Hi，my hisat2 run of paired reads resulted in the following report：
24615923 reads; of these:
24615923 (100.00%) were paired; of these:
9554401 (38.81%) aligned concordantly 0 times
11086995 (45.04%) aligned concordantly exactly 1 time
3974527 (16.15%) aligned concordantly >1 times
9554401 pairs aligned concordantly 0 times; of these:
4616966 (48.32%) aligned discordantly 1 time
4937435 pairs aligned 0 times concordantly or discordantly; of these:
9874870 mates make up the pairs; of these:
3846849 (38.96%) aligned 0 times
3981801 (40.32%) aligned exactly 1 time
2046220 (20.72%) aligned >1 times
92.19% overall alignment rate
There are quite a bit of reads aligned discordantly 1 time.
So i wonder is this mapping rate OK?
Hi，my hisat2 run of paired reads resulted in the following report：
There are quite a bit of reads aligned discordantly 1 time.
So i wonder is this mapping rate OK?
Thank you!