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Why are there differences between Google Analytics And Google Webmaster Tools in external links data? Generally this data do not coincide with each other.

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2 Answers

Google Analytics and Google Webmaster Tools are collecting different kinds of data, and they are sampling the data differently. That's why it's different.

Google Analytics "Referrals" measure a person who clicks a link to get from the external site to get to yours. Their browser must report that referral via HTTP_REFERER, and it must execute the Google Analytics JavaScript to report that. Some mobile browsers are no longer reporting the HTTP_REFERER value, so you will see those numbers start to go down.

Google Webmaster Tools "Links to Your Site" measure links to your site that the Googlebot spider finds when crawling the web. That is entirely different than what Google Analytics is measuring.

Also, neither Google Webmaster Tools nor Google Analytics will ever give you exact numbers. Both databases contain a ridiculous amount of data, so they need to sample it. You're supposed to be looking at this sampled data for trends over time to see if your marketing is helping or hurting your efforts.

Also, I've had this suspicion that Google never really wants to give you all the data. They ultimately don't want you monkeying around with your SEO too much because it undermines what they're trying to do in providing objective, relevant results.

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The difference is because Google Webmaster data is updated monthly whereas in Google Analytics you can see the daily activity.

Google webmaster tools has all the data, even if it does shows in Webmaster dashboard

Check out the following links to see the answers from the Google itself

http://support.google.com/webmasters/bin/answer.py?hl=en&answer=1213138

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But even if I take this into account I still have discrepancy with some external links which refer to the site ie. some of links are on GW but not on GA... –  nemat Jan 12 '13 at 9:50
    
Ya, true even I faced the similar problem. One of my sites is getting a back-link from Microsoft.com (Home page of Microsoft official site) as per the GW, which is no where possible in any case. Bro, to me it seems as a bug in GW. –  Sidh Jan 13 '13 at 18:04
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