# Seeking clarification on genome.Variant coordinate and strand conventions

**URL:** <https://www.alphagenomecommunity.com/t/seeking-clarification-on-genome-variant-coordinate-and-strand-conventions/789>\
**Category:** Help & Support\
**Created:** [February 15, 2026, 4:12am UTC](https://www.alphagenomecommunity.com/t/seeking-clarification-on-genome-variant-coordinate-and-strand-conventions/789 "2026-02-15T04:12:09Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Khalid\_Smith](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/khalid_smith/32/982_2.png) [@Khalid\_Smith](https://www.alphagenomecommunity.com/u/Khalid_Smith)\
**Post date:** [February 15, 2026, 4:12am UTC](https://www.alphagenomecommunity.com/t/seeking-clarification-on-genome-variant-coordinate-and-strand-conventions/789/1 "2026-02-15T04:12:09Z")

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Hello AlphaGenome community,

I am currently using the library to model genetic variants and have a question regarding the coordinate system and strand orientation used in the `genome.Variant` function.

I am working with a gene located on the reverse strand (negative strand). When defining a multi-base substitution (e.g., 20bp), I want to ensure I’m following the library’s expected conventions. Could you please clarify the following:

1. Position Indexing: Does the `position` parameter always default to the forward strand coordinate system, specifically requiring the minimum numeric index of the affected range, regardless of the gene’s actual orientation?.

2. Reference Bases: For a gene on the negative strand, should the `reference_bases` be the sequence as it appears on the forward strand (i.e., the reverse complement of the negative strand sequence)?

Thank you very much for your time and help.

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**Author:** ![Tumi\_Makgatho](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/tumi_makgatho/32/703_2.png) [@Tumi\_Makgatho](https://www.alphagenomecommunity.com/u/Tumi_Makgatho)\
**Post date:** [February 26, 2026, 11:27am UTC](https://www.alphagenomecommunity.com/t/seeking-clarification-on-genome-variant-coordinate-and-strand-conventions/789/2 "2026-02-26T11:27:36Z")

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Hi There,

Thanks for reaching out.

Yes, the `position` parameter in `genome.Variant` relates to the forward strand using 1-based indexing. For a 20bp substitution, the `position` is the coordinate of the first base of that block on the forward strand. Note that AlphaGenome uses 0-based indexing for its output tracks and intervals (like BED files or Python), whereas the position attribute for specifying variants is 1-based to maintain compatibility with common public variant formats (see documentation [here](https://www.alphagenomedocs.com/colabs/essential_commands.html)). Both the `reference`and `alternative` sequences of `genome.Variant` also relate to the forward strand.

You can still create a `genome.Interval` on the negative strand - the internal logic of AlphaGenome will flip the interval to the positive strand, insert the `genome.Variant` reference/alternative bases, then reverse complement back to the negative strand to pass into downstream functions like `predict_variant` or `score_variant`

Kind regards,  
Tumi