Genome sc|0001668

Genomics

Accession

NCBI Assembly:GCA_016708345.1

Type

Metagenome-Assembled Genome (MAG)

Estimated Quality Metrics

• Completeness: 96.31%
• Contamination: 4.13%
• Quality: 75.66

Ribosomal and transfer RNA genes

• 2 16S rRNAs (up to 100.0%)
• 2 23S rRNAs (up to 100.0%)
• tRNAs for 19 amino acids

Sequencing depth

17.8 ×

Source

• BioSample: SAMN16425705
• BioSample: SAMN14825675

Other features

• G+C Content: 57.55%
• Coding Density: 87.26%
• Codon Table: 11
• N50: 213,974 bp
• Contigs: 44
• Largest Contig: 698,924 bp
• Assembly Length: 4,960,954 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

Sample Metadata

BioSample entries

• BioSample: SAMN16425705
• BioSample: SAMN14825675

Date

Collection Date: 2018-08-29

Location

Lat Lon: 55.649286 N 12.058568 E

Toponym

Geo Loc Name: Denmark: Bjergmarken

Environment

Sample Type: metagenomic assembly

Isolation Source: activated sludge from Bjer_18-Q3-R1-45 • activated sludge

Env Broad Scale: aquatic biome [ENVO:00002030]

Env Local Scale: Waste Water [ENVO:00002001]

Env Medium: Activated Sludge [ENVO:00002046]

Other

Depth: 1m

Package

Ncbi Submission Package: MIMAG.wastewater.5.0 • MIMS.me.wastewater.5.0

Biosamplemodel: MIMAG.wastewater • MIGS/MIMS/MIMARKS.wastewater

All retrieved samples

• SAMN16425705: MIMAG Metagenome-assembled Genome sample from Rhodoferax sp.
• SAMN14825675: MIMS Environmental/Metagenome sample from activated sludge metagenome

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Metadata retrieved 6 months ago