That is what we call Sun Colored Amethyst or SCA for short, here's why you clear glass bottle turned this color...
There's a natural process that transforms some forms of glass to purple, the principal additive in glass that produces these varying shades of purple is manganese. Manganese, when measured properly, was used as a clarifying agent in glass to neutralize the blue-green coloring effects of the naturally occurring iron impurities in raw glass, thus producing a clear or off-clear glass (at least as we perceive it within the wavelength that reaches our eye). Manganese is a sensitive reactor to electromagnetic radiation. Within the scope of electromagnetic radiation there is a low level amount emitted by our sun in the form of ultra violet light. Over a prolonged period of time, moderate to higher levels of manganese in glass will react to the ultra violet light from the sun, causing a “purpling” effect. Dependant upon the levels of manganese in the glass, this purpling or solarization can produce multiple graduations in color from a pink tint to moderately dark purple.
That being said they can also be 'helped' along by "nuking" them, by either running them thru an industrial food sterilizer or putting them in a closed box with a high intensity UV blulb for a week or two, this will turn them extremely dark and bottle collectors hate those bottles AND the people that NUKE them... Jim