Fig. 5

HMGA2-CNV. a IGV screenshot of the HMGA2-CNVR locus (in blue) and the visualization of the alignment of paired-end reads. Sample1_No_CNV shows the aligned reads of a composite animal presenting no CNV; Sample2_CNV shows the aligned reads of a Brahman animal presenting the duplication event. Paired-end reads in green imply duplication with respect to the reference genome. These read pairs are oriented towards the outer sides of the predicted insert. Red colour reads indicate paired end reads with an insert size larger than expected (possible deletion). b Contingency table of SNP rs447470311 (chr5:47,726,121) versus HMGA2-CNVR (chr5:48,074,233–48,080,443 (~ 6.2 kb) genotype