Frederick14Va is correct.
The muskets used by Virginias state troops were (by far) Virginia Manufactory muskets. Produced between 1802 and 1821, nearly 60 thousand of the muskets were made. Virginia militia often stored thier regimental arms nearby at the courthouse, sheriff's office, etc. Virginia was slow in replacing and altering these arms to percussion, which is why so many are still found in flint. Simply, the legislature did not want to spend the money... Late in 1861 the Confederate government took control of these arms and sent thousands abroad in flint and contracted to have others altered to flintlock. Later Virginia demanded that their arms to be returned, admitting that arms not marked as Virginia Manufactory (on the lock) could not be returned. The Confederate govenment complied for the most part. At that point Virginia began her contracts for percussion alterations. I have included photos of a short infantry musket (39" barrel) that was altered by S.C. Robinson in Richmond and later the front band replaced with an M1822 (1816) musket and fitted for a M1842 bayonet and ramrod by the (at this time) Confederate arsenal in Richmond. Yes Virginia had US M1816s, but nowhere near as many at Manufactory muskets. They also had a handful of early post RevWar muskets and contract muskets, but also this numbered maybe two thousand in 1861. Virginia was very well armed as a state!!! Possessing roughly 60k stands of arms, and 300 cannon! Not counting various swords and pistols.
These arms were be replaced as soon as possible for federalized (Confederate) state troops (1st VA Vol. Inf.) vs 98th Virginia Militia (designations changed multiple times but generally retained thier pre-war nomencature) which largely kept, or reissued "old state arms." This persisted until the end of the war due to the want of firearms. Even veteran units were haphazardly armed near the end, esp. in the valley. Even unionist western Virginia maintained "old state arms" until well after the end hostilities.
Ok, the post is about Virginia militia rifle companies. The reason I went through that detail is that depending on what period of the war you are covering, the company designation was in name only. If they did not, essentially grab, or lucky enough to have rifles at the beginning of the war, they were issued muskets. When Virginia federalized her troops, those arms were now in Confederate service and no longer the stayes. There are two types of Virginia Manufactory rifles and several contracts. These were along the lines of a long rifle and relatively few were made, fewer altered to petcussion or even for a bayonet. Virginia had Halls rifles and M1817 Common rifles as well. Again, few were altered 8th to percussion... I included my excellent condition William B. & Cyrus Fisher altered Common Rifle, a true Army of the Valley gun. After the vast majority of statd troops became Confederate regiments, they were armed in a variety of ways usually with federal captures. The militia in state service were generally armed with old smoothbores which were generally still in flintlock until mid-war. Like most military companies, you were issued what you were issued... state troops often had to let go of thier newer arms for federalized troop use.
VMI guarded the state arsenal at Lexington. VMI never had 1500 cadet muskets, a few hundred (cant remember the number offhand) M1851 Cadet musket, the first batch from Springfield, and 100-150 Harpers Ferry Model 1817 Artillery/Cadet musket as a stop gap after the cadet musket craze begining with the 1841 Cadet muskets were made for West Point. They did at times use the states' Halls rifles located at the arsenal. I have included my example of an M1817 Artillery/Cadet musket. So far it's the only one in existance with Virginia provenance, altered by Union Mfg Co. in Richmond. Many if not most of these muskets went further south. Sorry the lock is upside down... but you can clearly see the bolster conversion.
Hope this helps, there is much much more that can be discussed. At some point I will complete my book on this subject.