Genome sc|0000458


Database

NCBI Assembly

Accession

GCF_030412265.1

Genomics

Accession
NCBI Assembly:GCF_030412265.1
Type
Isolate Genome
Estimated Quality Metrics
  • Completeness: 98.92%
  • Contamination: 0.86%
  • Quality: 94.62
Ribosomal and transfer RNA genes
  • 0 16S rRNAs
  • 1 23S rRNA (up to 100.0%)
  • tRNAs for 20 amino acids
Sequencing depth
1437.35 ×
Source
Other features
  • G+C Content: 43.65%
  • Coding Density: 84.2%
  • Codon Table: 11
  • N50: 1,390,346 bp
  • Contigs: 16
  • Largest Contig: 1,557,022 bp
  • Assembly Length: 4,967,627 bp
  • Ambiguous Assembly Fraction: 0.004%
Submitter comments
Whole-genome sequencing was performed using the Illumina HiSeq 2500 platform. Genomic DNA (gDNA) was used for paired-end libraries (2 × 150 bp) with NEBNext® Fast DNA Fragmentation and Library Preparation Kit (New England Biolabs Inc., MA, USA). The final library quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, CA, USA) and agarose gel electrophoresis. We performed the quality control of raw sequences obtained from Illumina HiSeq sequencing by using FastQC v0.12.1, considering as good sequences that ones with phred score equal or higher than 30. These sequences underwent de-novo assembly using SPAdes v3.15.5. We employed QUAST v4.4 to measure the assembled genomes' quality metrics and perform statistical analysis. Pair-end reads were aligned to the assemblies using the Burrows-Wheeler Aligner (BWA) tool. The average sequencing coverage was then calculated from the resulting BAM file using SAMtools. Taxonomic classification was first performed with GTDB-tk. When GTDB-tk was insufficient for detailed species taxonomy, FastANI v1.33 was implemented as a supplementary tool. When species-level classification was not achieved using GTDB-tk, we downloaded all available assemblies for each identified genus from NCBI. Species were considered the same if their Average Nucleotide Identity (ANI) values exceeded 95%. Finally, the annotation of functional genes in each genome was carried out using RAST-tk.

Automated checks
Complete

Sample Metadata

Date
Not detected
Location
Not detected
Toponym
Not detected
Environment
Not detected
Other
Not detected
Package
Not detected
All retrieved samples

Metadata retrieved about 1 month ago


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