GWAS poly issue to show the effect of each marker

[RezwanCAAS]

Hi gwaspoly team,
I ran the gwaspoly on roses (mixed ploidy, diploids, triploids, and tetraploids). GWASpoly does not show the effect of a few significant SNPs as given below. Can you please guide how to fix it, or is it normal?

Regards
Rezwan

[jeekinlau]

Hi Rezwan,

Please look at page 3 of the user manual. general model does not estimate effects

[RezwanCAAS]

Hi Jeekin,
Thank you for sharing this. Now it makes sense to me.

Regards
Rezwan