I was confused at first too, but, I think this is what it means...
The time in the top left corner indicates the time the phone has been on the battery since the battery was at 100%. So, if you don't charge it back to 100%, the time will continue to elapse while unplugged. Once it charges to 100% again, that time will reset.
The time at the bottom of the graph is the total time between 100% charges, so it shows the length of time of the graph...as well as the colors below:
The colors at the bottom indicate the signal strength, when the phone was awake, when the screen was on, and when the phone was charging during the time between 100% charges.