Your account fund balance might show negative because of various possible reasons. Each is mentioned below.
Account Maintenance charge(AMC) is deducted from your account. Which is deducted quarterly.
You might have bought shares with all the available margin not leaving any balance for deduction of Govt taxes and brokerages.
Overutilization of collateral Margin. You should maintain at least 50% of the funds from cash for taking any futures and options position.
MTM loss:- If you have any open futures and options positions, which are settled on an MTM basis. So if you incur any losses they will be deducted from your available cash, so the balance may become negative.
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