Summary

This page contains the results overview.

Where does this data come from?

The data used for each pie chart comes from selecting the best blast hit of each contig in the sample (The contigs are assembled in the Assembly step from the reads previously mapped to an organsim database). The best hit is determined by getting the maximum value after sorting by Bit score, e-value and nucleotide identity, in that order.

Toy example...

Given the following blast result:

• Contig1
  Contig1 has aligned 3 times, the best hit by Bit score is Organism1 (425).
• Contig2
  Contig2 has aligned twice, the best hit by Bit score is Organism2 (484).
• Contig3
  Contig3 has aligned only once with Organism1, so that is it's best hit.
• Contig4
  Contig4 has aligned 4 times. 3 hits have the same Bit score so we use the E-value to select the best hit. As the E-value is 0 in all the 3, we have to use the % of nucleotide identity. We select the hit with the highest % (97.75%), which corresponds with Organism4.
• Contig5
  Contig5 has aligned 2 times, the best hit by Bit score is Organism1 (926).
• Contig6
  Contig6 has aligned once with Organism1, so that is it's best hit.
• Contig7
  Contig7 has aligned once with Organism4, so that is it's best hit.

If we now count the number of times each organism is Best Hit we get the following:

• Organism1 = 4 (Contig1, Contig3, Contig5, Contig6).
• Organism2 = 1 (Contig2).
• Organism3 = 0
• Organism4 = 2 (Contig4, Contig7).

With that we can generate the pie chart...

This is done for each sample and divided by organism group (Bacteria, Virus, Fungi, Protozoa, Invertebrate).

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