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 mr1869 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
vg1117156319 sf1116690171 11 17156319 5.12E-08 5.15E-08
vg1004977357 sf1004993894 10 4977357 1.04E-06 1.05E-06
vg1117163217 sf1116697069 11 17163217 1.05E-06 1.05E-06
vg1117141737 sf1116675589 11 17141737 1.26E-06 1.25E-06
vg0224823901 sf0224818032 2 24823901 1.54E-06 1.53E-06
vg1110037503 sf1110032080 11 10037503 2.24E-06 2.25E-06
vg0220988854 sf0220982986 2 20988854 2.53E-06 2.54E-06
vg0618316811 sf0618315814 6 18316811 2.71E-06 2.72E-06
vg1122522843 sf1122056714 11 22522843 3.15E-06 3.17E-06
vg0327979488 sf0327972542 3 27979488 4.01E-06 4.04E-06
vg0715173240 sf0715172247 7 15173240 4.07E-06 4.09E-06
vg0812018246 sf0812017251 8 12018246 4.25E-06 4.27E-06