Having seen CTR reported in Search Queries much lower than what I would have expected, I have done some tests in order to understand how Google calculates it.
I looked at a branded search in a small period of time where I know the site is ranking as #1 but where CTR was being reported as only 26%. For branded searches I would normally expect this percentage to be close to 100%.
So for this specific search, filtered on the country of Austria, Google WMT reports the following:
Impressions 89, Clicks 23, CTR 26%, Avg. pos #1
Drilling down by clicking on this specific search query and amalgamating information on page that ranked and a position in search results, I get the following info:
#1 German Home Page, Impressions 23, Clicks 12, CTR 52%
#2 German About Us Page, Impressions 21, Clicks 9, CTR 39%
#3 German Product type list page, Impressions 21, Clicks 2, CTR 9%
#4 Site Home Page (English), Impressions 23, Clicks 0, CTR 0%
#5 German a particular product page, Impressions 1, Clicks 0, CTR 0%
Adding up all impressions reported above results in 89 impressions and adding up all clicks results in 23 clicks.
However, being this a brand name search, and knowing that the home page will always rank for it, it was easy to figure out that there were only 23 searches for this query, which resulted with 23 clicks.
So out of 23 searches, every one resulted in click through to a site. The 100% CTR would be more appropriate number to report.
The additional 66 impressions were result of multiple pages being shown in SERPs for these 23 searches and they result in WMT understating CTR for queries where more than one page ranks for the same query.
Unfortunately, WMT does not show "Searches" column that would say how many times a query was searched for in a selected period, and then calculating CTR based on number of searches for a query instead of on number of impressions.
If you have only one page ranking for a specific query, WMT CTR would be more correct in terms of how many visitors that searched for that query, clicked through to your site.