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Table 2 Windows explaining the largest percentages of tick resistance genetic variance in Hereford and Braford cattle breeds

From: Tag SNP selection for prediction of tick resistance in Brazilian Braford and Hereford cattle breeds using Bayesian methods

Obs

Window

Start SNP name

End SNP name

N SNP

%Var

Cum Var

chr_Mb

Top SNP name

ModelFreq

t.like

Stand_effect

1

1621

ARS-BFGL-BAC-27751

ARS-BFGL-NGS-115263

17

1.67

1.67

15_37

ARS-BFGL-NGS-5811

0.7574

1.393

1.4036

2

1319

ARS-BFGL-NGS-112243

ARS-BFGL-NGS-12954

17

1.19

2.86

11_101

ARS-BFGL-NGS-111179

0.6731

1.243

1.1350

3

1164

ARS-BFGL-NGS-1854

ARS-BFGL-NGS-24556

27

1.13

3.99

10_51

Hapmap58695-rs29019899

0.5048

1.076

0.8828

4

1553

ARS-BFGL-NGS-115527

ARS-BFGL-NGS-1112

15

0.84

4.83

14_54

BTB-00915241

0.3045

0.982

0.4614

5

710

BTB-01688071

ARS-BFGL-NGS-58275

23

0.78

5.6

6_49

BTB-02002785

0.3176

0.986

0.4781

6

1283

ARS-BFGL-NGS-44192

Hapmap60779-rs29022104

14

0.74

6.35

11_65

Hapmap60779-rs29022104

0.3697

1.005

0.6143

7

531

Hapmap57291-ss46526771

Hapmap22875-BTA-155031

14

0.74

7.09

4_113

Hapmap22875-BTA-155031

0.4834

1.06

0.8291

8

553

Hapmap36482-SCAFFOLD163485_1458

BTA-87049-no-rs

12

0.68

7.77

5_14

Hapmap52967-rs29017027

0.4047

1.022

0.6210

9

1974

ARS-BFGL-NGS-13160

BTB-00774670

20

0.64

8.4

20_17

Hapmap34041-BES1_Contig298_838

0.327

0.988

0.5321

10

1429

Hapmap48542-BTA-97857

ARS-BFGL-NGS-27497

11

0.54

8.95

13_14

Hapmap44228-BTA-34185

0.3342

0.99

0.4960

11

1488

ARS-BFGL-NGS-107401

ARS-BFGL-NGS-4602

18

0.53

9.48

13_73

Hapmap40517-BTA-33731

0.3514

0.997

0.5201

12

1709

Hapmap54735-ss46526095

Hapmap56619-rs29009970

16

0.52

10

16_40

ARS-BFGL-NGS-40365

0.2408

0.956

0.3808

13

214

Hapmap25908-BTA-160304

Hapmap60963-rs29015781

26

0.47

10.47

2_55

ARS-BFGL-NGS-111213

0.1665

0.937

0.2428

14

1159

ARS-BFGL-NGS-113665

ARS-BFGL-NGS-10383

21

0.46

10.93

10_46

ARS-BFGL-NGS-60054

0.2224

0.953

0.3154

15

944

Hapmap41647-BTA-81135

ARS-BFGL-NGS-111988

20

0.46

11.39

8_50

BTB-01398754

0.0986

0.902

0.1449

16

1495

ARS-BFGL-NGS-83969

Hapmap41120-BTA-99310

20

0.46

11.85

13_80

Hapmap41120-BTA-99310

0.1838

0.942

0.2532

17

293

ARS-BFGL-NGS-22691

ARS-BFGL-NGS-17681

22

0.43

12.28

2_134

ARS-BFGL-NGS-113378

0.2608

0.956

0.4564

18

179

ARS-BFGL-NGS-39206

BTB-01168392

21

0.41

12.69

2_20

BTB-00082871

0.2273

0.953

0.3302

19

1001

Hapmap25843-BTA-146186

ARS-BFGL-NGS-20859

18

0.37

13.07

8_107

Hapmap40677-BTA-121871

0.1692

0.936

0.2455

20

2440

BTB-00980670

Hapmap34915-BES7_Contig278_1082

17

0.32

13.39

28_20

BTB-01129090

0.1208

0.923

0.1530

21

2028

Hapmap44700-BTA-34998

ARS-BFGL-NGS-118166

15

0.32

13.71

20_71

ARS-BFGL-NGS-13702

0.2361

0.947

0.3888

22

163

Hapmap43083-BTA-86781

BTA-47785-no-rs

17

0.3

14.01

2_4

BTB-00077766

0.1948

0.944

0.2567

23

1132

ARS-BFGL-NGS-94247

ARS-BFGL-NGS-32828

24

0.28

14.29

10_18

ARS-BFGL-NGS-107048

0.2059

0.947

0.3001

24

147

Hapmap30204-BTA-124882

BTB-01761180

28

0.28

14.57

1_147

BTB-01301015

0.1687

0.934

0.2423

25

515

Hapmap25270-BTA-142450

ARS-BFGL-NGS-12738

11

0.28

14.85

4_97

Hapmap25270-BTA-142450

0.1796

0.931

0.2960

26

1239

Hapmap43962-BTA-86597

Hapmap42711-BTA-87541

24

0.26

15.11

11_21

BTB-00464454

0.142

