Customers sometimes assume that this score refers to the number of pages on the site we've scanned, versus the total number of pages on the site. This is actually incorrect!
The score is essentially a "grade" from 0% to 100%, with 100% being the best score possible.
We give scores for each page we scan, along with an overall score for the entire website. Site audit scores are calculated using a formula that looks at both the type and number of issues we find. This is weighted so that critical issues have more influence than errors, and errors have more influence than warnings.
If a page has a "Critical" issue, the page is automatically given a score of 0%. "Errors" reduce the page's score substantially, while "Warnings" reduce the page's score slightly.
Page-level scores are combined to form your overall site-wide score. When calculating your site-wide score, page depth is also taken into account (deeper pages have less influence on your overall score).