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 mr1295 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
vg0432977710 sf0432792597 4 32977710 6.02E-10 6.49E-07
vg0432961214 sf0432776101 4 32961214 8.99E-10 6.16E-07
vg0520021162 sf0519958638 5 20021162 1.31E-08 NA
vg0824524218 sf0824521504 8 24524218 1.70E-08 NA
vg0303879599 sf0303878595 3 3879599 1.81E-08 NA
vg0431473866 sf0431288764 4 31473866 2.67E-08 NA
vg0104617666 sf0104616666 1 4617666 1.95E-07 NA
vg1003557200 sf1003556177 10 3557200 6.49E-07 4.04E-06
vg1118275729 sf1117809588 11 18275729 NA 2.51E-06
vg0608160267 sf0608159268 6 8160267 NA 3.57E-06