We examined 109.3 m of core in deformed crystalline rocks, acquired at 50 spots over 3013 vertical meters in the Cajon Pass deep drill hole, along with samples from nearby outcrops in southern California, to determine the nature of deformation and alteration near faults of the San Andreas fault system. The upper 3–3.5 km section of the crustal column is deformed by narrow brittle fractures and faults. The lower 1.5 km section of the core is cut by at least 25 steeply dipping faults, 11 of which are newly identified here. Altered damage zones up to 20 m thick along faults in the lower 1.1 km of the hole are composed of indurated foliated laumontite + chlorite ± epidote cataclasites and exhibit semibrittle to plastic deformation mechanisms, diffusive mass transfer, and solution transfer. Where the fault-related alteration produced lower-density rocks, well-defined borehole geophysical signatures and in situ stress measurements deviate from background levels. Some of the faults encountered in the shallower part of the borehole are probably related to the steeply dipping, slightly listric left-reverse Cleghorn fault, whereas indurate, sheared, and hydrothermally altered fault-related rocks cored near the base of the borehole, which sampled a damage zone of hydrothermally altered rock, are most likely to be related to subsidiary traces on the North American side of an ∼50° NE-dipping San Andreas fault zone, which has several traces nearby. Although the bulk of the fault rocks might be related to a steep downdip continuation of a planar Cleghorn fault zone, this interpretation is less likely because the Cleghorn fault is a reactivated reverse fault that is likely to be listric at depth. The Cajon Pass borehole intersected a complex suite of faults with pervasive fault-related damage and synkinematic hydrothermal alteration to at least 5 km depth. Fluids impacted all phases of deformation.

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