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 mr1452 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
vg0529437664 sf0529375019 5 29437664 8.56E-09 2.34E-06
vg0139783926 sf0139782883 1 39783926 1.94E-08 NA
vg0619806827 sf0619805830 6 19806827 2.50E-08 9.57E-06
vg0630306971 sf0630305973 6 30306971 4.48E-08 1.85E-06
vg0804887405 sf0804886408 8 4887405 7.17E-08 4.29E-06
vg0809115323 sf0809114327 8 9115323 3.73E-07 1.92E-06
vg0709128655 sf0709127661 7 9128655 5.75E-07 2.21E-06
vg0513549188 sf0513491735 5 13549188 1.72E-06 3.11E-06
vg1217798279 sf1217769713 12 17798279 4.61E-06 2.54E-06
vg1019960632 sf1019889132 10 19960632 NA 1.84E-06