Entering edit mode
5 months ago
analyst
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50
Dear all,
I am trying to find uniquely mapped and multi-mapped reads. Kindly guide how can I calculate.
I explored other related posts but they include unpaired reads information in the summary but I don't see those details here so please guide to find uniquely mapped and multi-mapped reads from this summary.
Thanks
37262625 reads; of these:
37262625 (100.00%) were paired; of these:
4112024 (11.04%) aligned concordantly 0 times
30821396 (82.71%) aligned concordantly exactly 1 time
2329205 (6.25%) aligned concordantly >1 times
----
4112024 pairs aligned concordantly 0 times; of these:
242020 (5.89%) aligned discordantly 1 time
----
3870004 pairs aligned 0 times concordantly or discordantly; of these:
7740008 mates make up the pairs; of these:
5295292 (68.41%) aligned 0 times
2149199 (27.77%) aligned exactly 1 time
295517 (3.82%) aligned >1 times
92.89% overall alignment rate
30821396 (82.71%) aligned concordantly exactly 1 time --> Uniquely mapped
2329205 (6.25%) aligned concordantly >1 times --> Multi-mapped
Shouldn't I add discordant and others (neither concordant nor discordant) to calculate unique and multi-mapped alignment?
Why are we not considering discordant or others for unique and multi-mapping reads?