Fig. 2

Strategy for detecting insertionally polymorphic ERV variants. a ERV allelic presence. Upper: full-length provirus; Mid: solo LTR recombinant; Lower, unoccupied (pre-integration) site. b Strategy for detection of reference ERV deletions. Illumina read pairs were mapped to the CanFam3.1 reference, deletion-supporting read pairs and split reads identified using the program Delly [37], and candidate calls then intersected with RepeatMasker outputs considering ‘CFERVF1’ repeats. Deletion calls within a size range corresponding to a solo LTR or provirus were selected for further analysis. c Strategy for detection of non-reference ERV insertions. ERV insertion-supporting anchored read pairs were identified from merged Illumina data mapped to the CanFam3.1 reference using the RetroSeq program [90]. Insertion-supporting read pairs and intersecting split reads were assembled, assemblies for which ‘CfERVF1’ sequence was present were identified by RepeatMasker analysis, and the assembled contigs then re-mapped to the dog CanFam3.1 reference for precise breakpoint identification