By Sample

Where does this data come from?

The data in this table comes from the combined results of running blast and calculating the coverage of each genome of the reference that aligned to the sample. A table is presented for each organism group in each sample with the following information:

• Reference Id:
  Accession used in the reference database for the genome which aligned to a contig of the sample.
• Reference name:
  Name of the organism.
• % of identical matches:
  % of the query sequence that aligned with the reference.
• Alignment length:
  Number of base pairs that where aligned to the reference.
• Number of mismatches:
  Number of base pairs in the aligned sequence that did not match the reference.
• Number of gap openings:
  Number of gaps in the alignment.
• Start of alignment in query:
  Position of the query sequence base pair in which the alignment started.
• End of alignment in query:
  Position of the query sequence base pair in which the alignment ended.
• Start of alignment in subject:
  Position of the reference sequence base pair in which the alignment started.
• End of alignment in subject:
  Position of the reference sequence base pair in which the alignment ended.
• Expect value (E-value):
  Hits that can be expected to occur by chance when searching a database of a particular size. For example, an E-value of 0.05 means that this similarity has a 5 in 100 chance of occurring by chance alone. It is a good measure of the background noise. The closer to zero the more 'significant', though the calculation of the E value takes into account the length of the query sequence and the size of the database, so shorter alignments always have higher values; even if the match is perfect, only because they have a higher probability of occurring in the database purely by chance.
• Bit score:
  The bit score gives an indication of how good the alignment is. A certain score is pre-assigned for match, mismatch and gap which the algorithm then uses to calculate the global score of the alignment. Matches have a positive value while mismatches and gaps have a negative one, so the higher the score, the better the alignment.
• Coverage mean:
  Mean value of the depth of coverage of a given genome.
• Coverage min:
  Minimum value of the depth of coverage of a given genome.
• Maximum coverage:
  Maximum value of the depth of coverage of a given genome.
• Coverage SD:
  Standard Deviation of the depth of coverage of a given genome.
• Coverage median:
  Median of the depth of coverage of a given genome.
• x1-x4 depth:
  x/1 of the genome with a depth between 1x and 4x.
• x5-x9 depth:
  x/1 of the genome with a depth between 5x and 9x.
• x10-x19 depth:
  x/1 of the genome with a depth between 10x and 19x.
• =>x20 depth:
  x/1 of the genome with a depth equal or above 20x.
• Total coverage:
  x/1 of the genome covered in at least 1x depth.
• Coverage graph:
  Pdf file with the graph of the genome coverage.

How does the samples.html look like?