IMPUTE2 -merge_ref_panels output

Hello all,

I was finally able to use the IMPUTE2 -merge_ref_panels functionality and got the merged panel.

As per the website, the merged panel is obtained by imputing one panel into the other and vise versa.

Now my question is this, should the resulting panel be the union of the two panels or not?

As per the results I obtained it is not the union, and I am worried that I am doing something wrong.