious 7.1.7 by repeated rounds of read mapping, primer design for contig ends and low-coverage regions and sanger sequencing. Completeness and contamination were assessed with CheckM, but as the genome consists of a circular chromosome, it should be complete without any contamination. 
Automated checks
Complete

Last modified 3 months ago

Sample Metadata

BioSample entries
Date
Collection Date: 2012-05-25
Location
Lat Lon: 47° 18′ 36″ N, 8° 34′ 48″ E
View map of sampling locations
Toponym
Geo Loc Name: Switzerland: Lake Zurich
Environment
Sample Type: cell culture
Env Biome: Freshwater
Isolation Source: Switzerland: Lake Zurich, 5 m depth
Other
Not detected
Package
Ncbi Submission Package: Microbe.1.0
Biosamplemodel: Microbe, viral or environmental
All retrieved samples

Metadata retrieved 3 months ago

Sequencing Experiments

Candidatus Nanopelagicus limnes MMS-21-122


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