Snedeker shared first place with Ted Potter Jr., with both players having played two rounds in 8-under par. Potter shot a 67 on the par-70 Monterey Peninsula Shore Course Friday while Snedeker posted a 68 at the par-72 Spyglass Hill Golf Club.
Each of the 156 players compete over the three courses being used for the tournament before a cut is made Saturday. Those surviving the cut will play the fourth and final round at the Pebble Beach Golf Links Sunday.
Mickelson, the defending champion, was 2-under through 36 holes in a tie for 39th place.
Snedeker finished four shots behind Woods two weeks ago at the Farmers Insurance Open, played at Torrey Pines, and then wound up four shots behind Mickelson last week at the Phoenix Open.
Although he has yet to win on the PGA Tour this year, Snedeker is out front in the FedEx Cup points list. He won the 2012 FedEx Cup and the $10 million that went with it.
Potter won on the tour for the first time last year at the Greenbrier Classic.
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