A Sonoma County voter or candidate staying up late to watch Tuesday's election results trickle in could be forgiven for having the impression that votes were being tallied slower than in previous years.

At midnight — a full four hours after polls closed — the county Registrar of Voters' website listed just 40 percent of precincts reporting, 149 out of 374.

But the reality was the count was actually much farther along than anyone realized.

In fact, 179 precincts that require voters to mail in their ballots had already been tabulated along with the absentee ballots, but the precinct count failed to reflect this. That didn't happen until after midnight.

If they had been registered, instead of 40 percent of precincts counted by midnight, the tally would have been 88 percent.

The result was the vote count looked far behind previous years, when in fact it was pretty well on track, said Janice Atkinson, Sonoma County's clerk, recorder, assessor and registrar of voters.

"Things came in pretty well last night, but it didn't look like we had as many precincts reporting as it had in the past," Atkinson said Wednesday.

The confusion stemmed from a change in election rules regarding mail-in precincts. In previous years, Sonoma County's 179 mail-in precincts — areas with too few voters to merit staffing a polling place — were reported at the same time as the absentee ballots received by Election Day.

But this year, the Secretary of State's Office asked counties to report their mail-in precincts separately from absentee ballots, Atkinson said. The ballots were still counted and reported to the public shortly after polls closed. But an election official didn't take the extra step necessary to ensure the early results reflected that those mail-in precincts had been published.

"We didn't run those through until the very end," Atkinson said. "It was the first time we've done it this way, and we didn't think about how other people would see it."

Atkinson, who is retiring but will remain through the November election, said the process will be changed this fall to better reflect the reality that the mail-in precincts are "in" soon after the polls close.

There are 248,216 registered voters in the county, 12,259 of whom are in mail-in precincts.

The mix-up left even seasoned political observers baffled.

Political consultant Terry Price, who advised Susan Gorin on her run for the 1st Supervisorial District, noticed around midnight that only 35 of the 93 precincts were listed as being reported. This led him to conclude that a load of ballots from the Sonoma Valley had yet to arrive for processing at county election headquarters. That gave him hope that Gorin, who was running just 130 votes behind fellow Santa Rosa City Council member John Sawyer, might yet be able to overtake her rival.

Price even sent out an email to his team at 12:08 a.m. alerting them to that possibility, he said. Price then watched the precinct count "zoom up" after midnight and hit the 93 districts reporting at 12:38 a.m., but only 1,600 new votes had come in. Gorin picked up only a few dozen votes.

Aside from that glitch, the election went reasonably well, Atkinson said. There were some delays at precincts that held up delivery of the ballots to election headquarters.

The county is large and geographically diverse, with polling places in far-flung places like Sea Ranch and Annapolis needing to get their ballot boxes back to Santa Rosa. The last ballots were delivered from the West County at 11:40 p.m., due in part to a problem at one polling place where tired workers couldn't reconcile something and just threw everything into the ballot box for election officials to sort out, Atkinson said. Since ballots from multiple polling places are returned to an area return center before being driven to Santa Rosa, a problem at one polling place can hold up a whole section of the county's results.

The Secretary of State's Office reported Sonoma County turned in its results at 3:15 a.m., the third-slowest county in the state. That's in part because the county's computers couldn't send the results the way state officials requested it, and results had to be faxed in, Atkinson said.

Generally turnout was very light, with many polling places having just a few dozen people show up. One polling place, at Sonoma State University, had just three voters all day.

"It was lackluster," she said of the primary. "It was hard to get people excited about it."

The trend toward an increasing number of people voting by absentee ballot continued.

There were 163,214 mail-in ballots issued for the election, or 66 percent of registered voters.

"It keeps creeping up," she said.

Of those, 65,082 had been counted by the time polls closed. That leaves as many as 98,000 mail-in votes that could have been dropped off at polling places, but that didn't happen. Atkinson estimated somewhere between 25,000 and 35,000 people dropped off their ballots on Election Day. Those votes will now be counted over the next three weeks before the county issues final results.

Atkinson expected turnout of between 50 and 53 percent, but now thinks that might be optimistic.

So far, 91,848 votes have been counted, or a turnout rate of 37 percent. To hit 50 percent, 32,000 mail-in ballots would have to be counted. Judging from the stacks of absentee ballots left to be tallied, Atkinson didn't think it would happen.

"By the end of the week we should have a pretty good handle on how many we have," Atkinson said.

She predicted few races would be impacted by the uncounted ballots.

"Overall, I don't foresee a lot of changes," she said.