5 thresholds for mapping

-n Number of selected subreads, 10 by default.

-m Consensus threshold for reporting a hit (minimal number of subreads that map in consensus) . If paired-end, this gives the consensus threshold for the anchor read (anchor read receives more votes than the other read in the same pair). 3 by default

-p Consensus threshold for the non- anchor read in a pair. 1 by default.

-M Maximum number of mis-matched bases allowed in each reported alignment. 3 by default. Mis-matched bases found in soft- clipped bases are not counted.