Fig. 5

Somatic SNV detection using short reads on GRCh38 and HCC1395BL_v1.0 references. A Higher numbers of overlapping SNVs between MuTect2 and Strelka2 detected from 12 paired tumor-normal replicates on HCC1395BL_v1.0 as reference as opposed to GRCh38. B Higher number of overlapping INDELs between MuTect2 and Strelka2 detected from 12 paired tumor-normal replicates on HCC1395BL_v1.0 as reference as opposed to GRCh38. C 40,768 (97.83%) of 41,669 GRCh38-based somatic SNVs were considered mapped with HCC1395BL_v1.0-based SNVs, including 36,773 (88.25%) identical SNVs and 3995 (9.59%) equivalent SNVs. In total, 682 SNVs (1.64%) were able to map onto HCC1395BL_v1.0 but without overlapping Strelka2/MuTect2 calls. A total of 219 SNVs (0.53%) were considered as “not-mapped” onto HCC1395BL_v1.0 due to the stringent mapping criteria. D KEGG pathway enrichment analysis of 71 genes overlapped with the 1017 novel SNVs detected with HCC1395BL_v1.0 as a reference. Shown here are the top 10 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