Additional data

Additional data for manuscript Nanopore sequencing reveals hidden landscape of short L1 transductions in colorectal cancer1) Methylation of source L1HS from nanopore sequenced colorectal cancer, normal colon, uterine leiomyoma and uterus samples. Coordinates are lifted to T2T and contain 100 bp of the internal and flanking sequence from 5' of the elements. Regarding phasing: allels 1 and 2 are randomly assigned and cannot be compared between samples. * means both allelels and N that no phasing was able to be performed.2) Sequences of detected somatic L1 insertions (including orphan transductions). We masked most of the flanking sequences to protect participant identity. However, we retained 50 bp of flanking sequence on both sides of each insertion to allow for contextual evaluation. We masked rather than removed the remaining flanking sequence to preserve the integrity of the annotation coordinates in file 3)3) Annotation of sequences in file 2. Description from Nummi et al. (2025). Structural features of somatic and germline retrotransposition events in humans. Mobile DNA, 16(1), 20.A region of the polished sequence is annotated as target if it maps to the reference genome within 3000 bp from the insertion breakpoint called by Sniffles. Insertion refers to sequences longer than 20 bp not recognized as target. Non-target area annotation refers to sequences mapping to the reference genome, but not in the target area. If the mapping to the reference genome results in multiple non-target areas near each other, the areas within 500 bp of each other are merged together. Transposons contain the sequence mapping to the consensus transposon sequence. PolyA and polyT are annotated if a stretch of A or T bases is detected by using sweep line technique (+1 for match, -3 for mismatch and 5 as the limit). Target site duplication or deletion is annotated when there is an overlap or a gap between target sequences on both sides of the insertion of size 5-25 bp. Endonuclease cut site is annotated when sequence within 10bp of the insertion breakpoint maps to any of the following motifs with the insertion breakpoint where the dash line is marked (TTTT/A, TTTT/G, TTTC/A).