I've sequenced two genes of 15 dogs for SNP analysis. the chromatograms of one gene looked perfect but the ones of the second gene didn't look as good. To be precise, the chromatograms of one exon looked relatively good with only a few spots where the bases seemed unreadable. But the chromatograms of the second exon were full of that. So there must have been an error somewhere and my question is where this could have happened. My hypothesis is that I simply made a mistake during the mixing of the chemicals at some point.
Further useful information: The error must have happened befor the first pcr since i checked the pcr product with a fragment analyzer and the bands were only barely or not visible. Additionally, I noticed that many imprecisions seen in the chromatograms were only found at either the forward or backward strand.
Here is an image of several of the chromatograms of the exon that didn't work: