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UMI counts of reads covering M. m. domesticus specific alleles were used to construct three profiles depending on whether they were associated with M. m. domesticus cell barcodes (endogenous counts, endo), M. m. castaneus cell barcodes (contaminating counts, cont) or empty droplet barcodes (empty). Counts from droplets that are not clearly assignable as cell-containing or empty were excluded from further analysis (other).
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