Suppose in a 10X genomics experiment, each bubble is equivalent of the human genome in a fixed length fragments. The genomic fragments in a bubble get a unique barcode, so each bubble gets a barcode. The fragments are broken up, ligated with barcode adapters, and sequenced. When read from a fragment are mapped to the reference, they will appear to form a cloud of contiguous reads. Can we assume that a contiguous cloud of mapped res with identical barcodes is sampled from the same chromosome?
The 10x platform partitions the material into the barcoded gel beads ("GEMs"). The way the technology is presented is usually simplified to imply that a single GEM is a single fragment, but that is not actually the case. From the 10x website:
Our GemCode Technology creates a unique reagent delivery system that partitions cells or arbitrarily long DNA molecules (including >100 kb) and prepares sequencing libraries in parallel such that all fragments produced within a partition share a common barcode.
The key part is "all fragments produced within a partition share a common barcode". Thus, a single barcode can have multiple fragments that likely would be from multiple chromosomes.