It was felt across the Bay Area from San Francisco to Castro Valley and much of the East Bay.
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The quake was originally reported as 4.2 in magnitude, but has since been downgraded.
The quake was centered just outside of San Leandro, in Ashland, and struck around 6:30 p.m.
"It was almost like you could feel it coming," said Vicky Esquivel, who was home watching TV in Hayward, about three miles from the epicenter, when she felt a jolt so strong she thought someone ran into her house.
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"With a big truck, not a car! I felt like my house was going to fall off the foundation. I was so scared and then I just screamed and ran into the living room and my husband and I both looked at each other and said earthquake."
Esquivel is a longtime Bay Area resident and remembers the 1989 Loma Prieta quake. "Usually you feel the shaking, this was totally different. So I wonder if the closer you are to it, the more you're going to get that bang, instead of all the shaking."
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"It was only about five miles deep and as far as earthquakes go, that's pretty shallow," said Robert de Groot, a scientist with the USGS Shake Alert project, who added the the quake "gave rise to likely greater shaking throughout the region."
De Groot saves five miles is about half the depth of an average California quake, of which he says there are about 50 a day.
Kate Larsen: "Was there anything about this quake that made it feel more like a jolt than a rolling or a shaking?"
Robert de Groot: "Typically if people are really close to where the earthquake source is, the epicenter, then likely they feel everything happening at once."
De Groot says BART, which ran its trains at reduced speeds while they inspected tracks after Monday's earthquake, is automated through ShakeAlert for safety actions.
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BART said there was a 10-minute delay in the transit system due to the earthquake.
De Groot says that as of Monday night, there is nothing to indicate anything out of the ordinary as far as aftershocks are concerned. He calls the 3.9 quake "a garden variety California earthquake."
But de Groot says when you feel an earthquake, it's always a good reminder to get prepared. he says there are four different ways to sign up for ShakeAlerts on smart phones - the wireless emergency alert system, Google alerts on Android phones, and the MyShake and QuakeAlertUSA apps.
The San Francisco Fire Department says no injuries or damage have been reported.