JSON

Genome sc|0001556

Name

Promineifilum glycogenicum

Database

NCBI Assembly

Accession

GCA_016707605.1

Genomics

Accession
NCBI Assembly:GCA_016707605.1
Type
Metagenome-Assembled Genome (MAG)
Estimated Quality Metrics
  • Completeness: 90.0%
  • Contamination: 4.55%
  • Quality: 67.25
Ribosomal and transfer RNA genes
  • 1 16S rRNA (up to 100.0%)
  • 1 23S rRNA (up to 100.0%)
  • tRNAs for 19 amino acids
Sequencing depth
16.0 ×
Source
Other features
  • G+C Content: 66.77%
  • Coding Density: 87.71%
  • Codon Table: 11
  • N50: 316,583 bp
  • Contigs: 26
  • Largest Contig: 1,110,292 bp
  • Assembly Length: 5,044,159 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
Although this MAG has a borderline completeness as assessed by checkM (v1.2.2, =90.00%, instead of >90.00%) and a contamination of 4.55%, the automatic assessment with MiGA estimates a slightly higher completeness and this MAG is the only one present under this GTDB R214 species (d__Bacteria; p__Chloroflexota; c__Anaerolineae; o__Promineofilales; f__Promineofilaceae; g__Promineofilum; s__Promineofilum sp016707605). When compared to all the 9 species representatives under this entire genus (g__Promineofilum), this MAG has very good quality by having low fragmentation (the 2nd lowest number of contig counts of 26, 2nd largest longest contig of 1.11 Mbp, 2nd largest N50 of 0.317 Mbp), and being present with 16S, 23S, and 5S rRNA genes, as well as 19 tRNA genes (>=18 as required by MiMAG standard), while having no ambiguous bases and gaps. All these suggests the high assembly quality of this MAG.
Automated checks
Complete
Last modified about 1 month ago

Sample Metadata

BioSample entries
Date
Collection Date: 2018-08-28
Location
Lat Lon: 56.21314 N 10.242467 E
Toponym
Geo Loc Name: Denmark: Ega
Environment
Sample Type: metagenomic assembly
Isolation Source: activated sludge from Ega_18-Q3-R5-49 • activated sludge from wastewater treatment plant
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.6.0 • MIMS.me.wastewater.6.0
Biosamplemodel: MIMAG.wastewater • MIGS/MIMS/MIMARKS.wastewater
All retrieved samples
Metadata retrieved about 1 month ago

Sequencing Experiments

Illumina sequencing of activated sludge metagenome
Nanopore sequencing of activated sludge metagenome


© 2022-2024 The SeqCode Initiative
  All information contributed to the SeqCode Registry is released under the terms of the Creative Commons Attribution (CC BY) 4.0 license