Fig. 2

Schematic of LINE-1 and read alignments. a Diagrams of example LINE-1 insertions types are shown: full length, 5′ truncated, 5′ truncated with inversion, and 5′ truncated with 3′ transduction. TIPseq is able to detect these types of insertions. The full length LINE-1 element includes 5′ and 3’ UTRs, including a 3′ polyA tail, all colored in light blue. The specific L1 primer binding site is shown as a black arrow in the 3’ UTR. The open reading frames (ORF1 and ORF2) are shown in two darker shades of blue. Flanking genomic DNA is shown as gray lines with target site duplications (TSDs) as black lines. The gold line represents a transduced region of gDNA. Arrows underneath each diagram illustrate the orientation of the sequence. b The types of reads that TIPseq generates are shown in the top of the diagram with a TranspoScope image capture below. Reads containing only LINE-1 sequence are colored blue. Junction reads which contain both L1 and unique genomic DNA and are colored orange. Uniquely mapped genomic DNA reads are shown in gray, purple, and green. Gray reads are genome reads in genome-genome pairs. Purple reads are genome mates in genome-L1 pairs. Green reads are genome reads with an unmapped or discordant pair. TranspoScope displays the read counts and positions for specific L1 insertions detected by TIPseq. The L1 insertion site is shown as a vertical blue line, and downstream restriction enzyme cut sites used in TIPseq are shown as gray triangles with vertical red lines