bowtie2: multi mapping Summary report

Question

[KVC_bioinfo]

Hello,

I am having a hard time figuring out the summary report from bowtie2.

16182999 reads; of these:
16182999 (100.00%) were paired; of these:
5731231 (35.42%) aligned concordantly 0 times
4522376 (27.95%) aligned concordantly exactly 1 time
5929392 (36.64%) aligned concordantly >1 times
----
5731231 pairs aligned concordantly 0 times; of these:
2381431 (41.55%) aligned discordantly 1 time
----
3349800 pairs aligned 0 times concordantly or discordantly; of these:
6699600 mates make up the pairs; of these:
3814736 (56.94%) aligned 0 times
1883429 (28.11%) aligned exactly 1 time
1001435 (14.95%) aligned >1 times
88.21% overall alignment rate

I am not able to understand which of the above % shows the multi mapping.

Thank you in advance.

Answer 1

[Devon Ryan]

There are 5929392 paired-end multimappers and 1001435 single-end multimappers. So you can get whatever appropriate percentage you want.

[KVC_bioinfo]

So it does not mention overall multi mapping?

[Devon Ryan]

It makes the most sense to report both numbers ("37% of the paired-end reads and 15% of the remaining singletons were multimapping").