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 mr1053 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
vg0412457639 sf0412448354 4 12457639 9.76E-11 4.98E-08
vg1009320430 sf1009249251 10 9320430 2.16E-10 1.21E-07
vg1009694705 sf1009623526 10 9694705 2.29E-10 5.83E-08
vg1009262901 sf1009191722 10 9262901 2.86E-10 4.06E-06
vg0407668419 sf0407663686 4 7668419 4.63E-10 3.11E-06
vg1005269476 sf1005286013 10 5269476 7.21E-10 2.90E-06
vg1005761243 sf1005777781 10 5761243 9.39E-09 4.27E-06
vg0519117648 sf0519055132 5 19117648 1.36E-06 NA
vg0706162756 sf0706161757 7 6162756 4.69E-06 1.25E-06
vg0334859631 sf0334852501 3 34859631 6.05E-06 NA
vg0805469573 sf0805468576 8 5469573 7.65E-06 NA
vg1004482065 sf1004498603 10 4482065 NA 1.70E-06
vg0916030541 sf0916029540 9 16030541 NA 4.04E-06
vg0518984986 sf0518922470 5 18984986 NA 4.87E-06