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Table 5 Details and allele frequencies of SNPs in the nine French cattle breeds, and genotypes in the three other samples

From: Gene-based single nucleotide polymorphism discovery in bovine muscle using next-generation transcriptomic sequencing

SNP

SNP ID1

Chromosome

Position2

Gene

Alleles

Frequency (allele 1)

Genotype

     

1/2

 

AUB

BLA

CHA

HOL

LIM

MAN

MON

NOR

SAL

WAT

BIS

KOU

1

rs43299525

2

29,938,364

ENSBTAT00000038441

T/C

 

0.18

0

0.23

0.28

0.23

0.17

0.45

0.25

0.41

T/T

T/T

T/T

2

rs41255286

3

90,246,130

ENSBTAT00000015460

C/T

 

0.23

0.14

0.18

0.36

0.27

0.42

0.45

0.67

0.14

G/G

G/G

G/G

3

rs43360668

3

100,666,640

ENSBTAT00000003878

T/C

 

0.09

1

1

0.04

0.14

0.17

0.18

0.25

0.04

G/G

G/G

G/G

4

rs43414903

4

115,404,252

ENSBTAT00000028347

C/T

 

0.18

0.09

0.27

0.09

0.14

0.08

0

0.25

0.09

C/C

C/C

C/C

5

rs43484023

6

109,946,655

ENSBTAT00000060963

G/C

 

0.18

0.32

0.36

0.14

0.45

0.25

0.68

0.17

0.09

G/C

C/C

C/C

6

rs42722878

8

101,639,394

ENSBTAG00000020243

T/C

 

0.18

0.04

0.36

0.04

0.59

0.25

0.41

0.17

0.04

T/C

C/C

C/C

7

rs42722887

8

101,642,585

ENSBTAG00000020244

G/A

 

0.27

0.09

0.36

0.04

0.59

0.25

0.41

0.17

0.04

G/A

G/G

G/G

8

rs42722900

8

101,645,192

ENSBTAG00000020245

C/T

 

0.04

0.04

0.14

0

0.41

0.25

0.27

0.08

0.04

C/C

C/C

C/C

9

rs42722901

8

101,645,255

ENSBTAG00000020246

C/T

 

0.24

0.09

0.35

0.04

0.59

0.25

0.41

0.17

0.04

C/T

C/C

C/C

10

rs42306198

8

111,749,876

ENSBTAT00000008586

G/A

 

0

0.04

0.09

0.04

0.18

0

0

0.08

0.04

G/G

G/G

 

11

rs17870317

9

34,687,597

ENSBTAT00000038044

T/G

 

0.33

0.32

0.45

0.45

0.41

0.50

0.32

0.67

0.32

T/T

T/T

T/T

12

rs17870361

9

61,258,934

ENSBTAT00000015037

C/T

 

0.24

0.14

0.04

0.73

0.14

0.17

0.32

0

0.04

C/C

C/C

 

13

rs43626955

10

51,842,959

ENSBTAT00000007206

A/C

 

0.36

0.41

0.23

0.14

0.82

0.92

0.54

0.17

0.68

A/C

C/C

C/C

14

rs43626956

10

51,843,008

ENSBTAT00000007207

A/G

 

0.36

0.41

0.23

0.14

0.82

0.92

0.54

0.25

0.68

A/G

G/G

A/G

15

rs43626957

10

51,843,101

ENSBTAT00000007208

A/G

 

0.59

0.50

0.32

0.27

0.95

1

0.54

0.25

0.77

A/G

G/G

 

16

rs42748012

10

90,111,114

ENSBTAT00000016066

C/T

 

0.64

0.50

0.68

0.77

0.50

0.33

0.86

0.33

0.68

T/T

C/C

C/C

17

rs42738663

10

90,126,463

ENSBTAT00000016067

A/G

 

0.36

0.50

0.32

0.23

0.50

0.67

0.14

0.67

0.32

A/A

G/G

G/G

18

rs42311164

11

47,748,651

ENSBTAT00000005725

G/C

 

