Thanks for writing to H.C.M. for your query.
I have gone through your query regarding your cough and dark brown sputum in morning hours. You are diabetic and tests for tuberculosis
is negative, and no organism is isolated in investigation.
If your chest is normal than possibility of sinus infection
should be ruled out by doing C.T.scan of paranasal sinuses
. In chronic sinusitis
also morning phlegm is well reported. since color of phlegm is dark brown that means it is having alterred blood.
Next possibility is of GERD (gastro esophageal reflux disorder) and LPR (laryngopharyngeal reflux
). These are related with hyperacidity and gastritis.
Now a thorough examination of your nose, throat, chest and abdomen is necessary to find out real pathology which can be accordingly manage.