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The real Amy was indeed pregnant for part of Series 6 & went into labour at the end of "The Almost People" (episode 6). The confusion about whether or not she was pregnant arose because the Amy we saw from the start of Series 6 until then wasn't the real Amy but a "ganger" -- a Flesh copy, controlled by the real Amy's mind. By the start of "A Good Man Goes to War" (episode 7), the real Amy had given birth & had named her daughter Melody Pond.