Discordinant aligment

Discordinant aligment

0

hi
my result of hisat2 alignment is :
23250959 reads; of these:
23250959 (100.00%) were paired; of these:
2462449 (10.59%) aligned concordantly 0 times
19974163 (85.91%) aligned concordantly exactly 1 time

814347 (3.50%) aligned concordantly >1 times
----
2462449 pairs aligned concordantly 0 times; of these:
  1511718 (61.39%) aligned discordantly 1 time
----
950731 pairs aligned 0 times concordantly or discordantly; of these:
  1901462 mates make up the pairs; of these:
    804577 (42.31%) aligned 0 times
    924548 (48.62%) aligned exactly 1 time
    172337 (9.06%) aligned >1 times

98.27% overall alignment rate

now my question is about 61%aligned discordantly 1 time. is a problem?? how can i reduce this???


Paired


end


HISAT2

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