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 mr1370 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
vg0235128943 sf0235123074 2 35128943 5.33E-07 5.33E-07
vg0622820572 sf0622819575 6 22820572 8.47E-07 8.47E-07
vg1005078438 sf1005094975 10 5078438 1.15E-06 1.16E-06
vg0910004814 sf0910003813 9 10004814 1.23E-06 1.23E-06
vg0630078359 sf0630077361 6 30078359 1.25E-06 1.25E-06
vg0905688587 sf0905687587 9 5688587 1.83E-06 1.83E-06
vg0431266543 sf0431081433 4 31266543 1.83E-06 1.83E-06
vg0416678941 sf0416506984 4 16678941 2.01E-06 2.01E-06
vg0413358188 sf0413348899 4 13358188 2.49E-06 2.49E-06
vg0414583385 sf0414574099 4 14583385 3.47E-06 3.47E-06
vg0711107694 sf0711106700 7 11107694 3.51E-06 3.51E-06
vg0913511852 sf0913510851 9 13511852 3.58E-06 3.58E-06
vg0715448699 sf0715447706 7 15448699 3.73E-06 3.73E-06
vg0608455356 sf0608454357 6 8455356 4.73E-06 4.73E-06
vg1117104360 sf1116638212 11 17104360 4.98E-06 4.98E-06