Most are due to those trace element impurities, but at least one is the result of radiation damage to the crystal lattice, which makes the quartz smoky colored or brownish (cairngorm, or smoky quartz). read more
Natural quartz is rarely used as found in nature (especially in electrical applications), except as a gemstone. Natural quartz crystals have too many chemical impurities and physical flaws. As a result, a commercial process of manufacturing pure, flawless, electronics-grade quartz was developed. read more