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More than 6,000 people have been killed in violence in Iraq so far in 2013.
The costs of the 2003 American invasion of Iraq continue with ongoing sectarian violence on a near daily basis, including 1,000 killed in the last month alone.
Another 3,000 were killed in 2012, and so far 2013 has seen more than 6,000 killed.
The study puts the overall number of deaths at nearly 500,000.
That number is higher than media estimates but lower than a controversial 2006 Lancet study that put the number between 400,000 and 655,000 deaths.
The study, published in PLOS Medicine, was compiled by researchers from Iraq, Canada and the United States, led by Amy Hagopian from University of Washington.
"We think it is roughly around half-a-million people dead. And that is likely a low estimate," said Hagopian, according to National Geographic.
"People need to know the cost in human lives of the decision to go to war."
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The website Iraq Body Count puts the number of civilian deaths by violence in Iraq between 114,000 and 126,000, and questioned the methods of the PLOS study.
Iraq Body Count said while the study made major improvements over past studies, earlier numbers still needed to be explained.
“Hopefully, the widespread reporting of this study can contribute towards a more mature and reflective attitude among those who may have too easily latched onto conveniently massive round numbers as political footballs,” Hamit Dardagan, an analyst for Iraq Body Count, said in an email to Al Jazeera.
“It might also help if the authors were a little more forthcoming in acknowledging and perhaps exploring the discrepancies between the earlier work and the new study, whose results are much less of an outlier amongst the various existing estimates for deaths from violence.”
The PLOS researchers surveyed 2,000 households in Iraq between May and July 2011, asking them about deaths among family members, BBC reported. It is believed that most of the deaths were attributable to violence, but as many as one-third may have been due to failures in health care or sanitation.
Violence has displaced nearly 1.1 million Iraqis, who are now living in camps or in other countries.