Fig. 2

Identification and characterization of HERV-K (HML-2) loci in the human genome using PTESHK. “P”, “W” and “Y” indicate the three different individuals, each with three replicates (marked as “1”, “2”, and “3”). a Venn diagram exhibiting all the HERV-K (HML-2) detected with at least one single read mapped in this study. Combining the 1063 reference loci and 35 novel loci detected in this study, there were in total 1098 loci. PTESHK detected 943 reference loci and 35 novel loci. In each individual, over 900 loci could be detected in at least one repeat (957 of “P”, 951 of “W”, and 958 of “Y”). b Linear graph, exhibiting the number of detected HERV-K (HML-2) loci with different numbers of raw reads extracted, shows a similar variation trend for all samples. With 15 million raw reads, PTESHK was able to detect about 800 loci in every sample. c Genome-wide distribution of HERV-K (HML-2) loci. There were 943 detected reference loci, 120 undetected reference loci, and 35 novel loci. The detected reference loci were subdivided into near gene loci, polymorphic integrated loci, and polymorphic integrated near gene loci. Novel loci could be divided into novel reference loci and novel non-reference loci. Different groups are highlighted with different symbols in the figure. The distribution of these HERV-K (HML-2) loci shows that HERV-K (HML-2), including the 35 newly detected loci, tends to be located in gene rich regions (some highlighted by red arrows)