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 mr1496 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
vg0421387824 sf0421215877 4 21387824 3.35E-23 4.24E-17
vg0336193973 sf0336186899 3 36193973 6.14E-17 5.88E-12
vg0727970899 sf0727969906 7 27970899 1.42E-16 8.11E-10
vg0504875404 sf0504875381 5 4875404 2.34E-16 4.62E-10
vg0308535729 sf0308534667 3 8535729 6.68E-16 1.67E-09
vg0728000317 sf0727999324 7 28000317 7.06E-16 5.32E-10
vg1016339056 sf1016267832 10 16339056 7.91E-16 4.47E-10
vg0515214258 sf0515156800 5 15214258 8.83E-15 1.18E-09
vg1001348300 sf1001347277 10 1348300 4.47E-14 1.58E-09
vg0504952991 sf0504952969 5 4952991 1.06E-13 1.95E-10
vg0424049928 sf0423864789 4 24049928 1.67E-13 1.58E-08
vg1201867679 sf1201866676 12 1867679 3.11E-13 1.63E-08
vg1004727190 sf1004743727 10 4727190 5.14E-13 2.72E-09
vg0918474400 sf0918473399 9 18474400 6.80E-12 2.99E-08
vg1002008736 sf1002007713 10 2008736 1.45E-11 2.97E-08
vg0222717674 sf0222711805 2 22717674 2.03E-11 2.43E-08
vg1227451463 sf1227417863 12 27451463 8.30E-11 8.46E-10
vg0819366916 sf0819364203 8 19366916 2.12E-10 3.99E-08
vg0403207821 sf0403203424 4 3207821 8.21E-10 2.62E-08
vg1117137503 sf1116671355 11 17137503 8.45E-10 1.25E-08
vg0714252447 sf0714251454 7 14252447 3.53E-09 2.30E-08
vg0714480545 sf0714479552 7 14480545 2.53E-08 3.83E-08