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When I'm viewing the Galaxy Map form the Normandy and selecting where to go with a mass relay, some of the systems appear to pulse or blink.

At first I thought this was to indicate mission locations, but some of them are blinking with no obvious missions to complete. It's clearly not the presence of the Reapers.

Why are some of the systems blinking?

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I thought it meant there are possibly quests and/or items to be scanned in those sectors but I also ran into a sector where its glowing blue but 100% explored. –  z ' Mar 13 '12 at 22:13
    
@yx. Did those sectors have quests in them? I'm quite certain it means there's a quest or item to recover –  Dave McClelland Mar 13 '12 at 22:25
    
@Dave nope, they were all scanned with no quests –  z ' Mar 13 '12 at 23:54
    
@yx. There seems to be one system that always blinks (I had it too, so did a few others). I can't remember the name, but it's north west of the citadel. –  Mr Smooth Mar 14 '12 at 0:30

2 Answers 2

Blinking indicates that you currently have an active mission in your log to complete there.

If you see no obvious mission, scan around the system and you should find a war asset or fuel depot to recover.

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Fairly sure this behavior is intended, but it doesn't work perfectly. I've had 100% systems with no active missions blink. –  LessPop_MoreFizz Mar 13 '12 at 22:25
    
There's a bug that's been talked about fairly extensively on the BioWare forums. Specifically for a system in the lower right portion of the map. –  Fluttershy Mar 13 '12 at 22:28
    
I currently only have 3 active missions: Eden Prime: Resistance (because I missed a piece of information), Citadel: Cerberus cyphers and Priority: Horizon. The Minos Wasteland is blinking for me though, where the wiki assures me I don't need to go for those. Additionally, it's 100% searched. –  staticbeast Mar 13 '12 at 23:43

I have a system always blinking too, About 10 o'clock if the milky way were a clock, near the outside of the sector with the Citadel. called Minos Wasteland. For me it's currently at 100%, no missions. I went there anyway and found two systems, one called Fortis, the other Arrae, and both are 100% explored with no active missions in either. A glitch maybe? That seems to be the only one for me currently outside my only other active mission.

To add one more thing, if you pick up on conversations around the Citadel people ask you to find crap for them (or you eavesdrop about it...) Sometimes systems with the items they require will blink too. These won't be 100% explored, but I'm not sure if you can find the item before gaining the quest...

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you can definitely find the item before getting the quest –  z ' Apr 7 '12 at 19:35

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