JSON

Genome sc|0001743

Name

Poseidonia alphaeTs

Database

NCBI Assembly

Accession

GCA_002505405.1

Genomics

Accession
NCBI Assembly:GCA_002505405.1
Type
Metagenome-Assembled Genome (MAG)
Estimated Quality Metrics
  • Completeness: 90.9%
  • Contamination: 0.0%
  • Quality: 90.9
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
54.6 ×
Source
Other features
  • G+C Content: 50.0%
  • Coding Density: 94.34%
  • Codon Table: 11
  • N50: 72,244 bp
  • Contigs: 50
  • Largest Contig: 249,938 bp
  • Assembly Length: 1,936,638 bp
  • Ambiguous Assembly Fraction: 0.17%
Submitter comments
The completeness and contamination estimates provided by CheckM are based on the presence of predefined lineage-specific marker sets [17]. These marker sets can be further refined using checkm qa --out_format 4 (list of marker genes and their counts), which allows screening a lineage, in our case Candidatus Poseidoniales (MG II), to identify markers which are absent from all MAGs in the lineage. Based on this workflow we excluded 11 marker genes (TIGR00537, TIGR02237, TIGR00422, PF01287.15, TIGR03677, PF09249.6, PF13685.1, TIGR00162, PF02649.9, PF03684.8, PF01849.13) that were absent across all 270 Ca. Poseidoniales MAGs, resulting in 177 marker genes being used for completeness and contamination estimates. 
Automated checks
Complete
Last modified about 1 month ago

Sample Metadata

BioSample entries
Date
Collection Date: 2011-04-28
Location
Lat Lon: 54.174167 N 7.900 E
Toponym
Geo Loc Name: North Sea
Environment
Env Material: Subsurface seawater
Sample Type: metagenomic assembly
Env Biome: Marine
Isolation Source: Subsurface seawater
Gold Ecosystem Classification: Environmental | Aquatic | Marine | Neritic zone/Coastal water | Unclassified
Other
Depth: 1 m
Package
Ncbi Submission Package: Microbe.1.0 • MIMS.me.water.6.0
Biosamplemodel: Microbe, viral or environmental • MIGS/MIMS/MIMARKS.water
All retrieved samples
Metadata retrieved about 1 month ago

Sequencing Experiments

Recovery of uncultivated bacterial and archaeal genomes substantially flesh out the tree of life: Sample Euryarchaeota archaeon UBA255
COGITO 998_met_07 Sequencing


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