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?
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?
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