$49,000 is the correct loss calculation, assuming that you yourself originally purchased the mutual fund shares for a total combined $54,000 purchase price, and you sold them last year at a large loss for only $5,000 in sale proceeds.
Gain/Loss = Proceeds - Basis
($49,000) = $5,000 - $49,000
As long as you "lost" the $49,000 in total share value over the life of the investment, then what the software is calculating for you is correct.
Did you have a more specific question about your cost basis and capital gain transaction for these shares? Did you purchase these yourself, or did your receive them from someone else?
Keep in mind that if you were not the original buyer of these shares, you may have a different cost basis than the original purchaser. This would result in a different gain or loss on your Form 8949 for the year. See this note from the IRS instructions for Form 8949:
The basis of property acquired by gift is generally the basis of the property in the hands of the donor. The basis of inherited property is generally the fair market value at the date of death.
Learn more about Form 8949 at this TurboTax video link.
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