Question about analyzing low-depth tetraploid resequencing data for auto vs. allo

[yokkkkl]

Hi GenomeScope team,

Many thanks for developing such a user-friendly and powerful tool!

I have some tetraploid resequencing data (~10× depth) for one tree species. The ploidy has already been confirmed by flow cytometry. I’d like to just determine whether this species is autotetraploid or allotetraploid based on heterozygosity patterns (i.e., aabb vs. aaab).

Would it be appropriate to combine data from ten individuals that come from the same population (same location) for this analysis?

Many thanks for your time and help!

Best,
Junyi

[mschatz]

In generally I would not recommend it since you could get a complex mixture of heterozygous variants across all the different haplotypes. But if the A and B genomes are very different you might see a well defined set of peaks. Have you tried it? Good luck! Mike

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On Thu, Oct 16, 2025 at 5:05 AM yokkkkl ***@***.***> wrote: *yokkkkl* created an issue (schatzlab/genomescope#162) <#162> Hi GenomeScope team, Many thanks for developing such a user-friendly and powerful tool! I have some tetraploid resequencing data (~10× depth) for one tree species. The ploidy has already been confirmed by flow cytometry. I’d like to just determine whether this species is autotetraploid or allotetraploid based on heterozygosity patterns (i.e., aabb vs. aaab). Would it be appropriate to combine data from ten individuals that come from the same population (same location) for this analysis? Many thanks for your time and help! Best, Junyi — Reply to this email directly, view it on GitHub <#162>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABP34ZT77K5KAFVJN6AFHD3X5NTZAVCNFSM6AAAAACJLCD4FOVHI2DSMVQWIX3LMV43ASLTON2WKOZTGUZDAOJXHAZTMNA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Artifice120]

SmudgePlot might be able to predict the ploidy. With only 10X coverage though it really is a gamble as to weather there are enough reads that smudgeplot can use as evidence