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ISLAMABAD, Pakistan — As U.S. authorities took a purported al-Qaeda operative to court on charges of attempted murder and assault Tuesday in New York, her family, the Afghan police and the Human Rights Commission of Pakistan cast doubts on the accuracy of the American story.

On Monday, the Justice Department announced that Aafia Siddiqui, a Pakistani woman who was educated in the United States, had been taken into custody in mid-July in Afghanistan.

She was arraigned Tuesday in New York, and her case has inflamed anti-American sentiment in Pakistan and triggered street protests against her detention.

According to the criminal complaint filed in the Southern District of New York, Siddiqui was arrested July 17 by Afghan security forces in Ghazni province in eastern Afghanistan with her 12-year-old son. She was found with documentation on explosives, descriptions of U.S. landmarks and various chemical substances, the complaint says. A day later she was handed over to U.S. intelligence and military officials.

The complaint says that she got hold of an officer’s M-4 rifle in an interrogation room and fired two shots, which missed. The officer reportedly used his pistol to fire back and hit her at least once.

Afghan police, however, said U.S. soldiers demanded that local police hand over Siddiqui, but they refused, according to a report from Ghazni by Reuters news agency. When the Americans disarmed the Afghan police at gunpoint, Siddiqui approached the Americans, complaining of mistreatment by the police, according to this account.

The U.S. troops, according to an unnamed Afghan police officer, “thinking that she had explosives and would attack them as a suicide bomber, shot her and took her,” Reuters reported.

Siddiqui’s family, meanwhile, alleges that she’d been in secret custody since she disappeared five years ago from the Pakistani city of Karachi with her three children, and the Human Rights Commission of Pakistan, an independent organization, called the U.S. account a “cock-and-bull story.”

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