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What cost basis do I report on the 1099?
You wouldn't fill out a 1099, your employer would or possibly whoever manages the stock account.   The 1099-B imported from E-Trade says I had a transaction with sell price ~$4,500.   Yes.  You sold ~$4500 of stock to pay income taxes.  Both the cost basis and the sale price would probably be ~$4500, so no capital gain.  This is because you received and sold the stock at the same time.  If they waited a little, you could have had a small gain or loss.   The remainder of the stock has a cost basis of ~$5500.   There are at least two transactions here.   In the future you may sell the remaining stock.  It has a cost basis of ~$5500.  Sale price of course unknown until then.  You may break that into different pieces.  So you might sell $500 of cost basis for $1000 with a ~$500 capital gain.  Then later sell the remainder for $15,000 for a capital gain of ~$10,000.