Map lines can be setup to show a variety of information.
Originally by: Player Guide
This is the place where you set how many of the lines connecting systems you want to see. You can also choose to color the lines in two different ways:
• By Jump Type - Blue means the jump is within the same constellation, red means it's to a different constellation, but within the same region, and purple means it's a jump to a different region.
• By Region - Gives the regions different colors so you can see the boundaries of each one.
Also when you have an autopilot route set, the lines will show when the route transitions to a low security system with classic "danger" colors.