Fig. 4

Query neighborhoods in HuSB1 contain sequence variants and new genes. a Left panel: gyrA has substantial minor sequence variation in several query neighborhoods. In this multidimensional scaling plot, each point represents a distinct gyrA sequence from the Plass assemblies of four representative query neighborhoods, colored by query binned genome. The triangles represent gyrA sequences originating from the query binned genome, if any are present. The inlays are visualizations of assembly graphs of reads that contain gyrA sequence in each neighborhood. Unitigs are colored by their cluster of origin; matches to gyrA sequences from the bin are highlighted using color from relevant triangle. b Right panel: genome neighborhoods re-associate annotated functionality to binned genomes. For each of 23 genome bins originating from HuSB1, we found the unbinned content by removing all orthologs found in the binned genomes in [39] and by counting distinct ortholog annotations once. Functional content is distributed throughout pathways present in the binned genomes and increases functionality associated with binned genomes by approximately 13%