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 mr1597 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
vg0325617211 sf0325615229 3 25617211 2.95E-08 2.96E-08
vg0619932719 sf0619931722 6 19932719 3.64E-08 3.65E-08
vg0323847195 sf0323845369 3 23847195 1.34E-07 1.34E-07
vg1122409633 sf1121943504 11 22409633 6.14E-07 6.15E-07
vg0620179417 sf0620178420 6 20179417 9.53E-07 9.55E-07
vg0431894404 sf0431709299 4 31894404 9.92E-07 9.93E-07
vg1002137501 sf1002136478 10 2137501 1.15E-06 1.15E-06
vg1212815464 sf1212812803 12 12815464 1.84E-06 1.85E-06
vg1121223361 sf1120757239 11 21223361 1.95E-06 1.96E-06
vg0813547545 sf0813545098 8 13547545 2.83E-06 2.84E-06
vg1001111430 sf1001110406 10 1111430 4.04E-06 4.04E-06
vg0317761716 sf0317760498 3 17761716 4.15E-06 4.16E-06
vg0810860589 sf0810859594 8 10860589 4.49E-06 4.50E-06
vg0225140996 sf0225135127 2 25140996 4.76E-06 4.78E-06