id and id $USER show different groups

I set my primary group as root in /etc/passwd, and I always do this when install a new system. I also add myself to other groups,eg. sudo, lp, dialout ... However, the id only shows I am in root group and no other groups shown.

So I change my primary group from root to chiao voila the problem is solved! The id and id chiao show the same groups. Futhermore, I can use thonny directly.