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 mr1295 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
vg0427788963 sf0427603823 4 27788963 8.85E-08 NA
vg0217658679 sf0217652809 2 17658679 9.23E-08 NA
vg0519921523 sf0519858999 5 19921523 9.81E-08 NA
vg1111162952 sf1111157269 11 11162952 2.14E-07 1.01E-07
vg0220310142 sf0220304274 2 20310142 3.17E-07 NA
vg0728456461 sf0728455469 7 28456461 6.20E-06 1.39E-06
vg1124957503 sf1124491343 11 24957503 NA 2.73E-06
vg0324677253 sf0324675332 3 24677253 NA 7.41E-06