So, after this step, we will have $k$ clusters, each of them associated with a centroid $C = \{ c_1, \dots, c_k\}$, where $C$ is the set of centroids (and $c_i \in \mathbb{R}^{128}$ in the case that SIFT descriptors have been used). These centroids represent the main features that are present in the whole training dataset $D$. In this context, they are often known as the codewords (which derives from the vector quantization literature) or visual words (hence the name bag-of-visual-words). The set of codewords $C$ is often called codebook or, equivalently, the visual vocabulary.
At the end of this process, we will have a vector $I \in \mathbb{R}^k$ that represents the frequency of the codewords in the query image $u$ (akin to the term frequency in the context of the bag-of-words model), i.e. $u$'s feature vector. Equivalently, $I$ can also be viewed as a histogram of features of the query image $u$, i.e. the feature vector of $u$. Here's an illustrative example of such a histogram.
From this diagram, we can see that there are $11$ codewords (of course, this is an unrealistic scenario!), and, on. On the y-axis, we have the frequency of each of the codewords in a given image. We can see that the $7$th codeword is the most frequent in this particular query image.