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Like the question says, what is the difference between Gate SCORE and marks out of 100? Why there are 2 different marks?

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GATE mark is out of 100 and is the actual mark one scored. Now, since there are 2 sessions this is normalized - based on average mark and marks of top 0.1% in each session.

GATE score (out of 1000) is another normalization technique to ensure same playing field for GATE takers across different years. So, even if you score less but gets a high score, it is better for admissions. Most IITs/IISc consider GATE score and not mark.