@jik, I think the trick here is to come up with a reasonable estimation. A full-blown accounting system would do this on a "tax lot" basis, meaning, it would aggregate your trades based on the tax rules. This can grow quite complicated if you are buying and selling a security over the course of a year or more. For example, because the tax code depends on the distance between purchase and sale dates, you have to adhere to a standard to how you connect buys and sells. This can get quite intricate.
So, a rule of thumb, such as apply X% tax on gains/losses each quarter, would be more appropriate.
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