How to understand Hisat2 aligment result

Question

[Bioinfonext]

I map pair end read using Hisat2 to genome:

[root@psgl hisat2]# /home/yog/software/hisat2-2.0.4/hisat2 -p 8 -x Radish_index -1

/data/SNU_work/Analysis/unmapped/unmapped/hisat2/unmap_Read1.fastq -2

/data/SNU_work/Analysis/unmapped/unmapped/hisat2/unmap_Read2.fastq -S unmap.sam

Result:

101038635 reads; of these:

101038635 (100.00%) were paired; of these:

6478970 (6.41%) aligned concordantly 0 times

45018304 (44.56%) aligned concordantly exactly 1 time

49541361 (49.03%) aligned concordantly >1 times

----
6478970 pairs aligned concordantly 0 times; of these:

  338196 (5.22%) aligned discordantly 1 time

----
6140774 pairs aligned 0 times concordantly or discordantly; of these:

  12281548 mates make up the pairs; of these:

    5865219 (47.76%) aligned 0 times

    4078697 (33.21%) aligned exactly 1 time

    2337632 (19.03%) aligned >1 times

97.10% overall alignment rate

What is the meaning of aligned 0 times?

What is the meaning of aligned concordantly?

Please help!

[GenoMax]

See Devon's answer: tophat output files containing the reads which mapped uniquely as a pair

Answer 1

[rbj]

Or alternatively this example with Hisat2 is also useful here