Question about rep_set_tax_assignmets output file

[JoeyKim (KwangminKim)]

I wonder about rep_set_tax_assignmets output file!! plz help me~!!

I got this results (file - below)

I can know that
1st column of output file - input sequence identifiers
2nd column - taxonomy
3rd column - quality score

what is the 4th column meaning???(there are just two number 1,3)

and also 3rd column has just 0.67 & 1 two number

what is the meaning about that number??

If you guys know plz help me!!

[colinbrislawn (Colin J Brislawn)]

Good morning,

What script did you run to make this taxonomy file? I think I know what these columns mean, but once I know the script I can make sure.

During Last Common Ancestor classification each OTU get’s searched agains the database, and the the top hits are recorded. In Qiime 1, the top 3 hits were recorded by default. Then, taxonomy is assigned to that OTU based on the fraction of taxonomy that is shared by some fraction of hits. In Qiime 1, shared taxonomy >50% was the default.

So the final column ? is the number of database hits recorded. (3 hits)
And the QS column is the fraction of hits that matched at that taxonomy level. (2/3 hits == .67)

I hope that helps!
Colin

P.S. Keep in mind that all these settings can be changed. You can record the top 15 hits, then keep the top 70%, as an example.