Fig. 2.

This figure illustrates the orientation of the chimera reads when they map on the human genome. For all examples, we orient the human-virus integration fragments such that the human reference is in +ve strain. a–c illustrate cases where human is on the 5’ side of virus. In such cases, for each read R _i aligned on the human genome, we have either the whole read R _i or its prefix aligns on the +ve strand of the human genome or only the prefix of R _i aligns on the -ve strand of the human genome. d–f illustrate cases where human is on the 3’ side of virus. In such cases, for every read R _i aligned on the human, we have either R _i or its suffix aligns on the -ve strain of the human genome or only the suffix of R _i aligns on the +ve strain of the human genome