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Constructing a pangenome gene graph
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Clarification on Interpretation of Genes with Empty Fill #12

Closed Evenlyeven closed 2 months ago

Evenlyeven commented 2 months ago

Thanks for the tool!

I had a hard time interpreting the gene with empty fill, like gene 001883909 in my case (top), and the gorilla LRRC37A3 in the pangene paper (bottom). Does the empty fill indicate a gene deletion, or is there another explanation?

Any clarification would be greatly appreciated!

image image

lh3 commented 2 months ago

See figure legend:

The LRRC37A3 alignment in gorilla has two in-frame stop codons

An empty box indicates in-frame stop codons or frameshifts in alignment.