trunc-q will truncate the sequence at the first instance of quality score X. It acts on both the forward and reverse sequences independently. Then trunc-len acts, and will truncate any sequences that are longer than trunc-len to that value, and throw away any sequences that are shorter than trunc-len. So I think the behavior above is explained by some reads being truncated earlier than trunc-len, mostly in the reverse reads, as trunc-q is increased, and therefore being discarded.
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