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 mr1453 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
vg0139482305 sf0139481262 1 39482305 5.95E-09 2.96E-06
vg0710883859 sf0710882865 7 10883859 1.15E-08 NA
vg1209158266 sf1209155675 12 9158266 1.42E-08 NA
vg0139108098 sf0139107055 1 39108098 5.53E-08 NA
vg1219543928 sf1219515398 12 19543928 7.14E-08 NA
vg0502177239 sf0502177214 5 2177239 9.65E-08 NA
vg0503179544 sf0503179520 5 3179544 4.35E-06 3.53E-06
vg0621146125 sf0621145128 6 21146125 5.38E-06 4.48E-07
vg0139341179 sf0139340136 1 39341179 8.49E-06 6.47E-06