Storage used by applications doesn't match between folder info and system report I'm running on Macbook Pro OS X 10.11. I'm curious that when I check my storage the system reports I've used for apps 100.15GB whereas the applications folder size is just 39.56GB. Is it probably counted for storage that apps use to store their data?. If so how could I inspect those data (e.g. location and size) to consider removing them? 

Thanks in advance.
Not all applications are stored in /Applications. That's the default install folder for most applications, but it doesn't include all applications. In fact, since applications are really just bundles of files, most applications can be run from anywhere. 

To demonstrate this, take a look in System Profiler at Software > Applications. You'll see lots of software that isn't in /Applications



With that said, using this as a method to eliminate large applications probably isn't the most efficient or easy. You'd be better off using a disk scanner like DaisyDisk, Disk Inventory X, or some other alternative.