This question is really about interpreting the output of the
df command, which is famously confusing and if you Google it, you'll see many questions about
How to interpret
df's results are inclusive of the 5% reserved space @chronitis told you about. This is the total absolute space. This number will approximate the size shown in the results of
fdisk -l for the partition which you're reviewing in the
Avail provides the total effective space and excludes the 5% reserved space. This is the space you can actually work with.
So nothing is missing. The disparity between
Avail totals in
df's output represents the 5% reserved space.
Free space not accounted for in
If you're scratching your head thinking "But I deleted that file(s), why can't I see the additional space in
df?!?", here's why:
If you delete a large file(s) but the process for it hasn't been terminated, this "free" space won't be reflected in the results of
sudo lsof +L1 will identify deleted files still showing a PID.