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 mr1173 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
vg0528670544 sf0528607899 5 28670544 3.47E-07 3.47E-07
vg1206433446 sf1206432336 12 6433446 7.58E-07 7.58E-07
vg0629345546 sf0629344548 6 29345546 9.79E-07 9.80E-07
vg0316249506 sf0316248154 3 16249506 1.17E-06 1.17E-06
vg1206433470 sf1206432360 12 6433470 1.47E-06 1.47E-06
vg0729464249 sf0729463257 7 29464249 1.73E-06 1.73E-06
vg1128487344 sf1127964123 11 28487344 3.21E-06 3.21E-06
vg0124422057 sf0124421013 1 24422057 3.21E-06 3.22E-06
vg0521838884 sf0521776326 5 21838884 3.45E-06 3.45E-06
vg0312973767 sf0312972485 3 12973767 3.52E-06 3.52E-06
vg0319619967 sf0319618478 3 19619967 3.91E-06 3.91E-06
vg1006722269 sf1006737892 10 6722269 4.49E-06 4.50E-06
vg1009824904 sf1009753725 10 9824904 4.87E-06 4.87E-06
vg1001445274 sf1001444251 10 1445274 9.25E-06 9.25E-06