Fig. 2
a LD Manhattan plot showing a zoom to the candidate region on CFA11. The plot indicates r2 values of each SNP in respect to the new GWA analysis top SNP. The fine-mapped region of association is highlighted with a grey shadow. b UCSC genome browser-based panel showing genomic location (bp), highly linked SNPs (r2 > 0.8) in the fine-mapped region colored according to their r2 (darker colors indicating higher LD) in respect to the fine-mapping top SNP, location of genomic gaps, and location of RefSeq protein coding genes. c Plot showing the –log10(p-value) of the difference in coverage between the LC case and control groups in the fine-mapped region. The green boxes represent the three CNVs (Del1, Del2 and Del3) predicted by CNVnator in the HC individuals. d Heatmaps showing fold coverage differences (M-value) between the LC case and control groups for the windows overlapping with Del1, Del2 and Del3, +/− 10 Kbs. The potential CNVs in the upstream region of Del3 were also predicted by CNVnator, but were discarded either because of overlap with a gap or repetitive sequences