FOXBORO — The second quarter is done here at Gillette, and the Niners hold a  17-3 lead. It is the largest deficit the Patriots have faced at halftime this year. The last time they were down by at least two touchdowns at the half was in Week 16 last year, when New England fell behind Miami 17-0 at the half zooming back to a 27-24 win.

Here are a few quick notes:

•As was the case in the first quarter, ball security was an issue for both teams. The wet weather affected both the Patriots and Niners, and will make it tough going the rest of the evening. (That, combined with some interesting officiating from Ed Hochuli and his crew, has made for a crazy first half.)

•The Patriots’ best drive of the second quarter came on their first series, when New England took over on its own 25 after the Niners’ turned the ball over on downs. The Patriots maneuvered into San Francisco territory, getting all the way to the Niners’ seven-yard line, but things stalled out after a Ray McDonald sack. Following the setback, Stephen Gostkowski connected on a 32-yard field goal to make it 7-3. (The highlight of the drive came when the Patriots faced a fourth-and-4 at the San Francisco 32, when a nine-yard completion over the middle to Deion Branch in his first game back allowed New England to pick up the first down. The drive went 16 plays and 62 yards and consumed 6:24 for the Patriots.)

•The Niners answered almost immediately, scoring on a three-play, 80-yard drive that ended with a 34-yard pass play from Colin Kaepernick to Delanie Walker to make it 14-3 with 6:59 left in the second quarter. The highlight of the drive for San Francisco was a 35-yard pass interference penalty on Aqib Talib on a pass play for Michael Crabtree got the Niners into New England territory.

•The Patriots were quickly forced to punt on their ensuing possession, but Ted Ginn Jr. appeared to botch the punt. After a lengthy review (compounded by a struggling Hochuli going back and forth to try and get the call correct), it was determined that he didn’t touch the ball, and possession reverted back to the Niners. San Francisco then marched back down the field, targeting Patriots cornerback Alfonzo Dennard on a series of plays and getting good, tough inside yardage with Frank Gore on the ground. (The highlight was a 19-yard pickup by Kaepernick on a third-and-3.) The 49ers took it all the way down to the two-yard line before settling for a 20-yard field goal from David Akers to finish the second-quarter scoring.