Yes, you would have passed the substantial presence test seeing that you are past your third year here. Your first 2 years as a J-1 Research visa holder would have been exempt. But if you had183 days here in the third year, you are no longer considered exempt and are treated as a US Resident for tax purposes.
Therefore you must file your taxes as a US resident would be required to file. This also means you must include income from all sources around the world.
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