Genome sc|0001743

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

• BioSample: SAMN06027172
• BioSample: SAMN03169783

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

Sample Metadata

Date

Collection Date: not applicable • 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

• SAMN06027172: Uncultivated Euryarchaeota archaeon UBA255 genome recovered from SRX802077
• SAMN03169783: MIMS Environmental/Metagenome sample from marine metagenome

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Metadata retrieved 14 days ago