Screen.seqs filtering all out - maxambig=0

Commands in mothur
1

breast skin swabs - v4 - 16s - 250cycles - paired end
Each sample was PCR amplified with two differently bar coded V4 fusion primers.
For about 30% of my samples, I get about 10 reads left after screen.seqs because of “maxambig=0”
summary after making contigs for one of the samples
http://pbrd.co/1oXHoke

What could be going on? Are these just bad data?

Thank you
-QQcumber

2

Looks like bad data, but it is suspicious that so many have exactly 2 ambiguous base calls. Are you using the Kozich method?

Pat