I wanted to generate consensus sequences for each OTU in my dataset based on a cutoff value of 75%. So I ran a test. I made up 10 sequences and run the command: consensus.seqs (fasta=test.fasta, cutoff=75). At one specific position there were 8 G’s and 2 A’s, which means 80% sequences support G while 20% support A. Since I set cutoff=75, it should report G. However, R is reported in this position. If I set cutoff=70, G is reported. So I am wondering if it is a bug or I missed something in my command. Thanks!
BTW the Mothur I am using is v1.27. The cutoff option was added to consensus.seqs since v1.20. Thanks!