Frequency of proviral insertion in genes and relative orientation of the provirus. (A) The proportion of proviruses inserted inside a RefSeq gene increased with UIS abundance (asterisks below the open black triangle; χ² test for trend). In low-abundance UISs, the proportion of proviruses inserted inside a gene was smaller than in UISs identified in vitro (vertical asterisks to the right of “vs in vitro”; χ² test). (B) When the provirus was inserted inside a RefSeq gene, it was integrated more frequently in the same orientation as the host gene in UISs identified in vivo; in contrast, the orientation of UISs identified in vitro was random (vertical asterisks to the right of “vs in vitro”; χ² test). Increasing UIS abundance was associated with an increased percentage of proviruses oriented in the same transcriptional sense as the host gene (asterisks below the ▵; χ² test for trend). Sample size: In vitro, n = 2135; AC < 0.1, n = 4544; AC 0.1 to 1, n = 8649; AC 1 to 10, n = 727; HAM-TSP < 0.1, n = 26 200; HAM-TSP 0.1 to 1, n = 36 377; HAM-TSP 1 to 10, n = 2931; HAM-TSP > 10, n = 39; ATLL 0.1 to 1, n = 9827; ATLL 1 to 10, n = 1659; ATLL > 10, n = 69; ATLL Major UIS, n = 19. ***P < .001. **P < .01. *P < .05. NS indicates not significant (P > .05).