Entering edit mode
17 months ago
ali
•
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
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2462449 pairs aligned concordantly 0 times; of these:
1511718 (61.39%) aligned discordantly 1 time
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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 that a problem? How can I reduce that?