0.926

0.2100

27

1238

ARS-BFGL-NGS-20053

BTB-00464777

19

0.26

15.37

11_20

BTA-104373-no-rsa

0.1533

0.922

0.2280

28

290

ARS-BFGL-NGS-54356

ARS-BFGL-NGS-77887

26

0.26

15.63

2_131

BTB-00117780

0.1469

0.931

0.1938

29

664

Hapmap30828-BTA-143720

Hapmap30881-BTA-159706

23

0.25

15.88

6_3

Hapmap30881-BTA-159706

0.171

0.937

0.2465

30

2515

Hapmap24672-BTA-140771

ARS-BFGL-NGS-29493

27

0.25

16.13

29_48

BTA-66199-no-rs

0.211

0.951

0.2818

31

329

ARS-BFGL-NGS-117560

Hapmap51025-BTA-67309

19

0.25

16.38

3_33

ARS-BFGL-NGS-119309

0.0962

0.91

0.1189

32

1758

ARS-BFGL-NGS-5880

BTA-122662-no-rs

23

0.25

16.63

17_7

ARS-BFGL-BAC-27352

0.1857

0.944

0.2496

33

2013

ARS-BFGL-NGS-55465

Hapmap51244-BTA-50863

19

0.24

16.87

20_56

Hapmap43377-BTA-85612

0.1385

0.927

0.1717

34

442

ARS-BFGL-NGS-113848

BTB-00169886

16

0.24

17.12

4_24

Hapmap45129-BTA-72713

0.1427

0.925

0.2042

35

1485

ARS-BFGL-NGS-118627

ARS-BFGL-BAC-15769

17

0.24

17.35

13_70

Hapmap57013-rs29019369

0.1502

0.934

0.1073

36

1656

ARS-BFGL-BAC-18252

Hapmap45825-BTA-25376

16

0.23

17.58

15_72

Hapmap45825-BTA-25376

0.1828

0.943

0.2411

37

261

Hapmap48190-BTA-114376

BTA-48503-no-rs

11

0.23

17.81

2_102

Hapmap36094-SCAFFOLD96944_22403

0.1323

0.928

0.1683

38

1190

ARS-BFGL-NGS-38839

Hapmap50492-BTA-86239

16

0.23

18.04

10_77

ARS-BFGL-NGS-111871

0.1883

0.945

0.2477

39

2294

ARS-BFGL-NGS-26313

ARS-BFGL-NGS-34801

17

0.23

18.26

25_15

ARS-BFGL-NGS-84660

0.1403

0.933

0.1543

40

2309

ARS-BFGL-BAC-3777

ARS-BFGL-BAC-47171

21

0.23

18.49

25_30

ARS-BFGL-BAC-37178

0.1584

0.911

0.3051

41

665

ARS-BFGL-NGS-56212

BTB-01468045

20

0.22

18.71

6_4

BTB-01280976

0.0959

0.922

0.1089

42

794

ARS-BFGL-NGS-93802

Hapmap57279-ss46526160

19

0.22

18.93

7_13

ARS-BFGL-NGS-111257

0.0898

0.91

0.1073

43

484

ARS-BFGL-NGS-26541

ARS-BFGL-NGS-44674

20

0.21

19.14

4_66

ARS-BFGL-NGS-36591

0.1501

0.932

0.2019

44

1976

BTB-00775794

Hapmap49633-BTA-50009

16

0.21

19.35

20_19

Hapmap28040-BTA-134983

0.1529

0.935

0.2100

45

1743

BTB-00661933

ARS-BFGL-NGS-99802

17

0.2

19.56

16_74

Hapmap48746-BTA-40116

0.1664

0.938

0.2172

46

282

ARS-BFGL-NGS-102874

ARS-BFGL-NGS-15468

22

0.2

19.76

2_123

ARS-BFGL-NGS-102874

0.1163

0.915

0.1622

47

2146

ARS-BFGL-NGS-118471

Hapmap38075-BTA-54630

18

0.2

19.96

22_45

BTB-00849206

0.1658

0.922

0.2876

48

364

BTA-68264-no-rs

Hapmap44273-BTA-68311

24

0.2

20.15

3_68

ARS-BFGL-NGS-33433

0.1601

0.912

0.2923

  1. Obs sequence number of the top 48 1-Mb non-overlapping windows, Window window coded number by GenSel according to physical map order, Start SNP name name of the first SNP flanking the window, End SNP name name of the last SNP flanking the window, N SNP Number of SNPs within the window, %Var percentage of genetic variance explained by the window, Cum Var cumulative percentage of genetic variance, chr_Mb BTA autosome and position of the window in Mb pairs, Top SNP name SNP name of the top SNP in the window (in terms of ModelFreq and or t.like statistics) and respective values of ModelFreq, t.like and standard effect (Stand_effect) of each top SNP
  2. aThis SNP was not included in the low-density panels proposed because it is in LD with BTB-00464454 and it has a low MAF
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Genetics Selection Evolution

ISSN: 1297-9686