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
|
- 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”.