Fig. 6

Characterization of MCPyV integration sites. a Location of integration events in the human genome labeled and colored by patient. b Coverage of reads corresponding to predicted overlapping integration sites in chromosome 1. Direction of virus-to-host fusion is shown by black arrows. c–e Representative assembly graphs for different types of viral integrations. Human DNA is a blue gradient and viral DNA is a red gradient representing different genomic segments. Human chromosome positions at the virus junctions are shown. Detailed assembly graphs for all virus-positive cases are in Additional file 3: Fig. S6. c Representative single linear assembly graph for integrated MCPyV from case MCC001 on chromosome 3. d Representative assembly graph of partially duplicated MCPyV genome integrated into the tumor genome of MCC025 on chromosome 1. Path for linearization of assembly graph shown by the dark gray line. e Representative assembly graph of MCPyV genome integrated into chromosome 7 of MCC071 supporting a circular DNA intermediate diagrammed on the right. f Barplot showing the frequency of microhomology lengths between 2 and 7 bp. Expected values are in black and observed are in gray. Asterisks representing p values from Fisher’s exact test are represented above the bars (* < 0.05, ** < 0.01). g Diagram of representative integration sites with viral sequence highlighted in yellow and host sequence in blue. Matching bases between host and virus are in red. h Barplot showing the frequency of repetitive elements within 2 kb of integration sites. Expected values are in black and observed are in gray. P values from Fisher’s exact test are represented above the bars