Table 1 Quality control criteria and number of SNPs discarded in each population
From: Linkage disequilibrium in crossbred and pure line chickens
Quality control | Population 1 | |||||
|---|---|---|---|---|---|---|
All | B | C | D | fBCD | pBCD | |
Chromosomes not included | 4522 | |||||
Mendelian inconsistency | 1456 | |||||
SNPs not called2 | 706 | 978 | 978 | 823 | 839 | |
Monomorphic SNPs | 7907 | 9888 | 7768 | 3467 | 3582 | |
SNPs with a call rate < 0.9 | 550 | 154 | 230 | 510 | 448 | |
SNPs with a MAF < 0.05 | 4914 | 4096 | 4300 | 3205 | 3149 | |
HWE (p value < 0.001) | 121 | 163 | 194 | NT3 | NT3 | |
SNPs in use | 37460 | 36379 | 38188 | 43653 | 43640 | |
Common SNPs | 26350 | |||||