After installing Cyanogenmod 12.1 or any custom rom if your storage is not summing up properly then you should try this fix.
After installing Cyanogenmod 12.1, my phone’s available and used space were not summing up properly. I was getting only 2.38 gb available though the used space was 5.56 GB out of 11.19 GB. After doing the math I realised I should be getting 5.63 GB space. To fix this below are the steps I performed.