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 mr1416 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
vg0225444889 sf0225439020 2 25444889 5.83E-08 5.83E-08
vg1213938357 sf1213935695 12 13938357 7.35E-08 7.35E-08
vg0216970148 sf0216964278 2 16970148 3.11E-07 3.11E-07
vg0221622425 sf0221616556 2 21622425 3.82E-07 3.82E-07
vg0118504134 sf0118503088 1 18504134 4.93E-07 4.93E-07
vg1218584234 sf1218555670 12 18584234 9.17E-07 9.17E-07
vg0413348505 sf0413339216 4 13348505 1.27E-06 1.27E-06
vg0220834541 sf0220828673 2 20834541 1.68E-06 1.68E-06
vg0818009619 sf0818006906 8 18009619 1.78E-06 1.78E-06
vg0403728255 sf0403723861 4 3728255 1.85E-06 1.85E-06
vg1210124111 sf1210121522 12 10124111 3.09E-06 3.09E-06
vg0315854657 sf0315853304 3 15854657 3.38E-06 3.38E-06
vg1222814459 sf1222780898 12 22814459 3.59E-06 3.59E-06
vg0407808783 sf0407804051 4 7808783 4.88E-06 4.88E-06
vg1223872471 sf1223838924 12 23872471 4.99E-06 4.99E-06
vg1223181515 sf1223147975 12 23181515 4.99E-06 5.00E-06
vg0308455093 sf0308454031 3 8455093 5.69E-06 5.69E-06