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 mr1528 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
vg0406713801 sf0406709248 4 6713801 2.95E-08 NA
vg0505634624 sf0505634562 5 5634624 1.43E-07 3.71E-07
vg0619254766 sf0619253769 6 19254766 7.61E-07 NA
vg0716091815 sf0716090822 7 16091815 1.15E-06 2.02E-06
vg0710361771 sf0710360777 7 10361771 1.45E-06 2.17E-06
vg0715234696 sf0715233703 7 15234696 1.46E-06 NA
vg1014030357 sf1013959123 10 14030357 6.04E-06 1.87E-06
vg1016652319 sf1016581092 10 16652319 NA 4.02E-07
vg0804827547 sf0804826550 8 4827547 NA 9.80E-07
vg0810477208 sf0810476212 8 10477208 NA 1.22E-06
vg1218127939 sf1218099375 12 18127939 NA 1.24E-06
vg0505490581 sf0505490559 5 5490581 NA 2.03E-06
vg1211597471 sf1211594807 12 11597471 NA 3.73E-06
vg0322975067 sf0322973555 3 22975067 NA 3.74E-06