Fig. 3

Characterization and genome coverage analysis of the 13,420-bp tandem duplication in the major associated region in JT goats and three European breeds with Swiss markings. a The visualization of several soft-clipped reads from WGS data reveals the 13,420-bp tandem duplication (CHI13:63,129,198-63,142,617 bp) in JT goats with non-classic Swiss markings using IGV. b PCR amplification and Sanger sequencing validated the presence of the duplication. c Genomic coverage at the duplication site in different phenotype groups of 24 JT goats (seven solid black goats vs. 17 goats with non-classic Swiss markings; adjusted for the genome-wide average coverage depth and calculated in 20-bp sliding windows). The smooth lines obtained with LOESS regressions are added to describe the trends of relative genome coverage depth along the genomic positions within each phenotype group. The same plots are shown for 5 BAL (d), 24 BST (e), and 24 TOG goats (f), respectively