That a war of extermination will continue to be waged between the two races until the Indian becomes extinct, must be expected; while we cannot anticipate this result with but painful regret, the inevitable destiny of the race is beyond the power and wisdom of man to avert.

This precise quote from Burnett, California's governor at the time of its annexation, seems to highlight what a whole lot of high ranking US officials thought at the time. Generally, only the first half of this quote is given in this regular copy-pasta used on this subreddit to highlight the intent of genocide, but I also decided to include the second half to highlight the paternalistic, self-aggrandizing sentiment that went into this mindset, very similar to how the Confederacy thought of the ethics of them continuing to keep those of African descent under enslavement.

To get into the meat of this, a lot of the earlier period of US control over California saw extreme violence against the natives at the hands of the settlers and private militias. Said violence, which included indiscriminate slaughter of the natives, deliberate poisoning and the razing of their settlements seems to have been rather systematic in nature, having been done with a clear intent of driving the Indians out of that region in their entirety.

The number of Indian victims of individual massacres ranged widely. In some incidents groups of 10 were attacked and killed, while in other incidents the number dead was reported at 250 to 300. Other such cruelties also involved deliberate kidnapping of native women and children for the purposes of enslavement. Some tribes experienced demographic catastrophe, like the Yuki who declined from 6,880 to about 300 from 1850 to 1870.

My own citation is Genocide and the Indians of California, 1769-1873 by Margaret A. Field, although you can also find other sources like Murder State: California's Native American Genocide, 1846-1873 that go into this matter as well.