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YDNA comparisons are normally made on the basis of the number of markers that differ between two test results. For example, if two 37 marker tests show 3 marker values that differ from each other, then the comparison is said to be "3-off" 37, or to differ from each other by 3/37. A problem arises if different test results make use of a different number of markers. Typical tests provide results for 12, 25, 37, and 67 markers. Since the cost of the test is dependent on the number of markers, different people choose different numbers of markers to be tested. This makes it difficult to directly compare test results when looking at kits that used different numbers of markers. The following table illustrates the problems that arise.

Kits B, C, D, and E differ from Kit A by 6, 1, 2, and 5 markers. Because you have to juggle both the number of difference in markers, and the number of markers tested, it is somewhat difficult to determine whether the various kits share a relatively recent common ancestor. For instance while Kit A differs from Kit B by 6 markers, and Kit E by 5 markers, its not obvious whether Kit B or E is more similar. True, Kit E differs from Kit A by few markers than Kit B, but fewer markers were tested to begin with.

yONE removes this uncertainty by using "dissimilarity indicies". Such indicies give a show the extent to which two YDNA test results differ from each other, but "normalize" the results allowing the user to temporarily ignore the number of markers being tested. The results are presented as "Percent Dissimilarity". When using the "One Step YDNA Model", the dissimilarity indices will range from "0.0" (Identical YDNA results, no difference in markers), to "1.0" (complete non-identical results).

From this it is clear that Kit E is in fact the most dissimilar of the four test kits compared to the target Kit A.