Indirect evidence is based on inference. The atomic structure, the structure of the solar system, and the theory of black holes are all based on indirect evidence.
In studying the structure of the atom, we do not directly observe the sub-atomic particles rather we draw inferences from several experiments and make conclusions. This is indirect evidence.
The solar system can be studied using several astronomical instruments that aid us in making useful inferences regarding the solar system.
The weight of evidence that substantiate the existence of black holes have also been amassed through indirect evidence.
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