Recently, Google made a change in the webmaster tool (search console) on 27th April 2016. It is clearly visible in the search console under Search Analytics option. You can see the graph something like below -
Google has made such kind of changes many times in the search console. The main reason behind this change is, Google wants to update the search console data – Clicks, Impression, CTR , etc. And due to this update, you may see changes in your search analytics data.
What google says about this -
"We refined our standards for calculating clicks and impressions. As a result, you may see a change in the click, impression, and CTR values in the Search Analytics report. A significant part of this change will affect website properties with associated mobile app properties. Specifically, it involves accounting for clicks and impressions only to the associated application property rather than to the website."
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