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I just did:
ffmpeg -i inputfile -r 30 -vcodec libx264 -an -s hd480 output_30.mp4
and
ffmpeg -i inputfile -vcodec libx264 -an -s hd480 output_60.mp4
on a 60fps file.
Why is the second file 27 MB and the first file 49 MB despite the fact that the first file contains only every second frame?
Did you actually get every second frame? My impression is that you got every frame, but you halved the framerate. Therefore, the length of the video in seconds is twice as long for the first compared to the second, and assuming equal rate controls (e.g. 1 megabit per second), the twice-as-long-file will thus be approximately twice as big, which is what you got.
