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Hello tramelliwe I can't really speak on whether the two peaks are common, but I can say that after doing a lot of amplicon sequencing I've had a lot of off-target amplification. Depending on what you're sequencing it can be expected and it happens even more with degenerate primers. Have you looked to see if any of your primers match up with that region? I can also check in with some friends that have more experience with this type of work. -
Thank you for your answer Ben3. Maybe I should clarify that my amplicon covers both peaks. I did check the specificity, but even with multiple mismatches, my primers do not bind other places on that locus. I did not do the library prep myself, maybe at that stage the fragments covering that zone were lost somehow?
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