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I recently got nexus 5 16GB, but I have weird storage problem. The OS should take about ~3.5GB, so I should have 12.55GB left for apps and stuff. BUT:

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4.66GB + 2.95GB + ~0.5GB IS NOT 12.55, but ~8GB. Where is the remaining 4GB space?

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    via a terminal app (or adb shell), execute df -h. This shows you all partitions, the used, and the free space along. My guess is the remaining space goes to /system (reserved space for possible future updates), /recovery, /boot, and /cache. – Izzy Jun 2 '14 at 9:15
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Thumbnail cache

Check the .thumbnails directory in sdcard/DCIM (Digital Camera IMages)/ notice that it is a hidden directory and only visible with certain file managers with the option to view hidden files.

This directory stores a lot of thumbnail data especially in the form of two large binary files.

Play Music (if you are using it)

Play Music caches your songs so Settings > Clear Cache.

App Data left behind

Delete some app data cache left behind by uninstalled apps from sdcard/ and sdcard/Andorid/data. Even apps such as Chrome, Maps, YouTube leave a lot of cached files in sdcard/Andorid/data. Clean those apps cache from sdcard/Andorid/data.

Storage Space

Install DiskUsage and check your devices storage by detail.

DiskUsage provides a way to find files and directories on storage card which consume a lot of space.

After pinpointing down apps and files that consume a lot of storage with DiskUsage. Simply deleting those files and going into Settings > Apps selecting and cleaning those apps would prove sufficient.

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