I'm not sure about this. I know that the --p-trunc-q parameter (with a default of 2) truncates reads with low quality sequences. But it says in the documentation that "If the resulting read is then shorter than 'trunc-len-f' or 'trunc-len-r' (depending on the direction of the read) it is discarded." So the read would not end up too short, it would just be discarded, in which case I would see the loss of reads in the filtered column of the dns.