The term 'rare' is relative and often misused and overused. Let's see if we can gain any insight using real data.
The following is my work an my work only. They are not authorized factory figures. Do not quote them as such and be respectful of the data. The data only says what is says on this date. Do not try and interpret it any other way.
The data is somewhat statistically volatile due to a small sample size. The values will change over time as I add cars but I do not anticipate wide swings in the results. I think it will remain stable overall. I don't anticipate 97 or 99 paint cars suddenly overwhelming the number of B5 cars. Yet, the numbers do help us visualize the relative distribution of colors based on a random sample.
I have 562 1969 GTXs from all three plants on file. Of that, I have 385 hard tops of which I'm reasonably sure represent the original colors (one must take into account that original looking tags with the exception of color changes could be in the sample thereby skewing the distribution.)
In this sample, X9 comes in about the middle of the pack in terms of frequency. It's not a particularly 'rare' color nor particularly 'common' either. It's in the middle with colors like F3 and Y2. It's far less common than B5 or A4 but certainly more prevalent than Y3 or L1.
The numbers for convertibles is far more volatile due to a very small sample size. Adding one or two cars to this small of a sample would affect the overall results. They included for entertainment purposed only.
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