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Table 2 GWAS Replication Testing

From: Whole genome sequencing identified a 16 kilobase deletion on ECA13 associated with distichiasis in Friesian horses

Name

Original sample p-value

Replication sample p-value

Combined p-value

ECA13:g.340918C > T

2.26 × 10−8

1.61 × 10−5

5.71 × 10− 14

ECA13:g.343850A > C

2.26 × 10− 8

1.61 × 10− 5

5.71 × 10− 14

ECA13:g.330462G > A

2.73 × 10− 7

2.34 × 10− 5

8.58 × 10− 13

ECA13:g.425443C > T

4.16 × 10− 7

1.45 × 10− 4

1.64 × 10− 11

ECA13:g.230097C > T

2.27 × 10− 7

2.30 × 10− 4

2.31 × 10− 11

ECA13:g.134040A > G

8.15 × 10− 8

3.07 × 10− 4

2.31 × 10− 11

ECA13:g.142416C > T

2.27 × 10− 7

3.07 × 10− 4

2.73 × 10− 11

ECA13:g.153435C > T

2.27 × 10− 7

3.07 × 10− 4

2.73 × 10− 11

ECA13:g.195278 T > C

2.27 × 10− 7

3.07 × 10− 4

2.73 × 10− 11

ECA13:g.198581G > C

2.27 × 10− 7

3.07 × 10− 4

2.73 × 10− 11

ECA13:g.200759 T > C

2.27 × 10− 7

3.07 × 10− 4

2.73 × 10− 11

ECA13:g.201534G > A

2.27 × 10− 7

3.07 × 10− 4

2.73 × 10− 11

ECA13:g.206996G > A

2.27 × 10− 7

4.06 × 10− 4

3.75 × 10− 11

ECA13:g.121325G > A

2.73 × 10− 7

1.07 × 10− 3

1.12 × 10− 11

ECA13:g.122064G > A

2.73 × 10− 7

1.07 × 10− 3

1.12 × 10− 11

ECA13:g.122243C > T

2.73 × 10− 7

1.07 × 10− 3

1.12 × 10− 11

ECA13:g.316346C > T

2.73 × 10− 7

1.07 × 10− 3

1.12 × 10− 11

ECA13:g.13611A > G

7.73 × 10− 7

1.10 × 10− 3

3.94 × 10− 10

ECA13:g.42897A > G

2.73 × 10− 7

1.10 × 10− 3

1.45 × 10− 10

ECA13:g.32112G > T

8.48 × 10− 7

1.39 × 10− 3

1.36 × 10− 9

ECA13:g.384663 T > C

5.94 × 10− 6

2.00 × 10− 3

5.77 × 10− 9

ECA13:g.15928A > G

8.15 × 10− 8

0.0288

2.04 × 10− 9

ECA5:g.39962594G > A

4.57 × 10− 6

0.404

4.65 × 10− 9

ECA5:g.39863319A > Ga

4.57 × 10− 6

0.478

1.28 × 10− 5

ECA12:g.3271275C > A

9.10 × 10− 6

0.716

6.75 × 10− 4

ECA12:g.3270900 T > C

1.57 × 10− 5

1

4.65 × 10− 4

ECA13:g.186975G > Ab

1

1

1

ECA13:g.189306C > Tb

1

1

1

ECA13:g.190216 T > Cb

1

1

1

  1. a This SNP was assessed through a PCR-RFLP analysis
  2. bAs these SNPs fall within the 16 kb deletion, they only yielded results in one case (see Fig. 5)