Genome sc|0003577


Database

NCBI Assembly

Accession

GCA_965236175.1

Genomics

Accession
NCBI Assembly:GCA_965236175.1
Type
Metagenome-Assembled Genome (MAG)
Estimated Quality Metrics
  • Completeness: 98.8%
  • Contamination: 0.0%
  • Quality: 98.8
Ribosomal and transfer RNA genes
  • 0 16S rRNAs
  • 0 23S rRNAs
  • tRNAs for 18 amino acids
Sequencing depth
259.11 ×
Source
Other features
  • G+C Content: 29.3%
  • Coding Density: 93.92%
  • Codon Table: 11
  • N50: 164,293 bp
  • Contigs: 12
  • Largest Contig: 228,517 bp
  • Assembly Length: 1,041,213 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
This is a metagenome-assembled genome (MAG) that was assembled with FLYE v2.9.1-b1780 (settings: --nano-corr –meta –no-alt-contigs) from combined long- and short-read sequencing (Oxford Nanopore and Illumina NovaSeq). Contigs ≥3 kbp were used for hybrid binning (tetranucleotide frequencies and coverage data) using MaxBin-2.2.7, MetaBAT and MetaBAT2 and DAS Tool-1.1.3 to combine their predictions. Bins were manually curated and CheckM v1.1.3 was used to estimate bin completeness, contamination, and strain heterogeneity. rRNA genes were predicted with barrnap v0.9, tRNA genes were predicted with tRNAscan v1.4. Although the fragmentation of this long-read MAG is low (it consists of only 4 contigs), and it is highly complete (98.8%), it does not contain any rRNA genes. 
Automated checks
Complete

Last modified 30 days ago

Sample Metadata

BioSample entries
Date
Collection Date: 2022-09-25
Location
Geographic Location Latitude: 37° 28′ 29″ N • 37° 28′ 29″ N
Geographic Location Longitude: 140° 5′ 56″ E • 140° 5′ 56″ E
View map of sampling locations
Toponym
Geographic Location Country And Or Sea: Japan
Environment
Isolation Source: Lake Inawashiro
Broad Scale Environmental Context: freshwater biome
Local Environmental Context: freshwater lake • freshwater lake biome
Environmental Medium: tectonic lake
Other
Ph: 7.08
Depth: 5
Temperature: 21.02
Chlorophyll: 0.54
Salinity: 0.05
Conductivity: 0.1163
Package
Ena Checklist: ERC000047ERC000024
All retrieved samples

Metadata retrieved 30 days ago


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