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 mr1345 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
vg0700312059 sf0700311059 7 312059 3.26E-11 7.38E-06
vg0315356877 sf0315355524 3 15356877 4.09E-11 NA
vg0818577556 sf0818574843 8 18577556 1.27E-10 NA
vg1122514350 sf1122048221 11 22514350 1.42E-10 NA
vg0520041619 sf0519979095 5 20041619 1.47E-10 NA
vg1128511488 sf1127988267 11 28511488 1.55E-10 5.52E-07
vg1013275525 sf1013204295 10 13275525 2.72E-10 3.85E-06
vg1127977155 sf1127505541 11 27977155 8.67E-09 2.92E-06
vg0818631289 sf0818628576 8 18631289 2.65E-07 1.66E-06
vg0432025550 sf0431840443 4 32025550 3.92E-07 NA
vg0402100710 sf0402096304 4 2100710 1.34E-06 2.73E-06
vg0434853783 sf0434668674 4 34853783 2.53E-06 NA
vg0217652051 sf0217646181 2 17652051 3.03E-06 NA
vg0819114273 sf0819111560 8 19114273 NA 7.04E-08
vg0819137940 sf0819135227 8 19137940 NA 2.10E-07
vg1016847285 sf1016776057 10 16847285 NA 7.51E-07
vg1016663184 sf1016591957 10 16663184 NA 4.55E-06