Genome sc|0002760

Genomics

Accession

NCBI Assembly:GCA_016709495.1

Type

Metagenome-Assembled Genome (MAG)

Estimated Quality Metrics

• Completeness: 96.58%
• Contamination: 2.24%
• Quality: 85.38

Ribosomal and transfer RNA genes

• 3 16S rRNAs (up to 100.0%)
• 4 23S rRNAs (up to 100.0%)
• tRNAs for 18 amino acids

Sequencing depth

10.101773 ×

Source

• BioSample: SAMN16425889

Other features

• G+C Content: 55.52%
• Coding Density: 89.0%
• Codon Table: 11
• N50: 120,675 bp
• Contigs: 54
• Largest Contig: 422,078 bp
• Assembly Length: 4,450,621 bp
• Ambiguous Assembly Fraction: 0.0%

Submitter comments

The binning in this project followed the mmlong v0.1.2 hybrid-metaflowpipeline after the assembly step. Metagenome contigs were translated into proteins using FragGeneScan v1.31, annotated taxonomically using Kaiju v1.6.0 against the proGenomes database (2017-05-16). DASTool v1.1.1 --search_engine diamond was used to dereplicate and select for the best representative bin. The dereplicated bins in the analysis were checked for completeness and contamination using CheckM --lineage_wf v1.0.11.
Genome taxonomy was determined using GTDB-Tk v1.0.2 and the refseq release 89 (2019-06-19) database, and the dependencies pplacer v1.1, FastANI v1.2, Prodigal v2.6.2, FastTree 2 v1.2, and HMMER v3.1b2. 

Automated checks

Complete

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Last modified 26 days ago

Sample Metadata

BioSample entries

• BioSample: SAMN16425889

Date

Collection Date: 2018-09-07

Location

Lat Lon: 55.488097 N 8.430505 E

Toponym

Geo Loc Name: Denmark: Esbjerg W

Environment

Sample Type: metagenomic assembly

Isolation Source: activated sludge from EsbW_18-Q3-R4-48

Env Broad Scale: aquatic biome [ENVO:00002030]

Env Local Scale: Waste Water [ENVO:00002001]

Env Medium: Activated Sludge [ENVO:00002046]

Other

Not detected

Package

Ncbi Submission Package: MIMAG.wastewater.5.0

Biosamplemodel: MIMAG.wastewater

Additional Accessions

SAMN14825690

All retrieved samples

• SAMN16425889: MIMAG Metagenome-assembled Genome sample from Dechloromonas sp.

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Metadata retrieved 26 days ago