Skip to main content

Table 1 The final integrated mapping results using step-wise regression. The estimates of the allele substitution effect under the single additive QTL model are included for comparison.

From: A combined strategy for quantitative trait loci detection by genome-wide association

SNP1 SNP2 a logPb "1/2" genotypec "2/2" genotyped Accumulated Variance (%) Single QTL allelic effect (simulated)g
196 - 18.65 0.33 0.62 1.78 0.71 (0.62)
402 - 5.59 0.08 0.23 2.28 0.85 (0.56)
540e 3219 10.51 (7.75) -0.18 (-0.09) -0.30 (0.08) 3.53  
778 - 7.34 0.23 0.45 4.18 0.42 (0.37)
1257f 3689 9.15 (6.63) -0.56 (-0.24) 0.46 (-0.17) 5.56  
1270 - 7.60 0.23 0.44 6.23 0.50 (0.35)
1483 - 10.02 -0.14 -0.36 7.13 0.43 (0.37)
2133 - 5.89 0.10 0.31 7.65 0.39 (0.30)
3033 - 20.52 0.31 0.66 9.54 0.68 (0.61)
3765 - 11.91 0.25 0.48 10.62 0.56 (0.58)
4935 - 18.38 -0.33 -0.71 12.35 0.70 (0.75)
  1. a: SNP2 column has a value only for epistatic pairs.
  2. b: the-LOG10 transformed P value for single significant SNPs, or the epistatic pairs in the nested test order. The -LOG10 (P) value for epistasis tests are in brackets.
  3. c: estimate of the "1/2" genotype in contrast to the "1/1" genotype. The estimates of SNP2 are in brackets.
  4. d: estimate of the "2/2" genotype in contrast to the "1/1" genotype. The estimates of SNP2 are in brackets.
  5. e: estimates of the pair-wise interactions: 0.51, 0.23, 0.07 and 0.66 for "1/2 × 1/2", "2/2 × 1/2", "1/2 × 2/2" and "2/2 × 2/2", respectively.
  6. f: estimates of the pair-wise interactions: 0.57, -0.55, 0.53 and -0.47 for "1/2 × 1/2", "2/2 × 1/2", "1/2 × 2/2" and "2/2 × 2/2", respectively.
  7. g: Estimated allelic effect from the single SNP GRAMMAR model; the simulated value is taken from the nearest simulated QTL as provided by the organisers.