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Fig. 2 | BMC Genomics

Fig. 2

From: Repetitive DNA content in the maize genome is uncoupled from population stratification at SNP loci

Fig. 2

Repeat Cluster layouts and Chromosomal Distributions. Graph layouts and chromosomal distributions are displayed for clusters 0, 2, 4 and 17 (a–d respectively). Cluster layouts, in 2D space, are calculated using the Fruchterman-Reingold algorithm and are shown in the top of each panel. Reads deriving from Stiff-stalk (SS) and Non-stiff-stalk (NSS) inbreds are indicated by blue and red vertices respectively. Edges, indicated in gray, represent sequence similarity hits between reads (vertices). The cluster name, most common hit to RepBase and the repeat family to which each cluster belongs is indicated. The most abundant k-mers from each repeat cluster were mapped to the maize B73 RefGen_v3 genome sequence, and the resulting loess smoothed profiles for each chromosome are displayed in the lower portion of each panel. Gene density profiles are also shown in blue, overlaying the repeat profiles

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