Hi Ariananda,

what you describe sounds like a bad sequence to me, not realy cause to suspect an indel. In case of an indel you should see a clean sequence up to the point of the mutation. 

the difference between your forward and reverse sequences is caused by differences in primer efficiencies during the sequencing. This is not uncommon. 

I would suggest you optimize your sequencing reaction (usually changing the input in the sequencing make a huge difference), the check whether you see a change from a clean to a messy sequence somewhere, that would be indictive of an indel. (and then you should be able to see the shifted sequence below the expected sequence, like a frameshift)

Thanks Arnoud! I finally use the method you suggested and it is quite acceptable (at least for me). I can guess the mutation type by using that method and by comparing with some references. Thanks a lot!

Hello Ariananda

I am totally agree with Arnoud, If you want good sequences, I suggest you clean very well your product before of the sequence, you can do that with some kits.

I use Big Dye Xterminator purification kit and after of purification I run an electrophoresis (I can not see more than my amplicon) and I quantify by spectrophotometry, my range A260/280 should be higher than 1.8 .

On the other hand, you have to use the exactly concentration of sample that the machine of sequence asking you, and the exactly amount of primers and normally that is in picograms; if you don't, you can have bad sequences.