You either removed the catalytic converter or you are running too rich.
backfiring.
carb or timing
Your cylinders could be backfiring on you. Bring it on to a mechanic. You could also have problems with your computer. But with a civic my guess is the cylinders.
The 2006 Honda Civic has 16 valves.
The 2006 Honda Civic has an inline 4 engine.
The 2006 Honda Civic has a 5-speed manual.
The 2006 Honda Civic is a gas-powered vehicle.
The 2006 Honda Civic has single overhead cam (SOHC).
The height of the 2006 Honda Civic is 4 ft. 5.5 in. (53.5 in.).
The 2006 Honda Civic's turning circle is 35.4 ft..
The 2006 Honda Civic runs on regular unleaded.
The curb weight of the 2006 Honda Civic is 2593 lbs..