The graph says you have 99% of the charge left (the line above the one you circled). Of the 1% of charge used, Android system used 26% of that (or 0.026% of the total battery charge), the screen used 15%, etc. The total, if all apps using any battery were listed, and the numbers went to about 3 decimal places, would always add up to about 99.99% - which means that all the power used from the battery was used. In your case, that's 1% of the total capacity. (The percentages for the apps aren't percent of battery capacity, they're percent of total power use.)
I don't know where you're getting that 5% loss number - the phone hasn't used 5% of the battery capacity yet.
Malik, other than when conditioning the battery, you should never let the battery get below 40%. 50% is the ideal charge point for maximum battery life. Constantly draining the battery to 30% kills the battery more than twice as fast as charging it at 50%.