Genome sc|0000339


Database

NCBI Assembly

Accession

GCA_028278785.1

Genomics

Accession
NCBI Assembly:GCA_028278785.1
Type
Metagenome-Assembled Genome (MAG)
Estimated Quality Metrics
  • Completeness: 85.9%
  • Contamination: 4.27%
  • Quality: 64.55
Ribosomal and transfer RNA genes
  • 1 16S rRNA (up to 80.0%)
  • 0 23S rRNAs
  • tRNAs for 20 amino acids
Sequencing depth
11.0 ×
Source
Other features
  • G+C Content: 65.92%
  • Coding Density: 91.44%
  • Codon Table: 11
  • N50: 9,022 bp
  • Contigs: 302
  • Largest Contig: 48,813 bp
  • Assembly Length: 2,243,157 bp
  • Ambiguous Assembly Fraction: 0.0029%
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.

We have not be able to reconstruct a better 16S rRNA gene sequence, but phylogenetic placement of the 16S rRNA gene is robust (see Nguyen et al., 2023).
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: Rhopaloeides odorabile
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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