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 mr1842 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
vg0331304089 sf0331296974 3 31304089 9.03E-37 3.60E-17
vg0331262164 sf0331255049 3 31262164 2.22E-35 2.26E-17
vg1006883184 sf1006898807 10 6883184 2.85E-20 NA
vg0518108159 sf0518047645 5 18108159 1.24E-19 NA
vg0807677059 sf0807676064 8 7677059 1.81E-19 5.81E-07
vg0321287390 sf0321285900 3 21287390 2.83E-19 NA
vg1000371326 sf1000370326 10 371326 2.92E-18 8.73E-09
vg0724575067 sf0724574073 7 24575067 2.25E-17 4.56E-09
vg0725312603 sf0725311609 7 25312603 7.67E-17 1.11E-10
vg0411669926 sf0411660632 4 11669926 8.02E-17 7.80E-08
vg0609019806 sf0609018807 6 9019806 2.65E-16 3.81E-07
vg0331256576 sf0331249461 3 31256576 NA 3.21E-12
vg0621137518 sf0621136521 6 21137518 NA 3.59E-10
vg0808289886 sf0808288890 8 8289886 NA 3.61E-08
vg0404387799 sf0404383403 4 4387799 NA 7.95E-08
vg0808279708 sf0808278712 8 8279708 NA 1.73E-07
vg0400999452 sf0400995004 4 999452 NA 1.78E-07
vg0609007802 sf0609006803 6 9007802 NA 2.98E-07
vg0806140348 sf0806139353 8 6140348 NA 4.95E-07
vg0411710445 sf0411701152 4 11710445 NA 5.06E-07
vg0609020767 sf0609019768 6 9020767 NA 7.92E-07
vg0401005726 sf0401001278 4 1005726 NA 8.09E-07
vg0401672905 sf0401668454 4 1672905 NA 9.13E-07
vg1109484212 sf1109478789 11 9484212 NA 2.52E-06
vg1107626177 sf1107621922 11 7626177 NA 2.71E-06