Yes he is. In the series finale when Jack picks Jen up and puts him on his shoulder she mentions "the time that CJ knocked me up and left me". I do believe that was something that was said or pretty close to it at least.
U kno what I dnt recall them ever saying CJ as the father, but I believe he was... That was the last guy we had seen jen with! I always had that same curiosity! (:
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