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 mr1240 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
vg0222725905 sf0222720036 2 22725905 1.54E-10 2.35E-09
vg0224628475 sf0224622606 2 24628475 3.08E-08 9.17E-07
vg1118246821 sf1117780680 11 18246821 3.87E-08 5.86E-08
vg0224723224 sf0224717355 2 24723224 1.76E-07 4.45E-07
vg0517986448 sf0517925934 5 17986448 4.90E-07 1.39E-06
vg0715467547 sf0715466554 7 15467547 9.16E-07 3.92E-06
vg1114410670 sf1113946987 11 14410670 1.28E-06 9.44E-07
vg0513969126 sf0513911670 5 13969126 1.52E-06 NA
vg0334419989 sf0334412859 3 34419989 2.44E-06 1.94E-06
vg1104837937 sf1104833839 11 4837937 2.63E-06 2.06E-06
vg0207854825 sf0207854824 2 7854825 2.97E-06 1.53E-06
vg0504460143 sf0504460120 5 4460143 4.47E-06 3.34E-06
vg1020189984 sf1020118466 10 20189984 4.81E-06 1.69E-06
vg0335631588 sf0335624457 3 35631588 5.49E-06 7.57E-07
vg1216221559 sf1216218855 12 16221559 8.25E-06 2.23E-06
vg1009464437 sf1009393258 10 9464437 NA 3.33E-06