mothur

Chimera.vsearch results for 18S v9

Hello,

My output from chimera.vsearch is as follows:

Reading file /Users/micah/Desktop/mothur_hm/HM.trim.contigs.good.unique.good.filter.unique.precluster.temp 100%
24340822 nt in 79193 seqs, min 254, max 354, avg 307
Masking 100%
Sorting by abundance 100%
Counting k-mers 100%
Detecting chimeras 100%
Found 38715 (48.9%) chimeras, 40253 (50.8%) non-chimeras,
and 225 (0.3%) borderline sequences in 79193 unique sequences.
Taking abundance information into account, this corresponds to
180676 (14.2%) chimeras, 1083503 (85.4%) non-chimeras,
and 3922 (0.3%) borderline sequences in 1268101 total sequences.

I have read through some of the papers suggested that I have seen in the forum, etc. but, I am not confident in my ability to interpret these results. They seem pretty high… Is there a reading/reference that shows what “normal/acceptable” values are depending on why type of wetlab was done or what sequence region you have? Perhaps I should run an alternative chimera analysis?

Thanks,

Micah

We genreally see 5-25% of all sequences being flagged as chimeras - your 14% is right there. I’d say that your results are pretty typical.

Pat

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