New to the DataHub ecosystem, What will be the best way to run sql query on Mysql database from Datahub ?

Can you elaborate more.. Do you want to query DataHub db?

No, so I have ingested a Mysql db to Datahub. I know we can query the metadata, but I am looking to query the actual MYsql data for some reliability checks.

oh, not sure if doable to query mysql directly in DataHub

You can docker exec into MySQL and see the relevant entries. Or do an cli ingestion and write it to file to see what is being written.