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Current trends show Mamata Banerjee is ahead of her main rival, the BJP's Priyanka Tibrewal, by over 56,000 votes, crossing her victory margin of 2011.
The Trinamool is also leading at Murshidabad's Samserganj and Jangipur seats, where by-elections were held after the deaths of two candidates.
Mamata Banerjee, who lost against her aide turned foe Suvendu Adhikari in Nandigram, must win the election to enter the state assembly before the end of her first six months as Chief Minister in this term.
The BJP candidate Priyanka Tibrewal is a lawyer and a long-time resident of the constituency.
Although the 41-year-old lost the recent assembly polls and the 2015 municipal polls, she has become well-known as one of the petitioners in the post-poll violence case against the state government.
Despite Trinamool Congress's tremendous victory in the assembly polls held this March-April, Mamata Banerjee lost the battle from Nandigram against Suvendu Adhikari, her former aide who joined the BJP in the run up to the elections.
While the Trinamool Congress has claimed that the party chief will win by a margin of over 50,000 votes, the BJP, claims it will be a "very good fight".
The Election Commission has arranged for a three-tier security system, deploying 24 companies of Central forces at the counting centre. More than 57 per cent voters cast their votes on Thursday.
Bhabanipur is the traditional seat of Ms Banerjee, which she quit to challenge Suvendu Adhikari from Nandigram, the area where her agitation had catapulted her to power a decade ago.
This time, Ms Banerjee's party leader Sobhandeb Chattopadhyay stepped down to make way for her in Bhabanipur.
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