Hi Ibro,

I could be wrong but you do not have a default setting for -v mode. From the manual:

In -v mode, alignments may have no more than V mismatches, where V may be a number from 0 through 3 set using the -v option.

Therefore in -v mode you must specify the number of allowed mistmatches. If you look at the usage:

-v <int> Report alignments with at most <int> mismatches. -e and -l options are ignored and quality values have no effect on what alignments are valid. -v is mutually exclusive with -n.

-n/--seedmms <int> Maximum number of mismatches permitted in the “seed”, i.e. the first L base pairs of the read (where L is set with -l/--seedlen). This may be 0, 1, 2 or 3 and the default is 2. This option is mutually exclusive with the -v option.