Fig. 1

Sample output from BreakAlign showing an illustrative HERV-K integration. The top line is the section of the host genome spanning the integration site. Numbered sequences below show individual NGS reads aligned to the host genome with viral DNA in lower case, red and underlined (viral sequences on the left are the 3′ end of the 3′ LTR; viral sequences on the right are the 5′ end of the 5′ LTR). Reads containing insertion/deletions (indels) are indicated, with insertions and substitutions shown in lower case and deletions shown as hyphens. The intervening 'TGGT' motif is the TSD—see Marchi et al. [9] for a detailed explanation of how the TSD is formed and the adjacent HERV-K LTR sequences in both forward and reverse orientation integrations. Note, in this integration there is a known A to G substitution in the upstream TSD [7, 8] which leads to the characteristic six nucleotide HERV-K TSD—in this case TGGTAA—appearing to be shortened to only four nucleotides. Image shown is the output HTML file, and a text version without colours or underlining is also output