CHICAGO — Illinois voters cast their ballots on Tuesday in the primary election for the November governor’s race, but the results remained murky yesterday with Gov. Pat Quinn leading his Democratic challenger by a narrow margin while state Sen. Bill Brady led the Republican field by an even slimmer number.

With 99% of the vote counted late yesterday, Quinn led state Comptroller Dan Hynes by only about 7,000 votes, with 451,871 votes for Quinn and 444,779 for Hynes.

Brady, from Bloomington, was ahead of state Sen. Kirk Dillard of Hinsdale by just 700 votes. Both Dillard and Hynes yesterday refused to concede. President Obama called Quinn to congratulate him on the presumed victory.

The general election, like the primary race, will likely focus on the Illinois’ fiscal turmoil. The state faces a combined deficit in fiscal 2010 and fiscal 2011 of at least $12 billion due to ongoing economic troubles, faltering revenue collections, and the use of one-time measures to balance the fiscal 2010 budget last June.

Illinois has suffered several rounds of downgrades. Fitch Ratings assigns an A to the state’s $22.4 billion of general obligation bonds and has it on negative watch. Moody’s Investors Service rates the state A2 and Standard & Poor’s rates it A-plus, both with negative outlooks.

Quinn last year proposed a 50% increase in the state’s income tax rate, but lawmakers refused. He has called for restructuring taxes, but has not provided details of any new proposal, while Hynes has said he would press for a graduated tax structure, with top earners paying more.

Both Dillard and Brady oppose any major tax increases. Fiscal analysts have warned that tax increases or cuts alone likely would not solve the state’s structural budget problems.

In Cook County, long-time Chicago Alderman Toni Preckwinkle won a decisive victory with 49% of the vote over board President Todd Stroger, who came in last place among the field of four Democratic candidates. Stroger’s loss ends nearly 16 years of county rule by a Stroger — his own election in 2006 was preceded by 13 years of control by his father, the late John Stroger.

Preckwinkle will face Republican Roger Keats in November’s general election to see who will run the ­second-largest county in the country, with a $3 billion budget. If Keats wins, it will be the first time in 40 years a ­Republican has led the 17-member county board.

Stroger’s loss likely spells the end of a controversial and highly unpopular sales tax increase that he implemented in 2008, making Chicago’s sales tax rate one of the highest in the nation.

Preckwinkle and Keats have vowed to repeal or roll back the tax hike, saying they would trim the 24,000-employee government to offset the loss of roughly $250 million in annual revenue that the new sales tax was estimated to bring in over the next few years.

“Now is the time to repeal the Stroger sales tax, now is the time to end patronage, now is the time to cut waste,” Preckwinkle said in her victory speech in Chicago Tuesday night.

In other ballot measures, voters north of Chicago in Lake County voted down a $174 million bond referendum to finance improvements at New Trier High School in Winnetka — one of the top high schools in the state — by a wide margin.

Supporters argued that the aging school needs the upgrades, including a new cafeteria, library, and field house, as well as wheelchair accessibility and other improvements. Opponents countered that the financing was too costly.

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