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 mr1224 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
vg0222833455 sf0222827586 2 22833455 5.10E-16 1.07E-12
vg0719007567 sf0719006574 7 19007567 5.27E-16 4.83E-12
vg1214075681 sf1214073021 12 14075681 6.79E-10 NA
vg0223078644 sf0223072775 2 23078644 1.25E-09 3.79E-07
vg0719443056 sf0719442063 7 19443056 1.87E-09 1.40E-07
vg0223062888 sf0223057019 2 23062888 5.18E-09 1.42E-06
vg0719446596 sf0719445603 7 19446596 2.20E-08 1.65E-06
vg0718888579 sf0718887586 7 18888579 4.87E-08 9.22E-07
vg0719274779 sf0719273786 7 19274779 6.77E-08 1.20E-07
vg0223038405 sf0223032536 2 23038405 3.08E-06 2.95E-07
vg0719127699 sf0719126706 7 19127699 3.99E-06 1.07E-06
vg0222835729 sf0222829860 2 22835729 5.10E-06 5.97E-07
vg0222314975 sf0222309106 2 22314975 NA 2.15E-06
vg0608480356 sf0608479357 6 8480356 NA 9.73E-06