M4A is an audio file format that is very similar to MP4. It is a proprietary file format of Apple. iTunes store contains the audios as M4A format. It uses MPEG-4 codec to contain audio files. One of the basic differences between M4A and MP4 is M4A does not contain videos like MP4.
FLAC is a lossless audio file format. It is similar to MP3 format but the main difference between these 2 formats is FLAC file compress the file size without changing the quality of audio. It can compress an audio file up to half of its original size using lossless compression algorithm.
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