SummonChimera detected recurrent HBV integration in HCC. (A) The human chromosome 5 region with the hTERT gene from the UCSC Genome Browser [http://genome.ucsc.edu/] view of the hg19 is shown . hTERT is a known recurrent HBV integration site. The red vertical lines indicate the positions of HBV integration, as predicted by SC, that are illustrated in B and C. (B) The T268 HCC sample HBV integration has been shown to be reference parallel. The red arrow points 5' to 3' on the virus reference strand and the numbers indicate the determined viral nucleotides included, keeping in mind HBVs circular genome. Green blocks represent the annotated gene coding regions within the integration. (C) The T198 HCC sample has an HBV integration that places the viral genes (green) in a transcription parallel orientation relative to hTERT.