a project in our group investigating the association between specific and drug resistance. One of these SNPs has been reported that the wild type alleles GG have been altered into TT. Using Sequencing, we found that the wild type allele GG have been altered into CC. How could we explain that regardless of ethnicity variations.
Thank you in advance.
Sorry to have to ask this but someone will. are you sure that you are sequencing the correct strand/direction?
Hi--I agree with Paul. If this is NGS derived make sure that you have the correct sense/antisense orientation settings with your variant caller. If you are getting CC>AA, this is the most likely issue. If there are any other SNPS is the region that have the compliment reference alleles, this almost surely the problem. Good luck.
Dear Paul Rutland and Shale Dames,
Thank you so much for your responses. They were very heplful and I am trying to solve the problem.
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