In some STM measurements the DNA appeared with negative contrast, i.e., ``submerged'' Under the metal background and darker. Here, we report controlled (using current and bias voltage settings) and spontaneous contrast inversions of DNA molecules in the STM images and dependence of the DNA apparent height on the bias voltage and current set. Using these characterizations, we formulate a model explaining the above phenomenon by the WKB approximation and resonant tunneling through virtual states in the tip-sample space.