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The difference between the Mastery Score Percentage in the AU and the Lowest Passing Score Percentage in the Test Settings is the following.
The Mastery Score determines if the score for the AU has been satisfied, while the Lowest Passing Score Percentage in the Test Settings only determines the test has been passed, granted these could be seen as the same if you only have one Test in your AU.
Also note that only included tests will affect the mastery score. This is done by making sure the check box ‘Include test score in overall score’ in Test Results Tab is checked on.