Hello,

Have you seen the description?

Clipping range: One of the parameters to control clipping of a poor end region of a read (-y)

If there are quality values, CAP3 computes two positions qualpos5 and qualpos3 of read f such that the region of read f from position qualpos5 to position qualpos3 consists mostly of quality values greater than Quality cutoff for clipping.

If there are no quality values, then qualpos5 is set to 1 and qualpos3 is set the length of read f.

The range for the left clipping position of read f is from 1 to qualpos5 + Clipping range.
The range for the right clipping position of read f is from qualpos3 - Clipping range to the end of read f.

I understand but by default the clipping range value is 100 and according to the definition if I apply this value then sort reads (about 200 pb) could dissapear, isn't it? Thank you.