The shot was fired around 1:45 a.m. on a train to Penn Station, which was due to depart at 1:51 p.m.
Witnesses say they saw a man in a hoodie fleeing the scene after the shooting.
The platform at Ronconcoma station was closed for morning trips.
On Wednesday morning, customers of the Ronkonkoma branch were told to delay for 5-10 minutes due to the fact that the track is not working.
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