Google gives a few reasons for this discrepancy:
To protect user privacy, the Performance report doesn’t show all data. For example, we might not track some queries that are made a very small number of times or those that contain personal or sensitive information.
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I don’t believe for a second that nearly half of the searches to all of these sites were private. That leaves the reason that some of the queries are being whatsapp number list made a small number of times—often called long-tail keywords. Google may have understated that just a bit. At any rate, 46.08% missing is way higher than I expected.
We know that 15% of all Google searches have never been seen before. I’m sure Google stores these queries. Otherwise, it won’t be able to come up with that statistic.
However, I’d speculate that the team behind GSC has limited resources, and it doesn’t bother to store or expose all of the data. It’s just the extent of the data that’s missing is surprising to me and may come as a shock to you.
You can figure out the kinds of terms that drive traffic to a page by using the Performance report in GSC or by checking the Organic keywords report in Ahrefs’ Site Explorer. The hidden data in GSC likely includes terms that are similar to the terms listed here.
For example, Google is missing data on 35% of the clicks for our post on keyword research. In the U.S., there are 327 terms listed in GSC and 426 in Ahrefs.
Keyword rankings as reported by Ahrefs' Site Explorer
Screenshot from Ahrefs’ Organic keywords report.
In all, 178 of these are duplicated in the datasets, but that leaves a number of unique terms in each dataset. While we can’t say for sure what the missing terms are, they’re likely similar to the terms included in these reports.