2 Information

You can check detail manual from here

2.1 How to use (General statistics)

2.1.1 Isolate summary table

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

2.1.2 Reads quality plot

  • X axis: Isolates, arranged by Completeness
  • Y axis: Data size [Mbp]
  • Green bar: High quality bases
  • Blue bar: Low quality bases

2.1.3 Completeness, Contamination, Novelty plot

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

2.1.4 Taxonomy profile

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

2.1.5 Isolate 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: Isolate quality, Complete, High, Medium, Low quality, and Contaminated
    6. Genome size [Mbp]: Isolate assembly size
    7. Nearest Reference: NCBI Assembly reference
    8. Taxonomy: Species name
  • You can:
    • change visible 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.

2.2 bitBiome