Genome sc|0003618

Genomics

Accession

NCBI Assembly:GCF_006363915.1

Cultures

Strain sc|0038982

Type

Isolate Genome

Estimated Quality Metrics

• Completeness: 100.0%
• Contamination: 2.88%
• Quality: 85.6

Ribosomal and transfer RNA genes

• 2 16S rRNAs (up to 100.0%)
• 2 23S rRNAs (up to 100.0%)
• tRNAs for 20 amino acids

Sequencing depth

352.0 ×

Source

• BioSample: SAMN11964623

Other features

• G+C Content: 49.8%
• Coding Density: 90.93%
• Codon Table: 11
• N50: 2,603,080 bp
• Contigs: 1
• Largest Contig: 2,603,080 bp
• Assembly Length: 2,603,080 bp
• Ambiguous Assembly Fraction: 0.0038%

Submitter comments

Genome of a culture that was harvested by centrifugation; DNA was extracted with the Quiagen MagAttract HMW DNA kit. Sequencing was done with Illuminia MiSeq (PE250), trimming of reads with trimmomatic, assembly with SPAdes. The genome was manually polished in Geneious 9 by repeated rounds of read mapping. Completeness and contamination were assessed with CheckM, but as the genome consists of a circular chromosome, it should be complete without any contamination. 

Automated checks

Complete

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Last modified 6 months ago

Sample Metadata

BioSample entries

• BioSample: SAMN11964623

Date

Collection Date: 2015-10-07

Location

Lat Lon: 50° 10′ 44″ N, 12° 34′ 59″ E

View map of sampling locations

Toponym

Geo Loc Name: Czech Republic: Lake Medard

Environment

Sample Type: axenic culture

Env Biome: freshwater lake

Isolation Source: Water column of Lake Medard, Czechia

Other

Depth: 0.5 m

Package

Ncbi Submission Package: Microbe.1.0

Biosamplemodel: Microbe, viral or environmental

All retrieved samples

• SAMN11964623: Microbe sample from Methylophilus medardicus

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Metadata retrieved 7 months ago