The aftershock was felt in Los Angeles, about 240 km to the south, and the surrounding area, with many residents posting on Twitter that they were awakened by it.
There had already been more than 80 smaller aftershocks since Thursday's 6.4 magnitude quake near the city of Ridgecrest, which was felt from Los Angeles to Las Vegas, USGS seismologist Lucy Jones said.
"We should be expecting lots of aftershocks and some of them will be bigger than the 3s we've been having so far," Jones told reporters on Thursday. "I think the chance of having a magnitude 5 ... is probably greater than 50-50."
Only a few injuries were reported in Thursday's quake, but two houses caught fire from broken gas pipes, officials said.
Water gushed from zigzagged cracks in the pavement from busted water lines. Deep fissures snaked across the Mojave Desert, with passersby stopping to take selfies while standing in the rendered earth.
The quake sent 30 residents of the desert community of 28,000 to emergency shelters, knocked some houses off their foundations and left many homeowners wondering if their insurance would cover the damage, Ridgecrest Mayor Peggy Breeden said.
"The most important thing is that we have not had any loss of life or any major personal damage to people," Breeden told CNN on Friday.
Breeden said officials were still assessing the extent of the damage, but added that emergency state and federal aid would enable the city's overwhelmed agencies to start the cleanup without worrying about their budgets.
The quake hit the edge of Death Valley National Park about 113 miles northeast of Los Angeles at about 10:30 a.m. on Thursday. It was very shallow, only 10.7 km deep, amplifying its effect, and was felt in an area inhabited by 20 million people, the European quake agency EMSC said.
The Ridgecrest Regional Hospital, where 15 patients were evacuated earlier, appeared intact apart from some new cracks in the walls.
The quake is the largest in Southern California since the 1994 magnitude 6.6 Northridge earthquake, USGS geophysicist Paul Caruso said. That quake, which was centered in a heavily populated area of Los Angeles, killed 57 people and caused billions of dollars of damage.
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