Can I have primary account holder as my mom (resident in India) and secondary account holder as me? How does it affect the tax rate?

No. In Depository Account, Status and Sub Status is captured of First Holder Only. There is no option in the software to capture status and sub status of Second and Third Holder. Legally, there is no bar in holding assets by resident Indian along with non - resident Indian. Tax on this is complex and depends on case to case basis. This depends on whose books holding is shown, who make the payment for acquiring shares etc. Best way would be to keep single holder and second holder as nominee.