Table 2 Description of AZI and KHU buffalo breeds genotypes available for analysis before and after filtering for cryptic quality control
From: A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds
| Â | AZI | KHU |
|---|---|---|
Number of individuals before filtration | 260 | 123 |
Number of SNPs before filtration | 73,935 | 73,935 |
SNPs with unknown position on genome | 19 | 19 |
SNPs with minor allele frequency (MAF) | 8830 | 8830 |
SNPs out of HWE (P-value <10e-6) | 198 | 124 |
Total genotyping rate in remaining individuals | 0.9974 | 0.9954 |
SNPs with Call rate (CRSNP) < 0.95% | 0 | 0 |
Individuals with call rate (CRIND) < 0.95% | 2 | 2 |
Replicate individuals | 2 | 3 |
Removed individuals by PCA output | 3 | 0 |
Removed individuals with IBS > 0.8 | 0 | 0 |
Number of individuals before filtration | 253 | 118 |
Number of SNPs after QC | 64,866 | 64,866 |