Probably the main reason why there are different results comes from the difference URLs that are analyzed.

OnPage for example analyzes the homepage URL with a backslash, i.e.http://www.domain.com/ and this page is indexable.


Please Check if the Yoast Plugin analyzes the homepage URL without backslash http://www.domain.com and if this page is not indexable as it uses a canonical tag which points to the URL http://www.domain.com/.

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