Mothur will generate two output files,
- A taxonomy file which gives a sequence-wise taxonomy at each level. The file has the following format.
- A tax summary file which gives consolidated summary of the taxonomic classification. The following lines gives a snapshot of the first OTU.
Here xyz is the bootstrap confidence score for the assigned taxonomy. A sample taxonomy file was created in a walk-through for using this database. Please click here to check the file generated in the walk-through.
Here xyz are natural numbers which will be equilvalent to the number of daughter levels or total abundance of that taxa level. Whereas, the alphabets a-h are whole number(s) denoting the rank ID. Please click here to check the a sample tax summary file generated in the walk-through.
Using the code avialable for download here one can parse the taxonomy file to generate abundance profiles at each taxonomic level. The abundance profiles are generated in the format shown below.
Abundance profile at Phylum level |
Abundance profile at Class level |
Abundance profile at Order level |
Abundance profile at Family level |
Abundance profile at Genus level |
Abundance profile at Species level |
Abundance profile at OTU level |
Using the OTUX IDs abundance profile user can map back the results to greengenes IDs. For details regarding mapping back please check this help page.
Following nomenclature has been followed for giving OTUX IDs
- First three characters is a prefix "OTX".
- Next two characters defines the v-region. For example, V4 database will have OTX04, whereas V3V4 database will have OTX34 as prefix.
- Final seven digits denote the OTUX IDs of that particular v-region database.
An example ID of V4 OTUX database is shown below.