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 mr1634 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
vg0315320771 sf0315319418 3 15320771 2.48E-10 NA
vg0317970682 sf0317969464 3 17970682 3.54E-09 NA
vg0607367426 sf0607366427 6 7367426 3.82E-09 NA
vg0124291514 sf0124290470 1 24291514 3.85E-09 NA
vg0700312059 sf0700311059 7 312059 5.96E-09 NA
vg0422558702 sf0422373587 4 22558702 4.22E-08 NA
vg0819114272 sf0819111559 8 19114272 NA 1.59E-07
vg1016851749 sf1016780521 10 16851749 NA 6.83E-07
vg0809201580 sf0809200584 8 9201580 NA 1.21E-06
vg1016625606 sf1016554379 10 16625606 NA 4.09E-06