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 mr1707 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
vg0918158744 sf0918157743 9 18158744 1.23E-23 6.64E-19
vg0916170774 sf0916169773 9 16170774 3.87E-12 3.38E-07
vg0704600543 sf0704599544 7 4600543 2.39E-09 2.54E-08
vg0210482475 sf0210482473 2 10482475 3.52E-09 NA
vg0717420887 sf0717419894 7 17420887 1.42E-08 1.74E-06
vg0112995841 sf0112994815 1 12995841 1.85E-08 9.46E-07
vg1117089560 sf1116623412 11 17089560 2.04E-06 3.10E-06
vg1208303450 sf1208300856 12 8303450 4.52E-06 2.17E-06
vg0407762610 sf0407757878 4 7762610 NA 1.72E-07
vg0412820231 sf0412810941 4 12820231 NA 2.94E-07
vg0116963933 sf0116962887 1 16963933 NA 6.96E-07
vg0116741597 sf0116740571 1 16741597 NA 1.10E-06
vg0820029453 sf0820026740 8 20029453 NA 1.87E-06
vg1205898444 sf1205897425 12 5898444 NA 2.12E-06
vg0117039557 sf0117038511 1 17039557 NA 2.53E-06
vg0607377849 sf0607376850 6 7377849 NA 3.12E-06
vg0808710581 sf0808709585 8 8710581 NA 3.16E-06
vg0219817547 sf0219811679 2 19817547 NA 3.33E-06
vg0704778806 sf0704777807 7 4778806 NA 6.16E-06