3 Information

You can check detail manual from here

3.1 How to use (General statistics)

3.1.1 MG summary table

  • Columns:
    1. Sample ID: Sample name
    2. Raw size [Gbp]: The number of total bases
    3. Clean size [Gbp]: The number of reliable bases used for analysis
    4. Assembly size [Mbp]: Total length of assembled contigs
    5. N50 [kbp]: Length of N50
    6. Number of CDS
    7. Shannon index: The higher the Shannon index, the higher the diversity
      • Effective number of species (ENS) = exp(Shannon index)
      • e.g. Shannon index = 3, ENS = exp(3) = 20
      • A community with Shannon index of 3 has an equivalent diversity as a community with 20 equally-common species.
  • 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.

3.1.2 Reads quality plot

  • X axis: Sample ID
  • Y axis: Data size [Gbp]
  • Hover text:
    1. Sample ID
    2. size: Data size [Gbp]
    3. Quality: Read quality level
      • high quality: reliable bases used for analysis
      • low quality: discarded bases
  • You can:
    • drag area to zoom in plot
    • hide color by single clicking legend text
    • highlight any color by double clicking legend text

3.1.3 Taxonomy plot

Relative abundance plot. (More interactive plot is here)

  • X axis: Sample ID
  • Y axis: Relative abundance
  • Color: Individual Phylum
  • Hover text:
    1. Sample ID
    2. Relative abundance
    3. Phylum

3.1.4 Taxonomy table

Taxonomy table of metagenome.

  • Columns:
    • Taxon: Taxonomy name
    • Sample ID: each sample
    • value: Relative abundance (% Total Reads)
  • 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 Stats:

  • Reads Stats:
    • Total Reads: Total number of MG reads
    • Total Length: Total number of bases
    • Clean Reads: High quality reads number of MG reads
    • Clean Length: High quality bases number
    • Shannon Index
  • Contig Stats:
    • Total Assembly Length
    • # Contigs: The number of assembled contigs
    • N50: weighted median statistic such that 50% of the entire assembly is contained in contigs or scaffolds equal to or larger than this value
    • # CDS: The number of CDS

3.2.2 Taxonomy profile:

  • Color: Indicate individual Phylum
  • Hover text:
    1. Taxonomy name
    2. Relative abundance (% Total Reads)
    3. Kingdom (Domain) name
  • You can:
    • click rectangle to zoom in clicked taxonomy
    • click top bar to zoom out plot

3.3 bitBiome