Genome sc|0000341


Database

NCBI Assembly

Accession

GCA_028283145.1

Genomics

Accession
NCBI Assembly:GCA_028283145.1
Type
Metagenome-Assembled Genome (MAG)
Estimated Quality Metrics
  • Completeness: 87.18%
  • Contamination: 0.0%
  • Quality: 87.18
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
22.0 ×
Source
Other features
  • G+C Content: 53.65%
  • Coding Density: 89.97%
  • Codon Table: 11
  • N50: 41,524 bp
  • Contigs: 90
  • Largest Contig: 92,812 bp
  • Assembly Length: 2,332,150 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
Completeness and contamination were assessed with CheckM v1.1.0 using a lineage-specific workflow.
This symbiont is from a sponge and we have seen previously seen that sponge-associated genomes which are closed (i.e. single, circular contig) have completeness estimates that are below the 90% threshold. For example, we have one completed MAG (2000x coverage, Q>50) for a sponge symbiont and gotten the following completeness estimates:
CheckM: 91 % complete
CheckM2: 81 % complete
Busco v5: 74 % complete
Clearly all pipelines are wrong and substantially underestimate the completeness. I believe this is also the case for this organisms.
Automated checks
Complete

Sample Metadata

Date
Collection Date: 2014-06
Location
Lat Lon: 18.816 S 147.633 E
Toponym
Geo Loc Name: Australia:Davies Reef
Environment
Sample Type: metagenomic assembly
Isolation Source: sponge microbiome
Env Broad Scale: coral reef [ENVO:00000150]
Env Local Scale: coral reef [ENVO:00000150]
Env Medium: sponge
Other
Host: Cymbastela coralliophila
Package
Ncbi Submission Package: MIMAG.host-associated.5.0
Biosamplemodel: MIMAG.host-associated
All retrieved samples

Metadata retrieved 5 months ago


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