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Lighthouse scores will vary each time you run it depending on how long certain resoruces take to process, it’s totally possible that the lighthouse systems are taxed for whatever reason when shopify runs them so your score is lower.
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The score shopify displays right next to your live them is an agreegrate of diferent page’s lighthouse score, when you say 56, are you talking about your homepage, or an aggregate score of your homepage, product page, and collection page?