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 mr1323 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
vg1218120371 sf1218091807 12 18120371 3.44E-08 3.44E-08
vg0104078758 sf0104077758 1 4078758 2.24E-07 2.24E-07
vg0104007398 sf0104006398 1 4007398 2.40E-07 2.40E-07
vg1002049340 sf1002048317 10 2049340 2.44E-07 2.44E-07
vg0208268939 sf0208268938 2 8268939 4.70E-07 4.70E-07
vg1214742719 sf1214740060 12 14742719 5.00E-07 5.00E-07
vg1226056282 sf1226022676 12 26056282 7.86E-07 7.86E-07
vg1217852416 sf1217823850 12 17852416 9.37E-07 9.37E-07
vg1206605318 sf1206604208 12 6605318 1.74E-06 1.74E-06
vg0527997931 sf0527935287 5 27997931 1.77E-06 1.77E-06
vg1200183647 sf1200182647 12 183647 1.82E-06 1.82E-06
vg0312535741 sf0312534459 3 12535741 1.99E-06 1.99E-06
vg0307401131 sf0307400129 3 7401131 2.06E-06 2.06E-06
vg1220235240 sf1220206682 12 20235240 3.53E-06 3.53E-06
vg1106528916 sf1106524668 11 6528916 4.57E-06 4.57E-06
vg0525243823 sf0525181244 5 25243823 4.87E-06 4.87E-06