  Superconducting thin films of niobium have been extensively employed in
transmon qubit architectures. Although these architectures have demonstrated
remarkable improvements in recent years, further improvements in performance
through materials engineering will aid in large-scale deployment. Here, we use
information retrieved from secondary ion mass spectrometry and electron
microscopy to conduct a detailed assessment of the surface oxide that forms in
ambient conditions for transmon test qubit devices patterned from a niobium
film. We observe that this oxide exhibits a varying stoichiometry with NbO and
NbO$_2$ found closer to the niobium film and Nb$_2$O$_5$ found closer to the
surface. In terms of structural analysis, we find that the Nb$_2$O$_5$ region
is semicrystalline in nature and exhibits randomly oriented grains on the order
of 1-2 nm corresponding to monoclinic N-Nb$_2$O$_5$ that are dispersed
throughout an amorphous matrix. Using fluctuation electron microscopy, we are
able to map the relative crystallinity in the Nb$_2$O$_5$ region with nanometer
spatial resolution. Through this correlative method, we observe that amorphous
regions are more likely to contain oxygen vacancies and exhibit weaker bonds
between the niobium and oxygen atoms. Based on these findings, we expect that
oxygen vacancies likely serve as a decoherence mechanism in quantum systems.
