new QTL when refine QTL in MQM

[Atoosa Samani]

Hi,

I have been exploring multiple QTL models for a subset phenotype in my F2 population. I have used scanone and scantwo to find QTLs that I made the MQMs with. One specific QTL  for a subset phenotype is refined to a very different position on the LG (on a different scaffold very far away) and it explains more than 20% of the phenotype. This refined QTL has not came up before. 

Should I consider this a new QTL? 

Thanks.

[Karl Broman]

I can't tell from the information provided. But I would look to see whether there is any association between the genotypes on the one scaffold and on the other.

karl