Table 2 Number of single nucleotide polymorphisms (SNPs) before and after the quality control for each of the scenarios evaluated
Dataset | Number of SNPs (before quality control) | Number of SNPs after the quality control and prior to LD pruning | Number of SNPs after LD pruning |
|---|---|---|---|
SNPs from the GGP-50 K SNP chip array | 50,697 | 30,872 (S1) | 9,210 (S5) |
SNPs from the RNA-seq data of the skeletal muscle | 2,591,269 | 74,812 (S2) | 18,933 (S6) |
SNPs from the GGP-50 K SNP chip array plus the SNPs from the RNA-seq data of the skeletal muscle | 2,701,417 | 104,699 (S3) | 30,037 (S7) |
Percentage of SNPs from the RNA-seq or GGP-50 K SNP chip array, respectively | 71% | 29% | 64% | 36% | |
SNPs from the GGP-50 K SNP chip array plus the SNPs from the RNA-seq data of the skeletal muscle, liver, and brain tissues | 6,675,049 | 135,996 (S4) | 105,870 (S8) |
Percentage of SNPs from the RNA-seq or GGP-50 K SNP chip array, respectively | 78% | 22% | 89% | 11% | |