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Table 1 Number of top 100 SNP effects from the least squares analysis without stratification correction that overlapped with the top 100 effects from EMMAX-IBS (E), GLS (G), and PCA (P) methods for stratification correction

From: Effect of sample stratification on dairy GWAS results

Traits

E

G

P

EG

EP

GP

EGP

MY

7

15

6

2

2

4

1

FY

4

2

0

1

0

0

0

PY

1

5

0

0

0

0

0

FPC

28

23

22

23

22

22

22

PPC

8

3

3

1

1

3

1

PL

6

10

1

3

0

1

0

SCS

6

7

0

0

0

0

0

DPR

7

8

2

3

2

2

2

SCE

8

3

2

0

2

0

0

DCE

3

3

0

1

0

0

0

SSB

8

6

6

2

6

2

2

DSB

6

11

2

0

0

0

0

NM

4

1

0

0

0

0

0

Total

96

97

44

36

35

34

28

STA

11

24

1

5

1

0

0

STR

5

12

0

1

0

0

0

BD

7

14

0

2

0

0

0

RW

12

31

2

6

1

1

1

DF

8

7

1

1

1

1

1

RA

19

22

6

10

4

6

4

FUA

6

13

1

1

1

0

0

RUH

9

13

4

2

2

0

0

UD

5

14

0

3

0

0

0

UC

13

10

3

2

3

0

0

FTP

17

16

5

6

4

2

2

RTP

12

13

3

2

3

0

0

TL

16

8

5

3

5

1

1

FA

6

15

4

4

1

2

1

RLS

2

2

6

2

1

1

1

RLR

5

18

3

4

0

1

0

FL

11

14

3

6

2

2

2

FS

10

21

4

0

2

0

0

Total

174

267

51

60

31

17

13

  1. E, EMMAX-IBS; G, GLS; P, PCA; MY, milk yield; FY, fat yield; PY, protein yield; FPC, fat percentage; PPC, protein percentage; PL, productive life; SCS, somatic cell score; DPR, daughter pregnancy rate; SCE, service-sire calving ease; DCE, daughter calving ease; SSB, service-sire stillbirth; DSB, daughter stillbirth; NM, net merit; STA, stature; STR, strength; BD, body depth; DF, dairy form; RA, rump angle; RW, rump width; FUA, fore udder attachment; RUH, rear udder height; UD, udder depth; UC, udder cleft; FTP, front teat placement; RTP, rear teat placement; TL, teat length; FA, foot angle; RLS, rear legs (side view); RLR, rear legs (rear view); FL, feet/legs score; FS, final score.