SAN JOSE, California, Oct 13, 2012 (AFP) - The 33-year-old had a 15-under 198 total at the CordeValle golf course. He equalled the course record 62 in the second round after opening with a 66 on Thursday.
"It was a little scrappy," said Mallinger, who has a two-shot lead. "I didn't have my best off the tee, but I started hitting some good shots coming in. I hit a lot of good putts that just didn't fall.
"Hopefully, I can straighten out the drive and make some putts tomorrow."
Mallinger had finished second twice, including losing in a playoff to Bo Van Pelt three years ago in Milwaukee.
Sweden's Jonas Blixt was second after a 66, while Americans Charles Howell and Jason Kokrak were another stroke back at 12 under. Howell shot a 66, and Kokrak fired a 67.
Fiji's Vijay Singh and Brazil's Alexandre Rocha were 11 under after both shot 66.
The 28-year-old Blixt birdied five of the last eight holes. He was even-par on the front nine with a birdie and a bogey. He shot up the leaderboard with birdies at 11 and 13 and then rolled in a birdie on 15 to get to 11-under.
Blixt birdied the 17th and followed with a six-foot birdie putt at 18 to finish two back. He finished third last week in Las Vegas.
"The front nine is a little harder. The back nine you can make a couple birdies," Blixt said. "Hopefully, I can finish like I did today."
Greg Owen (68), Scott Dunlap (70), Jhonattan Vegas (71), Danny Lee (67) and Russell Knox (65) share seventh at 10-under-par 203.
Leading scores on Saturday after the third round of the $5 million Frys.com Open (par-71, USA unless noted):
198 - John Mallinger 66-62-70
200 - Jonas Blixt (SWE) 66-68-66
201 - Charles Howell 66-69-66, Jason Kokrak 68-66-67
202 - Alexandre Rocha (BRA) 69-67-66, Vijay Singh (FIJ) 70-66-66
203 - Scott Dunlap 70-63-70, Russell Knox (SCO) 70-68-65, Danny Lee (NZL) 69-67-67, Greg Owen (ENG) 66-69-68, Jhonattan Vegas (VEN) 65-67-71
204 - Nicolas Colsaerts (BEL) 65-68-71, Jerry Kelly 69-68-67, Bryce Molder 71-67-66, Nick O'Hern (AUS) 62-71-71, D.A. Points 68-67-69, John Rollins 71-69-64, Gary Woodland 66-72-66
205 - Patrick Cantlay 67-70-68, Ben Curtis 69-71-65, Billy Horschel 67-65-73, Bill Lunde 69-67-69, Jeff Maggert 67-71-67, David Mathis 68-70-67, Zack Miller 70-69-66, Jeff Overton 68-69-68, Tim Petrovic 70-68-67