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 is 14 ft. 6.8 in. (174.8 in.) long.
The curb weight of the 2006 Honda Civic is 2593 lbs..
The 2006 Honda Civic's turning circle is 35.4 ft..