list of interval variants

[Jiseon623]

Hello, I performed mapping about two traits on CeNDR.
Two traits are similar, so the mapping results of them overlap each other.

The results have one common peak (common peak position and region), but the peaks have different numbers of interval variants.

And the two traits also have similar peaks (different peak positions but same region). They have different numbers of interval variants, too.

I thought that the list of interval variants would be the same if the regions were the same.
I wonder what made them different.

Best,
Jiseon

[synmuv]

Hi Jiseon,
Unless the traits are identical, then the correlations of genotype and phenotype are going to be different. This difference will go all the way to the variant level. Additionally, if the two traits have slightly different strains that were mapped, then the variants will also be different. If you would like to share your mapping reports with me (by DM), I can offer some more specific advice.
Best wishes and stay healthy,
Erik

[Jiseon623]

Hello Erik, Thank you for the quick reply. The difference of variants seems to be due to the difference in the mapped strains as you mentioned. Best, Jiseon 2020년 3월 24일 화요일, Erik Andersen <notifications@github.com>님이 작성:

…

Hi Jiseon, Unless the traits are identical, then the correlations of genotype and phenotype are going to be different. This difference will go all the way to the variant level. Additionally, if the two traits have slightly different strains that were mapped, then the variants will also be different. If you would like to share your mapping reports with me (by DM), I can offer some more specific advice. Best wishes and stay healthy, Erik — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#136 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANUZHDQ7GXQ7R6IX47QARSLRJAGPNANCNFSM4LRVVTIA> .

[synmuv]

Hi Jiseon,
Makes sense. I hope that it all works out for you.
Best wishes,
Erik