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 mr1679 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
vg0519489555 sf0519427039 5 19489555 6.57E-29 1.98E-07
vg0519465057 sf0519402541 5 19465057 1.02E-28 8.37E-08
vg0519486642 sf0519424126 5 19486642 2.00E-28 1.24E-07
vg0724428844 sf0724427850 7 24428844 6.32E-28 3.92E-13
vg1121888112 sf1121421983 11 21888112 7.38E-28 2.17E-09
vg0910121143 sf0910120142 9 10121143 3.00E-27 3.10E-06
vg0720025560 sf0720024567 7 20025560 4.96E-27 3.85E-06
vg0608112196 sf0608111197 6 8112196 3.74E-26 7.37E-09
vg1121900670 sf1121434541 11 21900670 4.53E-26 1.18E-09
vg0106808949 sf0106807949 1 6808949 9.57E-26 6.41E-07
vg1121882641 sf1121416512 11 21882641 9.82E-26 7.86E-08
vg0724501205 sf0724500211 7 24501205 1.39E-25 8.37E-17
vg0822936315 sf0822933602 8 22936315 6.69E-25 4.27E-08
vg0720122431 sf0720121438 7 20122431 1.88E-24 7.96E-07
vg1000264080 sf1000263080 10 264080 6.57E-22 7.77E-07
vg0917087568 sf0917086567 9 17087568 2.40E-21 3.39E-08
vg0127208150 sf0127207106 1 27208150 3.76E-21 2.81E-06
vg0724316306 sf0724315312 7 24316306 NA 3.33E-12
vg0724557235 sf0724556241 7 24557235 NA 7.11E-12
vg1204785483 sf1204784468 12 4785483 NA 3.67E-10
vg0215982412 sf0215976542 2 15982412 NA 1.49E-09
vg1204816499 sf1204815484 12 4816499 NA 2.05E-09
vg0729234628 sf0729233636 7 29234628 NA 2.14E-09
vg0724405048 sf0724404054 7 24405048 NA 2.47E-09
vg1204797152 sf1204775151 12 4797152 NA 6.29E-09
vg0729064560 sf0729063568 7 29064560 NA 1.33E-08
vg1117624559 sf1117158415 11 17624559 NA 5.18E-08
vg0608085803 sf0608084804 6 8085803 NA 7.52E-08
vg1221037385 sf1221003935 12 21037385 NA 3.43E-07
vg1227422436 sf1227388836 12 27422436 NA 5.54E-07
vg0724216200 sf0724215206 7 24216200 NA 6.43E-07
vg0314649425 sf0314648112 3 14649425 NA 6.49E-07
vg0817921068 sf0817918355 8 17921068 NA 6.88E-07