The train jumped its tracks near 11th Street and Borden Avenue.
As a result, there was limited LIRR service to Hunterspoint Avenue and no service to Long Island City.
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The Amtrak train did not have any passengers aboard it.
New York City Transit was cross-honoring LIRR fares on the E train at Jamaica and 7 line at Woodside.
There was no word yet on what caused the derailment.
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