Fig. 5: Categorization analysis of annotated transcripts uniquely discovered by Coral, as well as comparison of different basecalling tools in identifying fusion genes and allele-specific expression genes.

a Classification of reads assigned to the annotated transcripts identified by Coral but missed by other basecallers across three human cell lines. b Classification of the reads assigned to the most abundant transcript isoform discovered only by Coral across three datasets. c The detection status and proportion of spanning reads of 12 specific MCF-7 cell fusion genes (validated by RT-PCR and Sanger sequencing) using different basecallers. This analysis was performed on n = 7,230,921 reads. d Upset plot showing the intersection size of the genes with allele-specific expression (ASE) identified by the specific basecallers indicated by linked filled dots below each bar in the NA12878 dataset. The total number of ASE genes identified by different basecallers is shown in the left-hand horizontal bars. Intersection sets smaller than 9 elements are not displayed in the Upset plot. e Parental allele assignment for the genes HLA-C, GSTP1, CRYZ based on basecalling by Guppy, RODAN, GCRTcall, Dorado, and Coral. The number of reads assigned to maternal (M) and paternal (P) alleles at the heterozygous SNP with the highest total coverage of each gene is shown. Source data are provided as a Source Data file.