  We consider the Witten index ${\cal I}= Tr (-1)^F$ of SU(2) Super-Yang-Mills
quantum mechanics (SYMQ) with N=16, 8, 4 supersymmetries. The theory governs
the interactions between a pair of D-branes under various circumstances, and
our goal is to count the number of the threshold bound states directly from the
low-energy effective theory. The string theory and M theory have predicted that
${\cal I}=1$ for N=16, which in fact forms an underlying hypothesis of the
M(atrix) theory formulation. Also the consistency of conifold transitions in
type II theories is known to require ${\cal I}=0$ for N=8 and 4. Here, the bulk
contribution to ${\cal I}$ is computed explicitly, and for N=16, 8, 4, found to
be 5/4, 1/4, 1/4 respectively, suggesting a common defect contribution of -1/4.
We illustrate how the defect term of -1/4 may arise in the SU(2) SYMQ by
considering the effective dynamics along the asymptotic region.
