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 mr1506 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
vg0805963026 sf0805962029 8 5963026 2.03E-07 2.03E-07
vg0324965295 sf0324963375 3 24965295 3.47E-07 3.47E-07
vg0223170147 sf0223164278 2 23170147 3.82E-07 3.82E-07
vg0317372993 sf0317371803 3 17372993 5.94E-07 5.94E-07
vg0816086900 sf0816084186 8 16086900 6.35E-07 6.35E-07
vg0509233251 sf0509233180 5 9233251 1.34E-06 1.34E-06
vg0901298010 sf0901297010 9 1298010 1.61E-06 1.61E-06
vg0700837076 sf0700836076 7 837076 1.72E-06 1.72E-06
vg1124252852 sf1123786722 11 24252852 1.83E-06 1.83E-06
vg1001343441 sf1001342418 10 1343441 2.16E-06 2.16E-06
vg0401647321 sf0401642870 4 1647321 2.57E-06 2.57E-06
vg0223518691 sf0223512822 2 23518691 2.58E-06 2.59E-06
vg0318307997 sf0318306779 3 18307997 2.93E-06 2.93E-06
vg0408495393 sf0408490666 4 8495393 3.05E-06 3.05E-06
vg0335297514 sf0335290383 3 35297514 3.50E-06 3.50E-06
vg1001247868 sf1001246845 10 1247868 3.73E-06 3.73E-06
vg0307132377 sf0307131375 3 7132377 3.92E-06 3.92E-06
vg0724585298 sf0724584304 7 24585298 4.00E-06 4.00E-06
vg0223074046 sf0223068177 2 23074046 4.78E-06 4.79E-06