Find Chimeras - Outputs:

The results are summarized in the html output and provided as a tab-delimited text file. The titles and contents of the output columns are as follows:

1. Name:

   The given description of the sequence in the FASTA-formatted input file.

2. Classification:

   Taxonomic classification of the sequence according to the IDTAXA algorithm (60% confidence level).

3. Group:

   The name of the group in DECIPHER’s database, to which the sequence was assigned during the chimera test.

4. Nucleotides:

   The number of non-gap characters, including ambiguity codes, in each sequence.

5. Result:

   One of these three different outcomes: “Not deciphered as a chimera”, “Chimera”, or “Indecipherable”. The latter outcome indicates that the sequence was not evaluated since it could not be assigned to a group that meets the criteria for finding chimeras. Often indecipherables are sequences that are chimeric or are not SSU rRNA.

6. Chimeric Region:

   When a sequence is a putative chimera, this column indicates the group of the potential parents of the chimeric fragment, followed by the position of the fragment in the sequence (5’ and 3’ ends; numbering according to the original sequence without gaps). Otherwise, the chimeric region output is “NA”, meaning not applicable.