Splice Junction Plot - Please help me understand which ones are forward splicing(linear) and which ones are back splicing?

Help & Support
1

Screenshot 2025-12-23 012124
Screenshot 2025-12-23 0121241060×834 118 KB

2

Hi,

The model is only trained to predict forward splicing.

Best,

Jun

3

Thanks for this clarification Jun, What exactly can we interpret from this plot other than Splice junctions because the arcs and even the numbers are same for ref and alt

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The numbers above the arcs represent the strength of the splicing event (the predicted count of reads spanning that junction). If the numbers are the same for ALT versus REF then that means AlphaGenome has not predicted a difference induced by the variant. Perhaps consider visualizing other output tracks for your research question.