kbroman/Paper_qtlX: Final changes

A few more changes after studying the proofs

• some typos

• fix a problem in the Application section where we wrongly talked about a difference in degrees of freedom. The main effect penalty is smaller for the X chromosome than autosomes, but there is no difference in degrees of freedom. The difference in the penalty is likely due to reduced recombination (that mice have one recombinant X chromosome, vs two recombinant autosomes).