Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1550 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0209688142 sf0209688140 2 9688142 4.60E-09 3.40E-08
vg0709269240 sf0709268246 7 9269240 1.37E-08 1.63E-06
vg1000865327 sf1000864303 10 865327 1.75E-08 3.87E-07
vg0400004808 sf0400003808 4 4808 2.60E-08 NA
vg0207235631 sf0207235631 2 7235631 4.45E-08 NA
vg0400148574 sf0400147574 4 148574 7.84E-08 NA
vg0421328067 sf0421156121 4 21328067 8.76E-08 1.73E-06
vg0621414627 sf0621413630 6 21414627 1.12E-07 3.22E-08
vg1020625734 sf1020554213 10 20625734 1.30E-07 9.78E-07
vg0411851800 sf0411842511 4 11851800 2.43E-07 3.65E-07
vg0412663837 sf0412654547 4 12663837 2.99E-07 1.32E-07
vg0704746642 sf0704745643 7 4746642 5.41E-07 2.41E-06
vg0134578272 sf0134577229 1 34578272 7.45E-07 6.27E-07
vg0204738973 sf0204738970 2 4738973 7.72E-07 1.10E-06
vg0432167290 sf0431982183 4 32167290 NA 2.06E-07
vg0216167479 sf0216161609 2 16167479 NA 2.66E-06
vg0433052397 sf0432867284 4 33052397 NA 3.36E-06