Table 4 Outlier SNPs identified in the between-population component of association

From: Genetic heterogeneity underlying variation in a locally adaptive clinal trait in Pinus sylvestris revealed by a Bayesian multipopulation analysis

SNP name

All

North

Central

 

MaAF a

Outlier b

Regression c

MaAF a

Outlier b

Regression c

MaAF a

Outlier b

Regression c

   

P-value

Slope

  

P-value

Slope

  

P-value

Slope

FTL2_f1-356

0.95

95% (1)

0.14

−1.37

0.96

75% (3)

0.17

−1.07

0.94

   
      

50% (1)

      
      

95% (2)

      

UMN_2763_01-83

0.94

95% (2)

0.23

−1.76

0.95

   

0.94

   

PhyN-2120

0.94

95% (3)

0.06

−2.12

0.97

75% (2)

0.44

−1.70

0.92

   

CL1154Contig1_02-143

0.93

95% (4)

0.26

−0.52

0.98

75% (1)

0.22

−2.60

0.90

   
      

95% (1)

      

CL1848Contig1_01-69

0.93

   

0.95

95% (3)

0.36

−1.75

0.92

   

0_1453_01-517

0.92

   

0.91

95% (4)

0.84

0.24

0.92

   

2_3720_01-180

0.92

   

0.97

95% (5)

0.33

−3.66

0.89

   

CHCS-189

0.90

   

0.87

   

0.92

95% (1)

0.18

0.32

  1. The results are based on averages over nine MCMC chains with different prior combinations.
  2. Note that regression results were not used to identify these outliers, but only serve as additional information to illustrate the correlation between population phenotypic means and allele frequencies.
  3. aMajor allele frequency; average of population-specific frequencies.
  4. bOutlier type: SNP was identified as an outlier in the box and whisker plots of medians (50%), 75% quantiles (75%) and 95% quantiles (95%); corresponding rank in brackets.
  5. cRegression: p-value and slope coefficient of the linear regression phenotypic population mean vs allele frequency in percentages. Thus the reported slope corresponds to the change of the phenotype in bud set days, when the allele frequency increases by 1%.
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