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What does it mean when you have a situation where your D<0?

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Consider two bi-allelic loci, A and B with alleles A1, A2 for A and B1, B2 for B. Negative values for D means that A1 is more often associated with B2 than expected. Similarly, A2 is more often associated with B1 than expected.

More info on Wikiedpia > Linkage Disequilibrium or on any intro book to population genetics (see here for recommendations). If there is anything in particular you do not about the definition of LD, feel free to ask a question by highlighting what is unclear to you.

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