That is your taproot, the first root that comes from your seedling.
What do you mean by separate? Is it completely loose from your seedling? if so, start a new grow.
if not, try to put some dirt on it carefully and you will be fine.
This occurred because you might putted the seed in the dirt sideways instead of the root downwards.
or with feeding water the seed went sideways.
Goodluck growing :)