QTL effect size calculation in MapQTL

[Gina]

Hi everybody! I just start to learn the software MapQTL and here I have some questions about how to calculate the QTL effect size with the "Kruskal/Wallis test" analysis results. I hope you will kindly help me to figure these things out. Thanks.

For example, my sample population is F2 population and the parental genotypes for one QTL locus is [hk x hk].

1. Does the effect size of this QTL locus equal to the difference between Mean-hh and Mean-kk? I mean, is the QTL effect size estimated as the difference between the value of Mean-hh and Mean-kk?

2. Is it possible that the value of Mean-hk is not between Mean-hh and Mean-hk?

Thanks.