Philadelphia police had been searching for the gunman who shot the man multiple times on the Broad Street Line train around 2:40 p.m. in the city's Francisville section.
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The victim was taken to Temple University Hospital where he died a short time later.
Police said a 16-year-old male was shot in the arm during the incident. He was originally reported to be an innocent bystander, however, sources tell Action News that is not the case.
According to sources, the teenager got onto the subway at the Susquehanna Avenue stop and tried to rob the 21-year-old man.
Sources say a struggle ensued and the teenager shot the victim multiple times. Philadelphia police called the shooting a "targeted attack."
Fourteen fire cartridge casings were found at the scene. Earlier reports said the victim was shot 11 times, but sources say it may have been closer to six.
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The victim, who had a permit to carry, was also armed and shot the teenager in the arm.
There were at least a dozen passengers aboard the train car, but no other injuries were reported.
Sources say the 16-year-old later showed up at the hospital but told police he was shot on a basketball court. He denied being shot on the subway at Broad Street and Fairmount Avenue.
That all changed though when his mother arrived at the hospital, sources say.
The mother allegedly knew her son was lying and he eventually confessed to the shooting.
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Sources say he told police where he hid the gun.
The teen was released from the hospital and remains in custody.
Action News is told the 16-year-old has two prior arrests for theft.
There is no word on charges.