Fig. 4 | Scientific Reports

Fig. 4

From: Genetic distances and genome wide population structure analysis of a grain amaranth (Amaranthus hypochondriacus) diversity panel using genotyping by sequencing

Fig. 4

(a) Linkage Disequilibrium Plot. Markers were ordered on the x- and y-axes based on genomic location; hence, every cell of the heat map represents a single marker pair. (b) Linkage Disequilibrium (LD) decay plot across the genome. The x-axis represents the physical distance between SNP pairs in base pairs, while the y-axis shows the LD measure (r²). Each point represents a pair wise SNP comparison. The dark blue line indicates the LD decay threshold of r² = 0.1, which was used to estimate the average haplotype block size of 295,883 bp. The vertical (green) line signifies the average LD decay distance.

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