the "duf" output you posted does not show anything about actual disk, only the mounted partitions of the disk. Which is correctly reported.
For disk information see "lsblk" or "lsscsi", etc.
During the installation you were given a choice on how to partition the disk and the end result is what you see. You can either reinstall your OS or find a procedure on the net to expand the LVM slice and the ext4 file system inside the VM.
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