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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

  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