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Genome sc|0001890

Database

INSDC Nucleotide

Accession

JAPYMX000000000

Genomics

Accession
INSDC Nucleotide:JAPYMX000000000
Type
Metagenome-Assembled Genome (MAG)
Estimated Quality Metrics
  • Completeness: 83.0% (automated estimate: 73.6%)
  • Contamination: 0.18% (automated estimate: 0.9%)
  • Quality: 82.1 (automated estimate: 69.1)
Ribosomal and transfer RNA genes
  • 1 16S rRNA (up to 77.0%)
  • 0 23S rRNAs
  • tRNAs for 19 amino acids
Sequencing depth
20.0 ×
Source
Other features
  • G+C Content: 64.19%
  • Coding Density: 90.1%
  • Codon Table: 11
  • N50: 7,062 bp
  • Contigs: 167
  • Largest Contig: 29,836 bp
  • Assembly Length: 1,058,502 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
Assembly size is relatively small (~1 Mb). Given the completeness estimate of 83%, this indicates a reduced genome for this lineages compared to other gammaproteobacterial clades. This would also indicate that some marker genes used for completeness estimates are likely missing and thus completeness is potentially underestimated. Please also note the high tRNA number, which would support this point.
Automated checks
Complete
Last modified 6 months ago

Sample Metadata

BioSample entries
Date
Collection Date: 2014-06
Location
Lat Lon: 18.816 S 147.633 E
Toponym
Geo Loc Name: Australia: Davies Reef, Great Barrier Reef
Environment
Sample Type: metagenomic assembly
Isolation Source: sponge tissue, high temperature, high CO2 • sponge tissue
Env Broad Scale: coral reef [ENVO:00000150]
Env Local Scale: coral reef [ENVO:00000150]
Env Medium: sponge
Other
Host: Stylissa flabelliformis
Package
Ncbi Submission Package: Metagenome.environmental.1.0
Biosamplemodel: Metagenome or environmental
All retrieved samples
Metadata retrieved 6 months ago


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