COMMUTER LTT HELD SHORT OF THE WRONG RWY AT FAT IN THE FOG.

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AFTER RECEIVING OUR CLRNC TO TAXI; I TAXIED TO RWY 29L. WHILE HOLDING SHORT OF RWY 29L; WE HAD NOTICED THAT EVERYONE ELSE WAS TAXIING TO AND DEPARTING OFF RWY 29R. WE THEN CONTACTED THE TWR AND RPTED THAT WE WERE READY FOR DEP. THE TWR REPLIED HOLD SHORT. AFTER A FEW MINS; THE TWR CLRED ANOTHER ACFT FOR TKOF ON RWY 29R. THE TWR CTLR THEN STATED TO US; 'COMPANY ID AFTER COMPANY DEPARTS TAXI INTO POS AND HOLD.' AFTER WATCHING COMPANY DEPART RWY 29R I ASKED MY FO TO CONFIRM WITH THE TWR POS AND HOLD ON RWY 29L. BEFORE MOVING MY ACFT; MY FO STATED TO THE TWR; 'COMPANY ID IS GOING INTO POS AND HOLD ON RWY 29L.' THE TWR THEN ASKED US IF WE WERE AT RWY 29R. MY FO STATED; NEGATIVE WE ARE HOLDING SHORT OF RWY 29L. (WE NEVER CROSSED THE HOLD SHORT LINES FOR RWY 29L; AS I CONTINUED TO HOLD SHORT OF THE RWY). THE TWR THEN INFORMED US THAT WE WERE INSTRUCTED TO TAXI TO RWY 29R. I TOLD HIM THAT I THOUGHT WE WERE GIVEN RWY 29L. THE CTLR THEN GAVE US THE OPTION OF RWYS AND I TOLD HIM THAT WE PREFERRED 29R. THE CTLR THEN INSTRUCTED TO US TO CANCEL OUR PREVIOUS CLRNC AND TAXI TO RWY 29R. THIS INCIDENT TOOK PLACE ON A VERY FOGGY DAY SO THE TWR WAS UNABLE TO SEE THE RWYS. BEING VIGILANT AND CONFIRMING INSTRUCTIONS SAVED US FROM A POSSIBLE RWY INCURSION.