Fig. 5. Structural variants mediated by TE insertions.

a xTea called out several structural variants promoted by insertions of different types of TEs from the 20 long-read samples: 48 (31 Alu, 11 L1, and 6 SVA) deletions, 24 (18 Alu and 6 L1) duplications, and 6 (5 Alu and 1 L1) inversions. In addition, xTea called out 12 LTR recombination-caused dimorphic HERV events. b Compared to gnomAD-SV, more than 15, 40, and 50% of the TE-mediated deletions, duplications and inversions are novel. Each of these complex SVs are only called as one type of simple events, although the breakpoint positions are the or close to each other. c 6 HERV-K, 4 HERV-H, 1 HERV-L, and 1 HERV-W dimorphic HERV events are called out. Compared to a previously reported call set, 50% of the HERV events are novel. d Internal deletions occur in some dimorphic HERV insertions. Boxplot of each site shows the length of the HERV copy among different samples. While some copies are of full length (~7200 bp), some copies are only ~4000 bp although the front and tail parts exist. For the boxplots, the box demarcations represent the 25, 50, and 75th percentiles, and the whiskers extend from the box to the largest and smallest data points at most 1.5 times the interquartile range away from the median.