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Archaeologist Kevin Colls of Staffordshire University, who carried out the project with leading geophysicist Erica Utsi, concluded: "We have Shakespeare's burial with an odd disturbance at the head end and we have a story that suggests that at some point in history someone's come in and taken the skull of Shakespeare.
"It's very, very convincing to me that his skull isn't at Holy Trinity at all."
investigators went to another church, St Leonard's, in Beoley, Worcestershire, where legend has it a mysterious skull in a sealed crypt is that of Shakespeare's.
A forensic anthropological analysis revealed it to belong to an unknown woman who was in her 70s when she died.
Mr Colls said: "It was a great honour to be the first researcher to be given permission to undertake non-invasive archaeological investigations at the grave of William Shakespeare.
"With projects such as this, you never really know what you might find, and of course there are so many contradictory myths and legends about the tomb of the Bard.
"The amazing project team, using state-of-the-art equipment, has produced astonishing results which are much better than I dared hoped for, and these results will undoubtedly spark discussion, scholarly debate and controversial theories for years to come. Even now, thinking of the findings sends shivers down my spine."