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 mr1533 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
vg1013525472 sf1013454242 10 13525472 1.09E-34 7.05E-26
vg1013528269 sf1013457039 10 13528269 1.11E-34 4.62E-26
vg0803359178 sf0803358181 8 3359178 2.78E-11 7.31E-06
vg1013767614 sf1013696383 10 13767614 3.98E-11 6.25E-08
vg1013526752 sf1013455522 10 13526752 6.61E-11 2.01E-10
vg0803360078 sf0803359081 8 3360078 8.16E-11 2.99E-06
vg1013680813 sf1013609582 10 13680813 1.43E-10 1.51E-07
vg1013680144 sf1013608913 10 13680144 2.37E-09 1.02E-06
vg1013340402 sf1013269172 10 13340402 2.60E-09 3.17E-06
vg1013412160 sf1013340930 10 13412160 5.04E-09 2.00E-06
vg0301975407 sf0301974403 3 1975407 5.26E-06 NA
vg0827096536 sf0827093822 8 27096536 6.01E-06 NA
vg1013500622 sf1013429392 10 13500622 NA 8.06E-07