If a team on 3rd down gets a penalty via Defensive penalty

It just doesn't get factored in at that point. LIke a pass attempt that has holding or PI, the whole attempt gets erased. If you were 2/4 going into that third down, and there's a PI that gives you first down, you are still 2/4 on third down going forward.

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Does that count as a third down conversion? Or are you 0/1?

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yes, 1st down by penalty still counts as 1st down in the stats