Queries vs Keywords

[SoundinTheory]

Can anyone clarify why my list of queries from google webmaster tools varies so much from the keywords that have resulted in clicks?

I have a site that, according to Google analytics, has had clicks from 125 key phrases where as in webmaster tools (via analytics) allegedly only 17 queries have resulted in clicks. Is it becuase GA can't handle less than 5 clicks from the webmaster data or is it something else I am missing?

The site I am researching for has very little traffic from other search engines.

[Ben_Alvord]

This is because of Google's (fairly) recent change in reporting of search referrals within Google Analytics.  If the user who visits your site is using Google under SSL (so with a https prefix), their search term is hidden and shows up in Google Analytics as (not provided).  So when you look at the list of search queries in GA, you are only looking at the queries that people searched for when they weren't accessing Google through SSL.  Everything else gets lumped into (not provided).

In Webmaster Tools though, you're able to see ALL of the searches, even the ones from HTTPS searches.  That's what creates the discrepancy.

[SoundinTheory]

I understand about the Google log in but, unless I have misunderstood your response, this also applies to the keywords that have driven traffic to the site.

Why are so many more keywords showing in my analytics than queries that resulted in click? Is this not the same data? Is this where I am going wrong?

[Ben_Alvord]

Sorry about that, I misread your question.

I wasn't really sure of the answer once I reread your question, but I did find this link from Google Support after digging around a bit: http://support.google.com/webmasters/bin/answer.py?hl=en&answer=1213138

[SoundinTheory]

It really is bizarre, the number of unique keywords or queries is as follows:

Google Webmaster Queries (in webmaster) - 77

Google Webmaster Queries resulting in clicks (in analytics) - 18 (406 in total)

Keyword clicks to the site (in analytics) - 125

There must be something I'm missing!