Believe that the Federal government purchased around forty-six hundred of the Northern manufactured .56 cal. Colt revolving five-shot rifles, and most were used in the west.
The below link provides details of the number of Colt revolving rifles in service during the war:-
Colt's Model 1855 Revolving Rifle In The Civil War | An Official Journal Of The NRA (americanrifleman.org)
Below is a summary of the numbers in active use, at different points of time during the war, by the U.S. government:-
pre '61 - 700 rifles (deliveries received)
end '62 - 2,400 rifles (in field service)
fall '63 - 2,700 rifles (in field service)
mid '64 - 1,300 rifles (in field service)
end of war – 305 rifles (taken home)
Don't believe any Colt revolving rifles were issued to Confederate forces.
Thought any Confederate officer (or soldier) possessing such a rifle, might have captured the weapon in the field. (e.g. At Chickamauga, the surrendered 21st Ohio Infantry had 167 Colt rifles; at Brice's Cross Roads, the routed 9th Illinois Cavalry carried around 140 of these weapons).
Wonder when it was that Sam Watkins saw his company Captain with a revolving rifle (pre or post Chickamauga?).