Have you taken a gravity reading? tasted the sample? Smelled it?
Did your recipe call for late addition of LME or honey? Or addition in secondary?
Was fermentation fairly vigorous?
My 1st thought was a late addition of extract wasn't well mixed. But if it's been in a fermentor for a few weeks and fermentation was active, the yeasties would have stirred it up I would expect.
Is it a light colored beer? Could it be just regular stratification as the beer clears?
Did you cold crash at all?
test the gravity, smell and taste the sample...
See if you can get samples from the clear layer and also the darker layer below.
Do they still seem different side by side in similar glass containers?
If all seems well bottle that bad boy.
Hell, bottle it anyway. May turn out to be a tasty accidental sour.