I am looking at a tumor/normal pair illumina HiSeq data paired end. When i open my normal and tumor bam files in IGV, i expect to see a mutation at a specific location(which i do see). But the base there is A. The mutation is suppose to change G -> T but what the reads show me only is A -> C and on the Reference sequence in IGV i see a "C" (so that is fine). How can I explain this to someone?
The codon i am looking at is "ACC" so the complement of that is "TGG"..right...why don't i see any T and G in my reads? Why are there only A and C?