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 mr1272 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
vg0330874284 sf0330867171 3 30874284 1.77E-14 2.64E-08
vg0330824537 sf0330817424 3 30824537 2.42E-14 9.69E-09
vg1102427650 sf1102423554 11 2427650 4.24E-12 NA
vg1218087584 sf1218059020 12 18087584 1.43E-11 NA
vg0714507911 sf0714506918 7 14507911 1.84E-11 NA
vg0423312779 sf0423127634 4 23312779 3.39E-11 NA
vg1000754606 sf1000753582 10 754606 7.70E-07 NA
vg0324081878 sf0324079957 3 24081878 1.39E-06 8.76E-06
vg0217864370 sf0217858501 2 17864370 NA 7.72E-07
vg0501597771 sf0501597755 5 1597771 NA 9.44E-06