Manhattan plot. Grand linear view applied to a Manhattan plot as part of a genome-wide association study in Angus cattle. The y axis shows genetic variance, calculated by sliding windows of five consecutive SNPs for the infectious bovine keratoconjunctivitis (IBK; a type of pinkeye) score. The x axis is the genomic coordinates with all the chromosomes side-by-side. The horizontal striping of color helps to indicate the end of one chromosome and beginning of another. The plot is faceted by three different analysis methods. There is one extreme variance in the middle facet, in the region of chromosome 23. There are also a few large values in other regions. According to the results from the paper, three of these regions, 2, 13, and 23 are found to be potentially indicative of a quantitative trait locus associated with IBK.
Yin et al. Genome Biology 2012 13:R77 doi:10.1186/gb-2012-13-8-r77