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 mr1571 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
vg0610138842 sf0610137843 6 10138842 6.38E-09 9.47E-08
vg1224308470 sf1224274923 12 24308470 1.01E-08 NA
vg0610001965 sf0610000966 6 10001965 2.82E-08 3.54E-07
vg0526033573 sf0525970993 5 26033573 7.33E-08 NA
vg1104256046 sf1104251948 11 4256046 3.36E-07 3.29E-06
vg1124660528 sf1124194368 11 24660528 3.52E-07 1.46E-06
vg0609857445 sf0609856446 6 9857445 9.70E-07 4.72E-08
vg0519591621 sf0519529105 5 19591621 4.71E-06 NA
vg1210022856 sf1210020267 12 10022856 5.87E-06 2.39E-06
vg0502151253 sf0502151228 5 2151253 6.82E-06 3.11E-06
vg0813419843 sf0813417396 8 13419843 NA 3.20E-06