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 mr1036 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
vg0205081512 sf0205081509 2 5081512 4.53E-10 NA
vg0404560956 sf0404556559 4 4560956 2.65E-09 NA
vg0330850180 sf0330843067 3 30850180 4.23E-09 NA
vg0802472843 sf0802471846 8 2472843 1.29E-08 NA
vg0331266260 sf0331259145 3 31266260 3.37E-08 3.31E-07
vg0331249150 sf0331242035 3 31249150 9.28E-08 1.09E-07
vg0205285361 sf0205285359 2 5285361 3.30E-07 NA
vg0815304114 sf0815301400 8 15304114 1.98E-06 3.05E-06
vg0303379797 sf0303378793 3 3379797 NA 1.01E-07
vg0721650261 sf0721649268 7 21650261 NA 1.55E-06
vg0725627256 sf0725626262 7 25627256 NA 2.74E-06
vg0217569334 sf0217563464 2 17569334 NA 2.95E-06
vg0617311491 sf0617310494 6 17311491 NA 4.68E-06