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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.