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Figure 1 | BMC Genomics

Figure 1

From: Detecting autozygosity through runs of homozygosity: A comparison of three autozygosity detection algorithms

Figure 1

Observed LD within 50 kb using 5, 000 pairwise SNP comparisons. LD patterns are measured by sampling the r2 of 5, 000 SNP pairs up to 50 kb away. The lines represent Lowess curves that track changes in mean r2 as physical distance increases between SNPs. Empirical r2 values are in blue, and simulated r2 values are in green. Because MAF strongly influences the r2 between SNPs, a floor effect often occurs after short distances due to SNP pairs with large MAF differences, making it difficult to compare LD patterns between datasets. Therefore, we included both closely matched MAF SNP pairs and SNP pairs with minimum MAF > .05. Darker hues represent matched MAF pairs and lighter hues represent SNP pairs with minimum MAF > .05.

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