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Did you use countermeasures?  Just curious.  As far as your question regarding your clearance, it depends on the agency and the potential work you may or may not perform.  Why do you ask that question in this forum?  You could simply ask personnel in whatever agency you are being potentially hired by.  The folks here are interested in the abolishment of polygraph and not a general source regarding the workings of security clearances.

ne,

Disregard Guest.  Some people are so insecure about everything an anti-polygraph person says, they tend to discredit even the non-polygraph related issues.

As your case goes, your hiring agency sounds similar to the FBI.  If that is the case then, what you need to realize is that the DoJ issues their own TS clearances.  I have a DoD TS, and I still had to go through the whole mess (which ended when I was labeled a spy during my polygraph).  So you have to check with the other agencies you are considering and see who their issuing agency is for clearances. 

The other issue is that if you opt out of the job you are currently seeking, your clearance with them may not be fully processed.  I don't know the agency you are applying for and if I did, I wouldn't know their clearance procedures.  But they may very well not process your clearance until the last minute before you hit the field, so be mindful of that if you decide to leave early.

Hope I helped you a bit,

Chris

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I don't think you will be granted the security clearance if you turn down the job.