Some of the Muslim dead were taken to the local mosque
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Niger has denied that any of its citizens were responsible for recent violence in neighbouring Nigeria.
Hundreds of people were killed in the city of Jos when clashes erupted after local elections last week and thousands remain in a makeshift camp.
Authorities in Plateau State had accused 16 men it arrested afterwards of being Nigerien mercenaries.
But the Niger government said there was no evidence those arrested were from Niger, or had been involved.
Earlier in the week, Niger's ambassador to Abuja, Isa Ibrahim, said that those arrested had been living in Jos "for several years as water vendors".
He also claimed that around 50 Niger nationals had been killed in the violence and warned against statements that could "fuel a dying fire".
Violence flared on Friday amid claims an election had been rigged.
Churches and mosques were torched as mobs from the Muslim Hausa community and mainly Christian ethnic groups armed with machetes went on the rampage.
Nigeria's 140 million people are split almost equally between Muslims and Christians and the two communities generally live peacefully side by side.
But Jos has seen repeated bouts of inter-communal violence, with more than 1,000 killed during riots in 2001.
The BBC's Alex Last in Nigeria says the real trigger for confrontation is usually competition for resources.
In Nigeria political office is perhaps the most powerful resource of all as it gives the holder access to some of country's huge oil revenues, he says.
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