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 mr1482 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
vg0431358556 sf0431173449 4 31358556 4.15E-09 NA
vg0527183886 sf0527121242 5 27183886 2.30E-08 NA
vg0908746391 sf0908745390 9 8746391 2.44E-08 NA
vg1210427460 sf1210424873 12 10427460 3.35E-08 NA
vg0920324119 sf0920323638 9 20324119 7.16E-08 NA
vg0304467332 sf0304466334 3 4467332 2.53E-07 5.24E-06
vg1002548618 sf1002547595 10 2548618 3.20E-07 9.04E-07
vg0327912257 sf0327905311 3 27912257 9.81E-07 NA
vg0319300846 sf0319299357 3 19300846 1.46E-06 5.17E-07
vg0105279447 sf0105278447 1 5279447 NA 7.86E-07
vg0706908766 sf0706907771 7 6908766 NA 2.09E-06
vg0103417535 sf0103416535 1 3417535 NA 3.96E-06