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 mr1193 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
vg1113418649 sf1112954971 11 13418649 5.29E-07 5.29E-07
vg0219802540 sf0219796672 2 19802540 5.72E-07 5.72E-07
vg0428951624 sf0428766482 4 28951624 7.92E-07 7.92E-07
vg0906245690 sf0906244690 9 6245690 1.11E-06 1.11E-06
vg0142380984 sf0142379940 1 42380984 1.16E-06 1.16E-06
vg0416097313 sf0415925346 4 16097313 1.24E-06 1.24E-06
vg0402649303 sf0402644907 4 2649303 1.76E-06 1.77E-06
vg0729077790 sf0729076798 7 29077790 2.00E-06 2.00E-06
vg1120464509 sf1119998434 11 20464509 2.19E-06 2.19E-06
vg0724426848 sf0724425854 7 24426848 2.79E-06 2.79E-06
vg0405742124 sf0405737563 4 5742124 3.85E-06 3.85E-06
vg0322365483 sf0322363972 3 22365483 4.14E-06 4.14E-06
vg0301146102 sf0301145100 3 1146102 4.83E-06 4.84E-06
vg0716578471 sf0716577478 7 16578471 4.88E-06 4.88E-06