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Table 3 Summary of panels designed from real data

From: mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

LD (r2 threshold) < 0.2 < 0.4 < 0.6 < 0.8
Number of different type of markers
Number of Markers 2067 3157 4278 5754
Number of STRs 47 64 83 115
Number of SNPs 2020 3093 4195 5639
Summary of r2
Min 0.000 0.000 0.000 0.000
1st Qu 0.000 0.002 0.003 0.006
Median 0.000 0.009 0.018 0.037
Mean 0.020 0.042 0.074 0.124
3rd Qu 0.020 0.042 0.084 0.159
Max 0.990 0.991 0.991 0.991
  1. This is the summary for panels designed out of real data. On the chromosome 22, 4 mixed panels have been generated from the SNP-STR reference haplotype panel of Gymrek’s lab [20]. The pruning was completed on plink/1.90 with threshold of pairwise correlation 0.2, 0.4, 0.6 and 0.8, with the code “--indep-pairwise”. The second part of Table 3 presents the summary of \(r^{2}\) values for each panel. The lists of \(r^{2}\) were calculated and exported with the code “ –r2 –ld-window-r2 0”.