Chimeric cases. (A) There are four possible cases of chimeric reads. Arrows point from 5' to 3' on the reference strand of the host. Blue arrows represent host genome and red is virus. The two columns indicate organism order cases, which as illustrated is always determined by comparison to the host reference strand. There are two possible strand orientations which are determined by the orientation of the host and virus reference strand to each other. (B) Three ambiguous cases for chimeric reads are possible. BLASTN finds a single chimeric read and thus there is potential for overlap or void positions in the alignment. Mapped chimeras are two reads with an unknown nucleotide distance between them, as such their ambiguous region is defined as the closest two nucleotides mapped from virus and host. (C) Reference parallel and anti-parallel integrations are reported if they are within the user defined host deletion size.