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I have a website hosted at .github.io subdomain that gets 40 daily visits from Google search according to Google Analytics. When I'm trying to find out which keywords were used using Search Console, I see 0 clicks and just 21 impressions (most of which are for (not set), which is fine) for the entire month.

For the other websites I host on my servers there is still a difference between Search Console and Google Analytics, but it's much lower, not more than 2x.

Does this happen because of being under a domain I don't own? Or it's a different problem?

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It's not a problem with the domain. Once registered in GSC, it'll give you all the attributes for that domain. In Google's eyes, that is your domain/site.

Numbers in Search Console are fudged by their sampling algorithm - the lower the absolute numbers you're dealing with, the less accurate they tend to be. It's likely the low amount of traffic giving you larger discrepancies.

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