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 mr1191 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
vg1125871704 sf1125405623 11 25871704 2.03E-10 2.03E-10
vg1125837262 sf1125371181 11 25837262 7.89E-10 7.89E-10
vg1209876262 sf1209873672 12 9876262 5.69E-08 5.69E-08
vg1126454396 sf1125982809 11 26454396 1.02E-07 1.02E-07
vg1016534305 sf1016463078 10 16534305 6.85E-07 6.85E-07
vg1125518645 sf1125052484 11 25518645 1.03E-06 1.03E-06
vg1126851649 sf1126380036 11 26851649 2.06E-06 2.06E-06
vg0826524537 sf0826521823 8 26524537 2.73E-06 2.73E-06
vg1217990202 sf1217961638 12 17990202 3.27E-06 3.27E-06
vg0225149137 sf0225143268 2 25149137 4.54E-06 4.54E-06