0.27

0.36

0.23

0.14

0.32

0.67

0.27

0.42

0.50

G/G

C/C

C/C

19

rs42613762

13

51,391,698

ENSBTAT00000025981

G/A

 

0.73

0.95

0.70

0.23

0.68

0.92

0.54

0.58

0.86

 

G/A

G/A

20

rs41255356

13

67,838,559

ENSBTAT00000018669

T/C

 

0.36

0.32

0.73

0.23

0.54

0.08

0.27

0.83

0

T/T

T/C

 

21

rs41774805

15

57,309,934

ENSBTAT00000006638

G/A

 

0.27

0.45

0.27

0.27

0.64

0.33

0.36

0.50

0.50

G/G

G/G

G/G

22

rs41720009

17

68,389,438

ENSBTAT00000053508

A/G

 

0.41

0.41

0.54

0.27

0.23

0.08

0.23

0.25

0.23

G/G

A/A

 

23

rs41905209

19

25,255,424

ENSBTAT00000061398

C/T

 

0.14

0

0.14

0.59

0.09

0.17

0

0.08

0

C/C

C/C

C/C

24

rs42803062

19

28,474,511

ENSBTAT00000044661

C/T

 

0.36

0.68

0.59

0.23

0.59

0.08

0.73

0.58

0.54

C/C

  

25

rs41969933

21

19,283,173

ENSBTAT00000014089

C/T

 

0.77

0.68

0.86

0.36

0.77

0.67

0.82

0.58

0.86

C/C

C/C

T/T

26

rs42013154

22

48,725,986

ENSBTAT00000019339

G/T

 

0.27

0.04

0.14

0.09

0.36

0.25

0.23

0

0.14

G/G

G/G

 

27

rs42016156

22

49,203,698

ENSBTAT00000045850

C/T

 

0.56

0.50

0.65

0.32

0.82

1

0.86

0.58

0.68

C/C

C/C

 

28

rs42015934

22

51,561,550

ENSBTAT00000007217

C/T

 

0.23

0.04

0.14

0.04

0.04

0.17

0.18

0.33

0.09

C/C

C/C

C/C

29

rs42451508

25

21,535,844

ENSBTAT00000008398

G/A

 

0.14

0.09

0.27

0.04

0.31

0.83

0.41

0.33

0.27

G/G

G/G

G/G

30

rs42174698

29

26,367,840

ENSBTAG00000001660

T/C

 

0.36

0.50

0.91

0.54

0

0.50

0.04

0

0.41

 

C/C

C/C

31

rs17871172

29

26,368,230

ENSBTAG00000001661

C/T

 

0

0.04

0

0

0.04

0

0

0.08

0

C/T

C/C

C/C

32

rs42188070

29

45,033,799

ENSBTAT00000023514

C/T

 

0.14

0.09

0.54

0.14

0.18

0.25

0.18

0.25

0.27

C/C

C/C

C/C

33

rs29024659

X

81,605,181

ENSBTAG00000002585

C/T

           

C/C

C/C

34

rs55617351

X

141,005,664

ENSBTAT00000029896

G/A

          

G/G

A/A

A/A

35

rs55617145

X

141,005,870

ENSBTAT00000029897

C/A

          

C/C

A/A

C/C

36

rs55617174

X

141,005,964

ENSBTAT00000029898

A/T

          

T/T

T/T

 

Mean MAF (autosomes)

      

0.25

0.22

0.25

0.19

0.27

0.20

0.26

0.24

0.20

   
  1. 1 rs number from dbSNP.
  2. 2 Position on the UMD3.1 cattle genome assembly.
  3. AUB, Aubrac, BLA, Blonde d’Aquitaine, CHA, Charolais, HOL, Holstein, LIM, Limousin, MAN, Maine Anjou, MON, Montbéliarde, NOR, Normande, SAL, Salers, WAT, Watusi, BIS, European bison, KOU, Greater Koudou.