Fig. 2: Spot swapping in human–mouse chimeric sample HM-1.

a Species annotation of sample HM-1, a chimeric tissue of human skin and mouse duodenum. Spots annotated as mixtures were removed prior to calculating the summaries in b–d in an effort to ensure that the effects shown are not due to spots containing a mixture of the two species. b The spot-specific proportions of spot-swapped UMI counts (human-specific UMIs in background or mouse spots; mouse-specific UMIs in background or human spots). Also shown are the proportion of human-specific UMIs in human spots and mouse-specific UMIs in mouse spots. For the six boxplots from left to right, n = 2962, 751, 1014, 2962, 751, 1014 spots, respectively. The lower whisker, lower hinge, line inside box, upper hinge, and upper whisker represent the minimum, lower quartile, median, upper quartile, and maximum calculated without outlier values which are more than 1.5*inter-quartile range away from the hinges and are shown in separate dots. Note that there may be spot-swapped reads in these latter proportions (e.g. reads from human spot t bound by probes at human spot t’), but they cannot be identified in this experiment. c–d The total UMI counts in human-specific genes and mouse-specific genes for HM-1. Similar plots for HM-2 and HM-3 are shown in Supplementary Fig. 11. Tissue spots on the perimeter as well as spots annotated as mixtures were removed prior to calculating the proportions in b in an effort to ensure that the effects shown are not due to spots on the tissue-background boundary.