Genome sc|0001744

Genomics

Accession

NCBI Assembly:GCA_003193925.1

Type

Metagenome-Assembled Genome (MAG)

Estimated Quality Metrics

• Completeness: 92.2%
• Contamination: 0.0%
• Quality: 92.2

Ribosomal and transfer RNA genes

• 1 16S rRNA (up to 100.0%)
• 1 23S rRNA (up to 79.0%)
• tRNAs for 19 amino acids

Sequencing depth

68.4 ×

Source

• BioSample: SAMN08159283
• BioSample: SAMN08159211

Other features

• G+C Content: 61.0%
• Coding Density: 93.6%
• Codon Table: 11
• N50: 104,796 bp
• Contigs: 23
• Largest Contig: 252,755 bp
• Assembly Length: 1,479,542 bp
• Ambiguous Assembly Fraction: 0.00047%

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: 2012-01-18

Location

Lat Lon: 18.23 N 81.48 W

Toponym

Geo Loc Name: not applicable

Environment

Sample Type: metagenomic assembly

Isolation Source: hydrothermal plume in the Mid-Cayman Rise

Other

Not detected

Package

Ncbi Submission Package: Microbe.1.0 • Metagenome.environmental.1.0

Biosamplemodel: Microbe, viral or environmental • Metagenome or environmental

All retrieved samples

• SAMN08159283: Microbe sample from Euryarchaeota archaeon
• SAMN08159211: procaryotic metagenome from Von Damm Rising plume

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Metadata retrieved 16 days ago