Where a lentivirus integrated, read from the junction between the vector’s LTR and the host genome. Reads that run out of the LTR carry the genome immediately outside it, and that stretch is what identifies the site.
The mates are not joined. An integration site is carried by whichever read crossed the junction, so R1 and R2 are two independent streams of reads over the same analysis. Nothing is uploaded — the files are read and analysed in this tab.
Which genome the junctions are placed in once they are found. Every position and gene in the result is relative to it. The reads themselves are never uploaded — only the short sequences either side of the junction, and only to be turned into a chromosome and a gene.
Asking which genomes this server has…
Both LTRs of a provirus have the same sequence, so one reference describes both junctions.
Found on either strand. The cleavage site is located from where the spacer sits in the LTR.
Which side of the cleavage site the host genome lies on. Auto picks the end the cut is closer to.
Bases of host genome taken past the indicator sequence. That stretch is what identifies the site, so a short one matches more places and a long one needs reads that reach that far — reads too short for it are counted and reported with the result.
Distinct junctions seen this many times or fewer are dropped.