The "magic icon 50%" means that the damage output of the spell scales with your magic stat at a rate of 50%. I don't think this means that 50% of your magic stat will be applied to the damage, rather I believe it is there to compare against other skills that may have different percentages here. The base damage of Ember Bolt at level 1 is 10-15, so I believe that the 11-16 in your case indicates an additional point of damage due to your magic stat level.
You are correct that the damage also is impacted by the power of your weapon, in this case 10% of the damage your weapon would normally do is applied to the damage you'd do with Ember Bolt.
Note also that this damage is per bolt, and you fire multiple bolts, which also can go up as you level the skill, I believe.
Once upon a time there was a skill calculator that I believe helped you play with the various statistics and determine the output damage you'd end up with, but the site's gone offline. It seems like Runic plays with the various formulae when they patch, so getting accurate, detailed information that is up to date is challenging. There's some info in the last post here, but I have no idea if it's accurate with the current revision of the game.