Fig. 6

Summary of somatic SV detections using tumor-normal paired short-read WGS data with HCC1395BL_v1.0 reference as compared to GRCh38. A Somatic SV counts discovered by GRIDSS2, Manta, Delly, and novoBreak with HCC1395BL_v1.0 reference as compared to GRCh38. B Somatic SV counts discovered by two or more somatic SV callers with HCC1395BL_v1.0 reference as compared to GRCh38. C 617 of 646 GRCh38-based somatic SVs (TRA excluded) were mapped to HCC1395BL_v1.0-based SVs, while 18 of 646 SVs were “unmapped,” and 11 of 646 SVs were mapped on HCC1395BL_v1.0, but no SVs in mapped locations on HCC1395BL_v1.0. D Somatic SVs supported by two or more callers were without mapped GRCh38-based SVs on HCC1395BL_v1.0. E KEGG pathway enrichment analysis of 17 genes overlapped with the 17 somatic SVs detected with HCC1395BL_v1.0 as a reference. Shown here are the top 7 enriched pathways with bar representing “odds ratio” (zScore) on the left side y-axis, dotted-line representing −log (p-value) on right side y-axis, and the numeric label showing counts of enriched gene versus the total genes in each pathway