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See here:

Go to my rep graph and notice that it only shows about 350 points...

Where's my other 4100?

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up vote 4 down vote accepted

I think this is not specific to Stack Apps, All the reputation graph on Trilogy site don't show bonus points. For your case, 100 is from Account Associations, 4000 is from Api Evangelist badge bonus point.

But I hope they could add those bonus info to reputation-graph as well.

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