In its charge sheet filed by the CBI before a special CBI court, the CBI has claimed that a detailed forensic analysis of the hard disc of the computer showed that there was no file carrying "CM" ever stored on it, CBI officials said.
The charge sheet filed by the CBI in connection with Pre Medical test for 2013 has listed 490 accused which includes three Vyapam officials - Nitin Mohindra, Ajay Kumar Sen and C K Mishra.
The CBI alleged that the racketeers arranged solvers for MBBS aspirants.
Congress leader Digvijaya Singh and whistleblower Prashant Pandey had alleged that the word "CM" found in the files in the computer of accused Nitin Mohindra was deleted or changed.
The CBI charge sheet comes as a major relief to Madhya Pradesh Chief Minister Shivraj Singh Chouhan as he has been given a virtual clean chit by the probe agency.
The state goes to polls next year.
The agency has also ruled out any tampering of the hard disc which was seized by Indore police on July 18, 2013 saying it was last switched off on July 15, 2013 and its records were not accessed thereafter, it said. "There is no grain of truth in the allegation that the HDD seized on July 18, 2013 from the office of then Principal System Analyst, Vyapam was tampered," CBI Spokesperson Abhishek Dayal said.
He also said that excel files provided by Mr Pandey in two pen drives to Delhi High Court and the CBI to purportedly show alleged tampering carried "false documents".
It is alleged that the then systems analyst in Madhya Pradesh Professional Examination Board known as Vyapam, Mohindra, who is an accused in the admissions scam had recorded details of payoffs to influential persons on his computer in the excel sheets.
His computer and hard disc was seized by Indore police on July 18, 2013.
It was alleged that solvers were arranged for candidates appearing for pre-medical admission tests conducted by Madhya Pradesh Profession Examination Board for a fee with the chain of payoffs reaching senior functionaries of the government.
The two had alleged, in their separate pleas, that the word "CM" was mentioned 48 times in an excel file stored on the disc which was either replaced or deleted.
Mr Dayal said the agency conducted investigation on the allegations made by the two in their writ petitions filed before the Supreme Court regarding tampering of disc.
The central forensic science laboratory experts prepared a mirror images of the hard disc at the local court on October 29 and 30, 2015 and the same process was videographed, Mr Dayal said.
He said the pen drives, as per the claims of Mr Pandey, contained the tampered and untampered versions of the impugned excel file.
After analysis, the CFSL submitted seven reports to the CBI, he said and added that as per the report, the computer with the hard disc in question was last shut down on July 15, 2013 and no file on the said disc was accessed after it.
The CBI spokesperson said the pen drive provided by Mr Pandey to the Delhi High Court as well as to the CBI contains "false documents created subsequent to seizure of the hard disc" in question.
Giving modus operandi of the Vyapam scam, the CBI said with the help of officials, the records were manipulated in such a way that roll numbers of candidates are immediately behind the solver which was codenamed as "engine bogey arrangement" with candidate being bogey and solver being the coach.
Using advanced softwares to identify facial features, the CBI matched the photographs in the admit card records to identify solvers, they said. The agency managed to identify 42 solvers, they said.
Based on its analysis, 61 engine and bogey students were named accused for the first time in the charge sheet filed today, CBI sources said adding that rest of the 490 accused have been named as accused in previous charge sheets filed.
Guardians of 22 beneficiaries have also been booked in the charge sheet along with one middleman. All these have been named for the first time, they said.