OK I put some green food colour in the tank , its been almost 1/2 hour ( 25 minutes so far) nothing has shown up in the bowl.
I have to add that when I first moved in, the shutoff valve was replaced by a local handyman, the reason being that the toilet did not work and their was no water in the tank, it was 'empty' so he fixed the toilet and I think he put in a new valve and some part in the tank as well ( I think, not sure)

Where are the tank levels? They should be 1/2" under the white overflow tube when the tank's filled and the ballcock's shut off. Back to you, Tom

The water level is about 3/4" below the white overflow tube

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I think it is my toilet, because when I turn it off ( the valve on the floor that is) the thumping sound I hear vibrating around that area disappears.

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You have llocalized the problem. I would replace the ballcock but if you want to repair it I'll need to know what you have in your tank. Which ballcock is yours? Back to you, Tom

Looks like the 'coloured' one.
Is the ballcock faulty because the water level is 3/4" vs 1/2 inch under the white overflow tube. I ask because there is also a toilet downstairs and am wondering if I should be checking that too.

OK! A little test. Remove the lid and push the float ball down. Now let it snap back up. Does that cause the noise? Let me know, Tom

Sorry my bad, it is the black and white one, not the coloured one as I previously stated