I am studying the effect of transposable elements in Saccharomyces cerevisiae populations. The outcome I have from Variant Effect Predictor is as follow:
Category Count Variants processed 414 Overlapped genes 1553 Overlapped transcripts 1553 Overlapped regulatory features -
What is the difference between overlapped genes and transcripts? If a transposon is overlapping a gene then I might not have a transcript at all or I can get a different transcript, depends where it is located. On the other hand, from literature, I know transposon can interrupt regulatory elements, does your database have annotations in yeast?
For all consequences predicted:
Upstream gene variant 49 Downstream gene variant 42 Intergenic variant 4 Transcript ablation 3 Coding sequence variant 1 Feature elongation 1 3' UTR variant 1
From above 1553 genes were overlapping to a transposon, but here how so many genes can be affected with the results above?
And finally, the information for the consequences on a protein sequence:
Stop codon lost 16 Coding sequence variant 84
Above coding sequence variants represent 1%, how is it possible that here the consequence is 84%?
I hope you could help me out. Thank you in advance for your time.