What Causes Brown Phlegm While Coughing?

I went to see my doctor today after having a cold/flu, etc. I've had symptoms for about 5 days. Yesterday I had severe chest tightness and head pressure. Last night I began coughing up brown phlegm and when I cough it hurts significantly in my throat and below. My dr. said my lungs are clear. I don't understand where the brown phlegm is coming from if my lungs are clear.