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 mr1210 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
vg0911559557 sf0911558556 9 11559557 2.56E-08 8.46E-06
vg0334788563 sf0334781433 3 34788563 5.82E-08 1.93E-06
vg0406038870 sf0406034309 4 6038870 7.58E-08 7.78E-07
vg0911067540 sf0911066539 9 11067540 2.47E-07 1.85E-06
vg0628393090 sf0628392092 6 28393090 8.32E-07 1.88E-06
vg0334986236 sf0334979106 3 34986236 1.44E-06 2.30E-06
vg1109060541 sf1109055154 11 9060541 1.69E-06 NA
vg0719818719 sf0719817726 7 19818719 2.19E-06 1.62E-06
vg0113688689 sf0113687663 1 13688689 2.26E-06 4.43E-06
vg0302703599 sf0302702595 3 2703599 9.45E-06 1.75E-06
vg0105186659 sf0105185659 1 5186659 NA 1.75E-06
vg0420880180 sf0420708223 4 20880180 NA 4.58E-06
vg0817501174 sf0817498460 8 17501174 NA 5.98E-06