Numbers in Parentheses in Taxonomy Files

Hi all! I am a high school student working on a project involving mothur.

I have a couple questions. What do the numbers in parentheses indicate in mothur taxonomy files? For example, Archaea(100);Euryarchaeota(88);Thermoplasmata(87);Thermoplasmatales(79);BSLdp215(77);unclassified(77);
I’ve noticed that in some of my taxonomy files the only difference between two OTUs is the number in parentheses.

Occasionally, mothur seems to list some OTUs separately, in the same taxonomy file, even though it appears that they are the same OTU. Has anyone experienced this issue before? I can send the files to anyone who is interested in helping. I’d appreciate any advice.


Thanks for your interest in mothur - it’s great that as a high school student you’re already thinking about research and learning about microbial ecology.

If this is from the output of classify.seqs the numbers indicate the confidence one has in the classification. Generally, you want a confidence score over 80.

If this is from the output of classify.otu (which is what I think this is) the numbers indicate the percentage of sequences in the OTU that have that classification. Here we want something over 50%.

So this OTU would seem to be an unclassified member of the BSLdp215 in the Thermoplasmatales.

Good luck and let us know if you need anything else!