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I noticed that each time I save a jpg file in PHP, it is saved with sub-sampling. How to remove that? I'm using GD library.

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I believe newer versions of libgd disable chroma-subsampling if you set the quality to 90 or higher.

Failing that, you could consider using PHP Imagick and disabling chroma sub-sampling with:

$img->setSamplingFactors(array('1x1', '1x1', '1x1'));
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