Mothur will generate two output files,

  1. A taxonomy file which gives a sequence-wise taxonomy at each level. The file has the following format.
  2. SEQUENCE_1 k__name(xyz);p__name(xyz);c__name(xyz);o__name(xyz);f__name(xyz);g__name(xyz);s__name(xyz);u__otuID(xyz);
    SEQUENCE_2 k__name(xyz);p__name(xyz);c__name(xyz);o__name(xyz);f__name(xyz);g__name(xyz);s__name(xyz);u__otuID(xyz);
    SEQUENCE_3 k__name(xyz);p__name(xyz);c__name(xyz);o__name(xyz);f__name(xyz);g__name(xyz);s__name(xyz);u__otuID(xyz);
    .          .
    .          .
    .          .
    SEQUENCE_N k__name(xyz);p__name(xyz);c__name(xyz);o__name(xyz);f__name(xyz);g__name(xyz);s__name(xyz);u__otuID(xyz);

    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.

  3. A tax summary file which gives consolidated summary of the taxonomic classification. The following lines gives a snapshot of the first OTU.
  4. taxlevelrankIDtaxondaughterlevelstotal
    0aRootxyzxyz
    1a.bk__namexyzxyz
    2a.b.cp__namexyzxyz
    3a.b.c.dc__namexyzxyz
    4a.b.c.d.eo__namexyzxyz
    5a.b.c.d.e.ff__namexyzxyz
    6a.b.c.d.e.f.gg__namexyzxyz
    7a.b.c.d.e.f.g.hu__namexyzxyz

    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

Phylum_1 <abundance>
Phylum_2 <abundance>
Phylum_3 <abundance>
. .
. .
. .
. .
Phylum_N <abundance>
Abundance profile at Class level

Class_1 <abundance>
Class_2 <abundance>
Class_3 <abundance>
. .
. .
. .
. .
Class_N <abundance>
Abundance profile at Order level

Order_1 <abundance>
Order_2 <abundance>
Order_3 <abundance>
. .
. .
. .
. .
Order_N <abundance>
Abundance profile at Family level

Family_1 <abundance>
Family_2 <abundance>
Family_3 <abundance>
. .
. .
. .
. .
Family_N <abundance>
 
Abundance profile at Genus level

Genus_1 <abundance>
Genus_2 <abundance>
Genus_3 <abundance>
. .
. .
. .
. .
Genus_N <abundance>
Abundance profile at Species level

Species_1 <abundance>
Species_2 <abundance>
Species_3 <abundance>
. .
. .
. .
. .
Species_N <abundance>
Abundance profile at OTU level

OTUXID_1 <abundance>
OTUXID_2 <abundance>
OTUXID_3 <abundance>
. .
. .
. .
. .
OTUXID_N <abundance>

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


An example ID of V4 OTUX database is shown below.

OTUX ID Nomenclature