Figure 6
Variant curation and transcription factor binding site analysis.
MGST1 gene expression Manhattan plot (6A) using a re-imputed 2 Mbp interval of sequence variants following reference assembly refinement and discovery of additional variants at the chromosome 5 milk composition locus. Gap variants are indicated by diamonds and coloured according to their linkage disequilibrium with the lead SNP (g.93945738C > T). The 8.2 kbp deletion variant is indicated, with its association representing haplotype-based results. Representative genome sequence alignments showing genotype classes of the biallelic deletion are also shown (6B). Figure 6C shows the evolutionary conservation of sequence flanking the g.93948718G > C and g.93949810G > A SNPs with predicted impacts on putative transcription factor binding sites. Bovine sequences within these alignments represent the minus strand and thus are reverse orientation to that depicted in Fig. 6A.
