**100**wrote:

hello every one, I have run

./bowtie2 -fr -x ATREFERENCE -q -1 R1.fastq -2 R2.fastq -S T2.sam

4088543 reads; of these:

4088543 (100.00%) were paired; of these:

```
1903298 (46.55%) aligned concordantly 0 times
1545760 (37.81%) aligned concordantly exactly 1 time
639485 (15.64%) aligned concordantly >1 times
----
1903298 pairs aligned concordantly 0 times; of these:
267481 (14.05%) aligned discordantly 1 time
----
1635817 pairs aligned 0 times concordantly or discordantly; of these:
3271634 mates make up the pairs; of these:
2469813 (75.49%) aligned 0 times
463625 (14.17%) aligned exactly 1 time
338196 (10.34%) aligned >1 times
```

69.80% overall alignment rate

Here I did not use -I and -X parameter because I am unable to interpret these parameters,though I read the manual but did not correlate -I and -X with improving mapping quality. any one can help me interpret and correlate -I and -X parameters with reference to improve mapping quality. basically I am interested in chimeric regions of chromosome because my library is Hi-C. suggestion are always welcome.