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 alignment whether concord. or discord., but both are aligned in paired-end mode. The rest of the reads either align as singles (i.e. Read1 in one locus & Read2 in completely different locus or one mate aligned and the other unaligned) or may not align at all. So the reads that are in this section is Total -(Concord.+Discord.). That is 16182999 -(10451768+2381431) = 3349800 reads.
  Since alignment, if any, here is in single fashion so we calculate in mates (readsx2).

Now to reach the overall alignment, count the mates in total (i.e. mates aligned in paired and mates aligned in single fashion). That would be -
(10451768 x2)+(2381431 x2)+1883429+1001435 = 28551262 mates
That is 28551262 mates aligned of total (16182999 x2) mates, which is 88.21%.