detailed explanation of bowtie2 mapping statistics

[Navy1991]

25870617 reads; of these:
25870617 (100.00%) were paired; of these:
2530173 (9.78%) aligned concordantly 0 times
22508388 (87.00%) aligned concordantly exactly 1 time
832056 (3.22%) aligned concordantly >1 times
----
2530173 pairs aligned concordantly 0 times; of these:
620049 (24.51%) aligned discordantly 1 time
----
1910124 pairs aligned 0 times concordantly or discordantly; of these:
3820248 mates make up the pairs; of these:
2960085 (77.48%) aligned 0 times
774150 (20.26%) aligned exactly 1 time
86013 (2.25%) aligned >1 times
94.28% overall alignment rate


This is an example output mapping statistics from bowtie2.

After reading the bowtie2 manual , I understood what concordant and discordant means (concordant refers to reads within the insert size and in correct orientation) .

aligned 0 times --> unmapped
aligned exactly 1 times --> unique match
aligned >1 times --> multiple match

Even after understanding this, I could not fully interpret the above summary?

what is the difference between the following two lines:

2530173 pairs aligned concordantly 0 times; of these:

1910124 pairs aligned 0 times concordantly or discordantly




Can anyone give your suggestions please?

[dpryan]

Please tell us what parts you don't understand, rather than just the parts that you do.

[Navy1991]

I have edited my question

[dpryan]

Bowtie2 found 2530173 read pairs that it couldn't align concordantly and looked for discordant alignments for them. It could align 620049 of them discordantly, leaving 1910124 still unmapped. It then tried to align each of the reads in those pairs separately (i.e., as singletons), which worked for about 23% of them.

[westerman]

2530173 pairs aligned concordantly 0 times; of these:
620049 (24.51%) aligned discordantly 1 time

This leaves

1910124 pairs aligned 0 times

At which point it is hard to say if the pairs are concordant or discordant thus the line:

1910124 pairs aligned 0 times concordantly or discordantly; of these:


-- or ... as Devon said.

[Navy1991]

Thank you. Its clear now.