Depends on who is doing the counting. Stanton's figures were acknowledged to be low for the number of prisoners prisoners kept in Southern prisons. A more complete 1903 estimate reported approximately 194,000 Union troops were held in Southern prisons while 215,000 Confederates were held in Northern prisons. See the following site:
As the site notes there should have been a much greater disparity in deaths between the two sides given the North's greater supplies of food, medicines, and doctors.
In the summer of 1864, the Confederate Agent of Exchange, Judge Ould, offered to buy medicines for Union prisoners at 2-3 times their cost and to let Federal doctors bring the medicines through the lines and treat the sick Union prisoners. The North never replied to this humane offer. Medicines were embargoed by the Federal blockade and were scarce in the South.
Records were not all that well kept on either side. One of my wife's ancestors died at Point Lookout prison in the North but he is not listed on the prison death rolls. There are claims on the web of severe undercounting of deaths at Point Lookout. While I don't know whether these claims are correct, there is evidence to support the undercounting.
The Charleston Daily Courier (December 3, 1863) reported that deaths were being substantially undercounted at the Fort Delaware Federal prison, but this report may not be correct. Who knows?
The number of prisoners kept at Andersonville is not certain. Those who were prisoners in the camp counted more than the somewhat PC park currently does. Fortunately for posterity, the prisoners carved their count into a stone monument at the park. The reduced number currently acknowledged by the Park Service has the effect of boosting Andersonville's death rate to more than the range claimed for Elmira Prison in New York.