Percentile depends upon the score of the topper. The topper's score is considered to be 100 percentile marks. If you get negative marks, it doesn't matter. The final marks scored by you will be compared with the topper's marks and thus you get a percentile score.

Suppose the topper from your shift of exam scores 340/360. Then 340 will be equal to 100 percentile.

Hope this helps. All the best.