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

**URL:** <https://www.alphagenomecommunity.com/t/splice-junction-plot-please-help-me-understand-which-ones-are-forward-splicing-linear-and-which-ones-are-back-splicing/753>\
**Category:** Help & Support\
**Created:** [January 29, 2026, 8:26am UTC](https://www.alphagenomecommunity.com/t/splice-junction-plot-please-help-me-understand-which-ones-are-forward-splicing-linear-and-which-ones-are-back-splicing/753 "2026-01-29T08:26:55Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Anjali\_Singh](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/anjali_singh/32/732_2.png) [@Anjali\_Singh](https://www.alphagenomecommunity.com/u/Anjali_Singh)\
**Post date:** [January 29, 2026, 8:26am UTC](https://www.alphagenomecommunity.com/t/splice-junction-plot-please-help-me-understand-which-ones-are-forward-splicing-linear-and-which-ones-are-back-splicing/753/1 "2026-01-29T08:26:55Z")

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![Screenshot 2025-12-23 012124](https://canada1.discourse-cdn.com/watermelon/original/1X/8100ffb62f8cf08706ad7c31914a7197531c1edc.jpeg)

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**Author:** ![Jun\_Cheng](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/jun_cheng/32/23_2.png) [@Jun\_Cheng](https://www.alphagenomecommunity.com/u/Jun_Cheng)\
**Post date:** [January 29, 2026, 4:32pm UTC](https://www.alphagenomecommunity.com/t/splice-junction-plot-please-help-me-understand-which-ones-are-forward-splicing-linear-and-which-ones-are-back-splicing/753/2 "2026-01-29T16:32:57Z")

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Hi,

The model is only trained to predict forward splicing.

Best,

Jun

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**Author:** ![Anjali\_Singh](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/anjali_singh/32/732_2.png) [@Anjali\_Singh](https://www.alphagenomecommunity.com/u/Anjali_Singh)\
**Post date:** [January 29, 2026, 6:19pm UTC](https://www.alphagenomecommunity.com/t/splice-junction-plot-please-help-me-understand-which-ones-are-forward-splicing-linear-and-which-ones-are-back-splicing/753/3 "2026-01-29T18:19:35Z")

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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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**Author:** ![Amanda\_Stafford](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/amanda_stafford/32/633_2.png) [@Amanda\_Stafford](https://www.alphagenomecommunity.com/u/Amanda_Stafford)\
**Post date:** [April 9, 2026, 9:23am UTC](https://www.alphagenomecommunity.com/t/splice-junction-plot-please-help-me-understand-which-ones-are-forward-splicing-linear-and-which-ones-are-back-splicing/753/4 "2026-04-09T09:23:44Z")

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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.