(A) Vlnplot of feature counts, unique molecular identifier (UMI) counts, and percentage of mitochondrial genes in cells after quality control. (B) Bar plot of doublet and singlet number. (C) Clustered heatmap of all cells copy number profiles estimated by CopyKAT. Warm colors represent the increase of copy number, while cold colors represent the loss of copy number. Columns represent genomic positions. In aneuploid cells, the copy number amplifications and deletions are more frequent: these are more consistent with the characteristics of malignant cells. (D) The aneuploid cells more highly expressed oncogenic markers than the diploid cells. ****p value < 0.0001. (E) The number of malignant cells of ATs, primary lesions (PLs), and lymph gland (LG). (F) Heatmap plot showing the SingleR result, higher score means higher Spearman correlations of the cells to be annotated with the expression levels of known cells in the reference set. (G) Chord diagram shows the correspondence between cell annotation results and cell cluster results. (H).Cell type Pearson’s correlation coefficient heatmap.