I have created security onion vm a distribution based on ubuntu in vmware work station with 52GB Hard disk space. But fdisk command shows me more space than I have allocated. 
It shows 55.8 which I dont know it came from.
Now I want to increase the root partition in guest OS for which I used fdisk utility after expanding it in VMware (now 55GB, again I am seeing 59.1). Following this link (till setp 7) I created a new partition, as can be seen below sda3
aneela@aneela-virtual-machine:~$ sudo fdisk /dev/sda
Command (m for help): p
Disk /dev/sda: 59.1 GB, 59055800320 bytes
255 heads, 63 sectors/track, 7179 cylinders, total 115343360 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x0002da52
Device Boot Start End Blocks Id System
/dev/sda1 * 2048 106954751 53476352 83 Linux
/dev/sda2 106956798 109049855 1046529 5 Extended
/dev/sda3 106954752 106956797 1023 8e Linux LVM
/dev/sda5 106956800 109049855 1046528 82 Linux swap / Solaris
However there is something wrong as all sectors mentioned by fdisk are not in use as the last sector in use is 109049855 and I have more than that. Are others sectors not in use or what? How can I include missing sectors so that I could expand to full capacity as after that I would simply merge partitions for which there are plenty of links available.
Thanks.
You created a tiny ( < 1mb ) partition in the small gap before your previously existing swap partition instead of using the free space at the end of the disk. Use
gpartedto delete this useless partition, and expand your extended partition to the right, then move your swap partition all the way to the right, then move the start of the extended partition as far to the right as it can, then you can just grow sda1.