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
-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.