Counting of ballots began amidst tight security in Parliament House here in the presence of authorised representatives of both Mukherjee and Sangma.
The ballot boxes of votes cast in Parliament House were taken up first for counting after which those from the states will be opened.
Authorised representatives inspected the seals of the ballot boxes and the counting began after ascertaining that they were not tampered with.
As many as 95 per cent of the 4,896 electors -- 776 MPs and 4,120 MLAs -- had exercised their franchise on Thursday at the polling centres set up in Parliament House and 30 other states and Union territories with assemblies.
All the ballot boxes from the states had reached Parliament House yesterday and were kept in a strong room.
Mukherjee appears set to win the election comfortably with UPA managers confident that he would bag over seven lakh of vote value of the total votes polled.
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The UPA constituents and its key supporting parties like SP, BSP, RJD and others had supported Mukherjee. Besides, he also got the support of opposition parties like Shiv Sena and JD(U).
BJP-backed Sangma is expected to garner a vote value of around three lakh.
The vote of SP chief Mulayam Singh Yadav had been declared invalid by the Election Commission on the ground that he violated the code of secrecy by revealing his ballot. Yadav had initially voted for Sangma and then tore the ballot paper when he realised his mistake.