This is a subject that I have always been interested in. There are lots of opinions and little proof. I did find this bit of info which I figure may be close. Sorry about the length.
By Stuart Wier
Two kinds of guns were the main reliance of the explorers. Lewis obtained fifteen rifles at Harpers Ferry Arsenal in the spring of 1803. Apparently these were the “1792 Contract Rifle,” modified for the expedition with Harpers Ferry model 1803 locks and patchboxes. They were plain, Pennsylvania-style rifles, with no ornamentation, hand-made by gunsmiths in Pennsylvania. Full stocked, they had an original barrel length of 42 inches, which was likely shortened a bit for the expedition, and caliber at least 49 and perhaps as large as 54.
The other gun of daily use was the “Charleville pattern” musket, the standard firearm of US soldiers of the period. It is a 69 caliber smoothbore, and is now called the “Model 1795 Springfield”
Clark brought a small 36 caliber “squirrel rifle,” and an “elegant fusil,” a light-weight gentleman's sporting smoothbore. Lewis brought a case of matched pistols, one of which he traded for a horse, and a "fowler," an extra-long smoothbore, also traded to the Indians for supplies. Both captains carried a “horseman's pistol” either the “US 1799 North and Cheney” model, similar to the French Charleville 1763 pistol, or the “US 1799 Contract” pistol (McCormick model), both now great rarities.
There are no known surviving guns from the expedition. Claims are made for three guns, but the claims are doubtful, lacking any definitive proof. None of the supposed expedition guns show the degree of wear expected from a two-year, 8000 mile, wilderness trip in small boats and horseback, and the arguments for their presence on the expedition come down to the enthusiast's "but could it have been" sort.
For more see Guns of the Lewis and Clark Expedition, Stuart Wier, published in "We Proceeded On," the journal of the Lewis and Clark Trail Historic Foundation, May 2006, vol. 32, no. 2, pp. 10-17, and see Letters, August 2006, vol. 32, no 3.