Fig. 4

IGV screenshots for Illumina short-read alignments spanning a structural variant (ASIP-SV1) associated with DHC in Nellore cattle. a Presents an overview of the 1155 bp deletion at CHR13:63,599,803–63,600,957. Carriers presented read pairs with RR (cyan) and LL (blue) orientation flanking the deletion. b Shows a close inspection of RR and LL paired-end reads at the chromosome 13 position 13:63,283,374, revealing chimeric and soft- and hard-clipped reads. Simulations presented in c and d show that these alignments are consistent with the ~ 1-kb deletion being an anchoring point for the insertion of a reverse complement of the CHR13:63,283,374–63,283,523 sequence, which shares high similarity with the Bov-tA SINE. The wild type and mutant alleles were determined based on comparative genomics analyses presented in Additional file 5