The way I understand it, during long-duration, fat-burning zone exercise (low- to moderate-intensity), you burn mostly muscle glycogen at first, but after about 15 minutes, your body switches to fat as it's main fuel. On the other hand, if you exercise harder (aerobic zone), you will burn more glycogen and less fat.
Of course, if you exercise aerobically a lot or do weight training, it builds muscle which burns more calories in your sleep or when you are not exercising. So I guess there's no real clear answer.
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