According to the USGS, at 5:36 AM an earthquake with a preliminary magnitude of 3.6 rattled the East Bay.
The quake, which they say had a depth of 6 miles, had an epicenter 1 mile east of Berkeley, and 11 miles northeast of San Francisco's Civic Center.
According to BART, they are having 10 minute delays due to the earthquake, as after a quake they must inspect the tracks. According to the SFMTA, "As a result of the earthquake, subway operating by procedure in manual to check track conditions."
The train is stopped wherever it is. My wife and I were on a BART train once that was stopped in the Transbay Tube after an earthquake along the Hayward Fault.
