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 mr1703 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
vg0325710457 sf0325708475 3 25710457 3.21E-07 3.21E-07
vg0314998474 sf0314997121 3 14998474 6.24E-07 6.25E-07
vg0724496335 sf0724495341 7 24496335 1.82E-06 1.82E-06
vg0714136537 sf0714135544 7 14136537 1.92E-06 1.93E-06
vg0414235746 sf0414226459 4 14235746 2.24E-06 2.24E-06
vg0408590224 sf0408585498 4 8590224 2.92E-06 2.92E-06
vg0719056367 sf0719055374 7 19056367 3.23E-06 3.23E-06
vg1121741517 sf1121275394 11 21741517 3.73E-06 3.73E-06
vg0325705952 sf0325703970 3 25705952 3.97E-06 3.97E-06