Queries regarding NGS

Hello everyone, I request you all to kindly help me by answering the following questions:
Would be very helpful if you do so.

1. How to select the threshold for the base quality parameters while processing the NGS reads till finding variants?
2. Difference between V3-V4 and V4 amplicon sequencing and its applications. Which one of the techniques can detect a large set of organisms?
3. Can you please explain the quality filters that can be used for processing microarray data in genome studio?

Thanking you in anticipation.