There are not only those physically injured in battle by enemy (or friendly) fire, killed, mortally wounded, or just wounded in some degree. There were also non-battle casualties, or those suffering injury on accident in camp, field, or due to illness.
Disease of course was deadlier than combat, and not a few men were physically weakened or wrecked by severe illness.
The Medical and Surgical History of the War volumes give many of the gory statistics.
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Livermore's "Numbers and Losses" gives the following calculation of killed and wounded, etc.
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p. 47-48.
Modern statistical data on Confederate losses suggests something more like half a million.
Historian J. David Hacker’s new estimate of Civil War dead challenges long-held views about the human and psychic costs of the conflict.
discovere.binghamton.edu
The U.S. Civil War was the nation's deadliest conflict, but debate remains over the total estimate of fatalities.
www.history.com
Folks often associate civil war battlefield surgery with amputation. They didn't always amputate, but did so lots of times. Here's a hair-raising account of the effects of having one's limb lopped off and its aftermath by Private Winchell of Company D, 1st US Sharpshooters was wounded in the arm at Gaines' Mill in the summer of 1862, and captured.
His arm was amputated without anesthesia...
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From Steven's history of the Berdan Sharpshooters, 1892, page 519 to read the whole gruesome tale...