Genome sc|0001698


Database

NCBI Assembly

Accession

GCA_009992655.1

Genomics

Accession
NCBI Assembly:GCA_009992655.1
Type
Metagenome-Assembled Genome (MAG)
Estimated Quality Metrics
  • Completeness: 85.0%
  • Contamination: 0.68%
  • Quality: 81.6
Ribosomal and transfer RNA genes
  • 1 16S rRNA (up to 100.0%)
  • 1 23S rRNA (up to 100.0%)
  • tRNAs for 18 amino acids
Sequencing depth
1000.0 ×
Source
Other features
  • G+C Content: 32.0%
  • Coding Density: 79.61%
  • Codon Table: 11
  • N50: 9,132 bp
  • Contigs: 223
  • Largest Contig: 35,706 bp
  • Assembly Length: 1,480,107 bp
  • Ambiguous Assembly Fraction: 0.024%
Submitter comments
We are aware of the fact that the genome is highly fragmented and is of low completeness. This has some biological reasons that I would like to explain here and based on which I'd like to receive an exemption for this submission.
a) The genome completeness is low because this is a deep-branching organism. We currently have a manuscript in preparation with the first complete genome and a genome in 5 contigs, both of which have a completeness of about 90%. Previous investigations have shown that there are multiple fused marker genes which are one reason for the low completeness.
b) The fragmentation of the genome is due to transposon propagation in the genome. We identified >30 transposons in the complete genome (manuscript in preparation) which results in fragmented assemblies. Yet, our assemblies have several thousand fold coverage and we are quite certain that we our genome analysis is fairly complete.
Automated checks
Complete

Last modified 8 months ago

Sample Metadata

BioSample entries
Date
Collection Date: 2015-05-29
Location
Lat Lon: 38.9383 N 110.1342 W
Toponym
Geo Loc Name: USA: Utah, Crystal Geyser near Green River
Environment
Sample Type: metagenomic assembly
Isolation Source: subsurface aquifer
Gold Ecosystem Classification: Environmental | Aquatic | Deep subsurface | Groundwater | Unclassified
Other
Not detected
Package
Ncbi Submission Package: Microbe.1.0Metagenome.environmental.1.0
Biosamplemodel: Microbe, viral or environmental • Metagenome or environmental
All retrieved samples

Metadata retrieved 8 months ago


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