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 mr1373 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
vg0112317208 sf0112316182 1 12317208 1.28E-07 1.28E-07
vg0608661476 sf0608660477 6 8661476 6.82E-07 6.82E-07
vg0918095326 sf0918094325 9 18095326 7.35E-07 7.35E-07
vg0135233075 sf0135232032 1 35233075 8.90E-07 8.90E-07
vg0606949718 sf0606948719 6 6949718 1.34E-06 1.34E-06
vg0103433293 sf0103432293 1 3433293 1.43E-06 1.43E-06
vg0600800938 sf0600799939 6 800938 1.52E-06 1.52E-06
vg0710562047 sf0710561053 7 10562047 2.53E-06 2.53E-06
vg0507051194 sf0507051136 5 7051194 2.60E-06 2.60E-06
vg0123862783 sf0123861739 1 23862783 2.72E-06 2.73E-06
vg0216113702 sf0216107832 2 16113702 3.80E-06 3.80E-06
vg0808585110 sf0808584114 8 8585110 4.32E-06 4.32E-06