Mississippi's football program was cited by the NCAA in nearly half of the 28 rules violations levied against the school in the Notice of Allegations the university recently received, said a person with knowledge of the investigation.
The person said Tuesday that 13 allegations involve the football program, and nine of those occurred during current coach Hugh Freeze's tenure. The person spoke to The Associated Press on condition of anonymity because the investigation is ongoing.
The violations are a mix of Level I -- which the NCAA considers most serious -- and Level II and III. Many have already been self-reported by the school.
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The school's women's basketball and track and field programs are also involved in the investigation.
Ole Miss has been under investigation since 2012 when women's basketball coach Adrian Wiggins and two assistants were fired after a school investigation found academic and recruiting misconduct. Two players were ruled ineligible and the school self-imposed a one-year postseason ban.
Ole Miss has 90 days to respond to the Notice of Allegations. School officials and legal counsel have not released the notice because they believe the documents should remain confidential while the investigation continues.
Some of the NCAA issues involving the football program are already known.
Left tackle Laremy Tunsil was suspended seven games during the past season after the NCAA ruled he received several improper benefits, including the use of three loaner cars over a six-month period.
A separate NCAA probe from last year involving Louisiana-Lafayette -- and former football assistant David Saunders -- also involved Ole Miss. Saunders worked at Ole Miss in 2010 under Nutt. Freeze became the Ole Miss head coach in December 2011.
Documents from the Louisiana-Lafayette case stated that Ole Miss legal counsel and NCAA enforcement staff interviewed Saunders in 2013.
Saunders was given an eight-year show-cause in the Louisiana-Lafayette case after the NCAA ruled he made an effort to arrange fraudulent college entrance exam scores for recruits.
Louisiana-Lafayette did not receive a postseason ban in its case, but was put on probation for two years and lost 11 scholarships over three seasons.
Ole Miss has already released some self-reported football violations over the past year, including that a "representative of athletics interests" provided transportation for potential recruits on six different occasions from 2011 to '14.
There was also a self-report where an assistant coach -- whose name was redacted from documents -- made improper contact with a recruit at a high school.