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 mr1559 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
vg0216741216 sf0216735346 2 16741216 9.41E-18 1.42E-10
vg0216858871 sf0216853001 2 16858871 1.30E-13 1.48E-08
vg0221849531 sf0221843662 2 21849531 2.22E-11 1.48E-07
vg0228175413 sf0228169544 2 28175413 3.72E-11 1.36E-07
vg0922209898 sf0922209417 9 22209898 4.90E-11 NA
vg0216679265 sf0216673395 2 16679265 1.69E-10 1.29E-08
vg0216714909 sf0216709039 2 16714909 2.50E-10 4.66E-08
vg0317023117 sf0317021991 3 17023117 4.68E-09 7.65E-08
vg0323673178 sf0323671352 3 23673178 5.30E-09 4.25E-06
vg1009283521 sf1009212342 10 9283521 4.25E-08 3.77E-08
vg1007924793 sf1007940403 10 7924793 4.81E-08 1.76E-06
vg0202719439 sf0202719437 2 2719439 5.53E-08 6.57E-07
vg0206304433 sf0206304433 2 6304433 1.57E-07 8.37E-08
vg0727492909 sf0727491915 7 27492909 2.87E-07 NA
vg0324795678 sf0324793757 3 24795678 1.88E-06 5.08E-07
vg0137962179 sf0137961136 1 37962179 NA 1.37E-06
vg1005695540 sf1005712078 10 5695540 NA 1.59E-06
vg0819940770 sf0819938057 8 19940770 NA 1.80E-06
vg0323687205 sf0323685379 3 23687205 NA 3.15E-06
vg1011003755 sf1010932575 10 11003755 NA 3.42E-06
vg0323900280 sf0323898454 3 23900280 NA 3.57E-06