Technically cas9 cuts DNA at 3 bp upstream of PAM sequence, but when the double strand break is repaired via NHEJ, unexpected various small insertions or deletions can be observed, that is completely possible. We always want to carry on with precise sequence after editing in mammalian cells, that is why we are trying to generate isogenic line by clonal selection (in order to eliminate cells carrying undesired seqs). Consequently, check your seq result, you should have seen an insertion consisting of random nucleotides added by NHEJ. 

Thank you Volkan Ergin for sending answer. 

I also things that its case of NHEJ. I will check the sequencing results again for insertion of bases. 

Dear Harshraj, what you describe is an event that is less likely. So i am asking you if you have seen the "expected" results and what the number of events are (btw: how did you analyse? Next-gen sequenceing?). If this is a single event, you may want to sequence the target region to ensure that the "mutation" hasnt been there from the very beginning already. You may also be interested to know that you can test your guideRNA in a transient assay before going through all the hassle of making the transgenic.

Also, if ur guideRNA works well, you can screen more descendents (but make sure the CRISPR/Cas9 cassette is integrated, e.g. check PCR, Southern blot) and you should also expect bi-or multi- allelic events.

Good luck with your experiments!

Anything can happen during the DNA repair. The target location may be retained if the editing is only transient, so cas9 does not cut back. It may only be transgenic for the selection marker gene and not the CRISPR system. Have you tested this?

@Markus Sack : I have tested my gRNA for transient expression and it works fine. For event i have analyzed two transgenic events by sequencing along with wild type. In wild type i didnt observed any change  in nucleotide sequence but transgenic events shows deletion of single base pair at downstream of PAM site. 

@Andras Kis : I have tested all positive events for cas9 by PCR. expression of cas9 has been observed in all events. I did pcr of selectable marker gene also, results are positive.