Genome sc|0003614


Database

NCBI Assembly

Accession

GCF_000981505.1

Genomics

Accession
NCBI Assembly:GCF_000981505.1
Cultures
Strain sc|0038781
Type
Isolate Genome
Estimated Quality Metrics
  • Completeness: 100.0%
  • Contamination: 1.29%
  • Quality: 93.55
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
481.6 ×
Source
Other features
  • G+C Content: 36.97%
  • Coding Density: 93.95%
  • Codon Table: 11
  • N50: 1,356,428 bp
  • Contigs: 1
  • Largest Contig: 1,356,428 bp
  • Assembly Length: 1,356,428 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
Genome of a culture with very slow growth and low yield. DNA was amplified by MDA (RepliPHI kit) prior to sequencing. Sequencing was done with Illuminia MiSeq (PE150), assembly was done with A5-miseq. 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 of PCR amplicons. Completeness and contamination were assessed with CheckM, but as the genome consists of a circular chromosome, it should be complete without any contamination. We have meanwhile isolated and genome-sequenced many additional strains of Methylopumilus, all of these are complete (one circular chromosome) with low completeness estimated by CheckM, which might be caused by the streamlined genome of this genus.
Automated checks
Complete

Last modified 2 months ago

Sample Metadata

BioSample entries
Date
Collection Date: 2010-10-14
Location
Geographic Location Latitude: 47° 18′ 36″ N
Geographic Location Longitude: 8° 34′ 48″ E
View map of sampling locations
Toponym
Geographic Location Country And Or Sea: Switzerland
Environment
Environment Biome: Freshwater
Environment Feature: Lake
Other
Temperature: 15.1
Geographic Location Depth: 5
Package
Ena Checklist: ERC000024
All retrieved samples

Metadata retrieved 3 months ago


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