It depends on how the ownership situation was established and what the papers at the time said. If this was a new purchase and the deed does not otherwise specify, it will be 1/3 share per owner. If you and your spouse owned the home prior, and made a gift to your daughter via quitclaim deed, you would have been required to file a gift tax return for the amount of the gift, and that would have established the size of the gift (perhaps as 1/3 the value of the house or something different).
You can't go back and now say that 98% of the home was your daughter's and 1% for each spouse just because it would reduce your taxable gain to say so. If audited, the IRS will also look at how the home was acquired and how the proceeds of the sale were divided. If the home was purchased 100% with parents' funds (as a place for the child to live while attending college, for example), and 100% of the sales proceeds go to the parents, then an auditor is likely to rule that the home was in actuality owned only by the parents and there is no allowable capital gains exclusion for it being the daughter's primary residence.
You may want to have your situation reviewed by a tax professional.
