> Japan’s often-cited conviction rate of over 99 percent is a percentage of all prosecuted cases, not just contested cases. It is eye-catching, but misleading, since it counts as convictions those cases in which defendants pleaded guilty. If the U.S. conviction rate were calculated in a similar manner it would also exceed 99 percent since so few cases are contested at trial (in FY 2018 only 320 of the total number of 79,704 federal defendants were acquitted at trial).[0]

[0] https://thediplomat.com/2020/03/carlos-ghosn-and-japans-99-c...

Edit: looking at your linked PDF I think the above quote is missing the thousands of misdemeanors dismissed by judges. This just goes the show the difficulty of comparing legal systems using a single number from each.