3 Information

You can check detail manual from here

3.1 How to use (General statistics)

3.1.1 MAG summary table

MAG = Metagenome-Assembled Genome

  • Columns:
    1. Sample ID: Sample name
    2. # MAGs: The number of MAGs
    3. # High quslity MAGs: The number of High quality MAGs
    4. # Medium quslity MAGs: The number of Medium quality MAGs
    5. # Low quslity MAGs:The number of Low quality MAGs
    6. # Contaminated MAGs:The number of Contaminated MAGs
    7. # High Novelty (>50%): The number of MAGs with high Novelty score
    8. # Low Novelty (<=50%): The number of MAGs with Low Novelty score
    9. # N/A Novelty: The number of MAGs with no reference sequence

3.1.2 Taxonomy plot

Relative abundance plot. (More interactive plot is here)

Unclassified is a MAG that could not be inferred phylogeny by GTDBtk.

Unclassified Bacteria is a MAG that could only be inferred to be a bacterium by GTDBtk.

Unclassified Archaea is a MAG that could only be inferred to be a archaea by GTDBtk.

  • X axis: Sample ID
  • Y axis: Relative abundance
  • Color: Individual Phylum

3.1.3 Taxonomy table

Taxonomy table of MAG.

  • Columns:
    • Taxon: Taxonomy name
    • Sample ID: each sample
    • value: Number of MAGs
  • You can:
    • save table as CSV format. (Click “Download as CSV” Button)
    • click Column name to arrange table.
    • input word at Search to filter table.
    • change visible rows of table. (Click “Show X” Button)

3.2 How to use (Individual DATA)

3.2.1 Completeness, Contamination, Novelty plot

  • X axis: MAGs, arranged by Completeness
  • Y axis: Completeness, Contamination, Novelty [%]
  • blue point: Completeness
  • Yellow point: Contamination
  • Gray bar: Novelty score, calculated using ANI and AF value

3.2.2 Taxonomy profile

  • Color: Indicate individual Phylum
  • Hover text:
    1. Taxonomy name
    2. Number of MAGs
    3. Kingdom (Domain) name
  • You can:
    • click rectangle to zoom in clicked taxonomy
    • click top bar to zoom out plot

3.2.3 MAG table

  • Columns:
    1. Genome ID: Genome name
    2. Completeness: Genome completeness (%coverage of single copy marker gene)
    3. Contamination: Genome contamination (duplication of single copy marker gene)
    4. Novelty: Genome novelty (calculated from ANI and AF value)
    5. Quality: MAG quality (Complete, High, Medium, Low quality, or Contaminated)
    6. Genome size [Mbp]: MAG size
    7. Nearest Reference: NCBI Assembly reference
    8. Taxonomy: Species name
  • You can:
    • change rows of table. (Click “Show X rows” Button)
    • copy table. (Click “Copy” Button)
    • save table as CSV and Excel format. (Click “CSV” or “Excel” Button)
    • click Column name to arrange table.
    • input word at Search or below Column name to filter table.

3.3 bitBiome