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Table 1 SNPs identified as associated with the phenotypic trait by different methods and approaches.

From: Data modeling as a main source of discrepancies in single and multiple marker association methods

 

SNP (P-value)

SNP (HQ-score)

SMA Additive effect (SE)3

Chromosome

SMA raw1

SMA corrected (QxPak)

Blossoc raw1

Blossoc corrected

raw

corrected

1

196

(52.2)2

196

(33.0)

200

(215.7)

200

(75.4)

0.74

(0.05)

0.71

(0.06)

 

323

(16.9)*

331

(10.4)

-

-

0.40

(0.05)

-0.69

(0.10)

 

415

(23.5)

402

(17.6)

416

(98.1)

402

(52.2)

0.46

(0.05)

-0.78

(0.09)

 

778

(14.9)

778

(11.5)

778

(51.7)*

778

(20.2)

0.40

(0.05)

0.40

(0.06)

2

1271

(15.8)

1270

(14.4)

1268

(94.6)

1267

(31.1)

0.36

(0.04)

0.43

(0.05)

 

1483

(28.3)

1483

(15.4)

1483

(113.2)

1487

(31.2)

-0.50

(0.04)

-0.45

(0.05)

3

2149

(17.2)

2133

(9.3)

2134

(65.8)

-

-0.39

(0.04)

0.35

(0.06)

 

-

-

2598

(37.9)*

2601

(17.6)

-

-

4

3048

(35.9)

3033

(27.4)

3032

(237.4)

3032

(104.4)

0.54

(0.04)

0.59

(0.05)

 

3765

(44.9)

3765

(23.4)

3765

(183)

3765

(47.5)

0.62

(0.04)

0.55

(0.05)

 

3953

(17.0)

-

3952

(103.2)

3952

(15.6)

0.37

(0.04)

-

5

4935

(23.7)

4935

(29.8)

4940

(94.8)

4935

(68.7)

-0.47

(0.05)

-0.63

(0.05)

Total # SNPs

33/15

10

49/19

10

  
  1. 1 – For analysis with raw data, only SNPs that coincide with those obtained with corrected data are listed in this table. A complete list of SNPs detected using raw data is in the Additional file 1.
  2. 2 – Between brackets are the significance level for methods: -log10 (p-value) for SMA and HQ score for Blossoc. Threshold for SMA is P < 10-8 and for Blossoc is HQ Score ≥ 15. The * shows SNPs that would not be selected using a bootstrap posterior probabilities (BPP) < 0.25 for SMA raw and an adjusted threshold for Blossoc raw <65, with a total of 15 and 19 selected SNPs for each method, respectively (Additional file 1).
  3. 3 – The direction of the additive effects is from genotype 11 to 22.