How to understand Bowtie2 mapping statistics
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 The Bowtie2 result summary is divided in 3 sections: Concordant alignment - In your data (4522376 + 5929392) reads align concordantly. Which is 64.59% of reads Discordant alignment - So now 5731231 reads remain which is 35.41% (100-64.59). Of these, 2381431 reads align discordantly. That is to say, of the non-concordant fraction, 41.55% of reads (2381431 reads) align discordantly. The rest - Now, remember that align