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 mr1655 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
vg0420385271 sf0420213315 4 20385271 4.45E-17 NA
vg0428506971 sf0428321824 4 28506971 8.15E-17 NA
vg0305033997 sf0305032999 3 5033997 8.83E-17 NA
vg0334657752 sf0334650622 3 34657752 1.06E-16 9.26E-06
vg0435311304 sf0435126185 4 35311304 1.73E-16 NA
vg0225012379 sf0225006510 2 25012379 7.96E-16 4.33E-06
vg1119446199 sf1118979887 11 19446199 NA 2.30E-07
vg0334694264 sf0334687134 3 34694264 NA 5.76E-07
vg1121176979 sf1120710857 11 21176979 NA 7.05E-07
vg0915670603 sf0915669602 9 15670603 NA 1.55E-06
vg0118543379 sf0118542333 1 18543379 NA 2.06E-06
vg1214515514 sf1214512855 12 14515514 NA 2.26E-06
vg0910300794 sf0910299793 9 10300794 NA 2.57E-06
vg1002965621 sf1002964598 10 2965621 NA 3.59E-06
vg1002965249 sf1002964226 10 2965249 NA 6.06E-06