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Table 1 Number of animals and amount of SNPs excluded during the quality control procedure of the genotype data

From: Characterization of linkage disequilibrium, consistency of gametic phase and admixture in Australian and Canadian goats

Breed

 

Excluded SNPs*

Remaining SNPs

 

N

MAF < 0.05

SNP CR < 0.90

HWE

Het.

Total3

 

AL1

403

3,828

2,358

39

1

6,820

45,268

SA1

318

4,155

2,358

45

2

7,140

44,946

  

MAF < 0.15

SNP CR < 0.90

HWE

Het.

Total3

 

LN1

81

10,321

2,358

54

156

13,436

38,650

NU1

54

16,013

2,379

21

242

19,233

32,853

TO1

53

15,388

2,362

63

870

19,233

32,863

BO1

67

13,282

2,374

17

185

16,438

35,648

BO2

61

11,562

55

81

471

15,029

37,057

CA2

48

9,508

147

33

689

13,272

38,814

RL2

66

4,695

57

52

274

7,980

44,106

  1. 1Canada, 2Australia, 3It was excluded 2,958 SNPs without chromosome number and/or position information or SNPs located in the sexual chromosomes. AL: Alpine, SA: Saanen, LN: LaMancha, NU: Nubian, TO: Toggenburg, BO: Boer, CA: Cashmere, RL: Rangeland; *some SNPs were excluded due to more than one criterion,, MAF = minor allele frequency; CR = call rate; HWE = χ 2 test for Hardy-Weinberg equilibrium (p-value < 10−6). Het: excess of heterozigosity (>0.15)