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 mr1973 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
vg0218644733 sf0218638864 2 18644733 2.78E-08 2.78E-08
vg0611318612 sf0611317613 6 11318612 6.91E-08 6.91E-08
vg0711196143 sf0711195149 7 11196143 1.13E-07 1.13E-07
vg0707590206 sf0707589211 7 7590206 2.08E-07 2.08E-07
vg0404978718 sf0404974157 4 4978718 2.10E-07 2.10E-07
vg0822651774 sf0822649061 8 22651774 2.42E-07 2.42E-07
vg1004566041 sf1004582579 10 4566041 2.73E-07 2.73E-07
vg0619432377 sf0619431380 6 19432377 3.31E-07 3.31E-07
vg1209876216 sf1209873626 12 9876216 5.84E-07 5.84E-07
vg0714215236 sf0714214243 7 14215236 1.12E-06 1.12E-06
vg0616129303 sf0616128305 6 16129303 1.19E-06 1.19E-06
vg0819366594 sf0819363881 8 19366594 1.58E-06 1.58E-06
vg0711201792 sf0711200798 7 11201792 1.59E-06 1.59E-06
vg0231324042 sf0231318173 2 31324042 1.91E-06 1.91E-06
vg1122427075 sf1121960946 11 22427075 2.23E-06 2.23E-06
vg0812584594 sf0812582419 8 12584594 4.62E-06 4.62E-06
vg0803968574 sf0803967577 8 3968574 4.66E-06 4.66E-06
vg0208678737 sf0208678736 2 8678737 7.89E-06 7.89E-06