In August, more than 15 million people cast their ballots, representing 78 percent of the registered voters.

Kenya 's electoral board, which oversees the voting and counting in the country said that as of 5pm on Thursday, voter turnout during the rerun of the presidential elections was at 48 percent.

One of the fatalities was a man who was shot in his thigh and bled to death, our correspondent said.

Al Jazeera's Catherine Soi has reported that three people have been confirmed dead following clashes between groups of men and police in the western city of Kisumu and Homa Bay.

Voting has ended, but polling stations will be open in some areas on Saturday.

Polls have closed in #Kenya -s presidential election but voting in at least 4 locations, including Kisumu & Siaya postponed to Saturday

"We have faced and continue to face challenges, which are largely security related in certain electoral areas. The commission is keenly following the security situation and continues its consultations," said Wafula Chebukati, chairman of the electoral body.

The Independent Electoral and Boundaries Commission (IEBC) has suspended voting in several areas, including Kisumu, Migori, Siaya, and Homa Bay.

"We don't use excessive force, we respond to (the) breaking of law and order. In every instance our response has been proportionate," says senior Kenyan police official, Inspector General of Police Joseph Boinnet.

"Today will go down in history as a 'Day of Infamy'. A nation's destiny depends upon its freedom to elect leaders."

At least one person has died from a gunshot wound in Kibera.

There have been violent confrontations between security forces and youths in several parts of the country, with the deprived Nairobi suburb of Kibera and the western city of Kisumu, particularly effected.

President Kenyatta strikes a more celebratory tone in keeping with a candidate in the midst of a vote, posting pictures of himself with supporters at a polling station.

There's a notably stark difference in the language the two dominant figures of Kenyan politics are using on social media.

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Javas Bigambo, a Nairobi-based political analyst, told Al Jazeera: Today's violence and reports of ballots not being delivered on time "contribute to the conclusion that this election may not be very credible in the end … It is a failed rerun because so far, from a spot-check across the country, it is evident that the boycott is successful.

"If close to half the country will not participate in this election, then the very question of legitimacy of this election upon its conclusion may arise."

"Kenyatta may be compelled to find a way of bridging that divide and extending an olive branch to the opposition leadership to take this country forward."