Permanent marker can easily be removed from glass using either WD-40, rubbing alcohol, or acetone-based nail polish remover.
If you have some acetone based nail polish remover that would be the best thing to use to get the permanent marker removed from the glass.
Just take a washcloth or paper towel or sponge and apply the nail polish remover to the cloth, paper towel or sponger and then wipe the permanent marker spot with it.
It may take a few tries to get the permanent marker off but it will work eventually.
You can also spray some WD 40 you can spray the WD 40 onto the glass and then allow it to sit for a few minutes and then scrub the permanent marker off the glass.
The rubbing alcohol will also work and you can just get the paper towel wet with the rubbing alcohol and wipe the glass down and the permanent marker should come right off.