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 mr1949 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
vg0719011406 sf0719010413 7 19011406 1.88E-17 8.47E-12
vg0718989547 sf0718988554 7 18989547 9.24E-17 1.25E-18
vg0719133785 sf0719132792 7 19133785 3.27E-14 3.47E-10
vg0719188413 sf0719187420 7 19188413 1.95E-12 1.83E-09
vg0918593583 sf0918592582 9 18593583 1.83E-11 4.99E-07
vg1201579861 sf1201578861 12 1579861 2.95E-11 7.37E-06
vg0336402152 sf0336395022 3 36402152 6.17E-11 2.80E-08
vg1201345907 sf1201344907 12 1345907 4.16E-10 2.13E-07
vg0336302808 sf0336295678 3 36302808 5.53E-10 5.11E-09
vg0719100263 sf0719099270 7 19100263 5.66E-09 3.80E-06
vg0719466613 sf0719465620 7 19466613 2.35E-08 8.29E-07
vg0335349500 sf0335342369 3 35349500 3.66E-08 5.31E-06
vg0503853547 sf0503853524 5 3853547 1.51E-07 2.18E-06
vg0718984454 sf0718983461 7 18984454 NA 4.50E-12
vg0502034831 sf0502034813 5 2034831 NA 3.66E-07
vg0624862159 sf0624861162 6 24862159 NA 1.66E-06