Discordinant aligment

Question

[ali]

Hi

My result of hisat2 alignment is:

23250959 reads; of these:
  23250959 (100.00%) were paired; of these:
    2462449 (10.59%) aligned concordantly 0 times
    19974163 (85.91%) aligned concordantly exactly 1 time
    814347 (3.50%) aligned concordantly >1 times
    ----
    2462449 pairs aligned concordantly 0 times; of these:
      1511718 (61.39%) aligned discordantly 1 time
    ----
    950731 pairs aligned 0 times concordantly or discordantly; of these:
      1901462 mates make up the pairs; of these:
        804577 (42.31%) aligned 0 times
        924548 (48.62%) aligned exactly 1 time
        172337 (9.06%) aligned >1 times
98.27% overall alignment rate

Now my question is about 61%aligned discordantly 1 time. Is that a problem? How can I reduce that?

Answer 1

[Istvan Albert]

The error message is quite difficult to parse,

.... aligned 0 times concordantly or discordantly ...

What does that even mean?

... long story short, note how only 10% of your data aligned non-concordantly, out of those 61% percent were discordant ...