I was surprised to learn that, according to the research of an organization of orthodox Torah scribes, more than 50 percent of the Torah scrolls they checked contained scribal errors; see the comments of Moshe Sokolow in Jewish Book World 15:3 (Winter 1997), p. 16.
The edition used most commonly by biblical scholars, the Biblia Hebraica Stuttgartensia, reproduces a single Masoretic manuscript and includes an unsystematic collection of textual variants at the bottom of each page. The massive Hebrew University Bible (of which only Isaiah and Jeremiah are completed) includes a fuller collection of textual variants. Neither edition attempts to note consistently which variant readings are preferable and which are secondary.
A preliminary attempt is in my book, The Text of Genesis 1–11: Textual Studies and Critical Edition York/Oxford: Oxford Univ. Press, 1998).