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 mr1123 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 4.11E-19 1.66E-14
vg0336193973 sf0336186899 3 36193973 8.05E-14 1.86E-10
vg0504875404 sf0504875381 5 4875404 1.16E-13 2.35E-08
vg0727970899 sf0727969906 7 27970899 3.36E-12 4.42E-08
vg0308535729 sf0308534667 3 8535729 6.98E-12 2.78E-07
vg1126461419 sf1125989832 11 26461419 1.40E-11 3.14E-08
vg0424049928 sf0423864789 4 24049928 3.41E-11 1.51E-07
vg1016339056 sf1016267832 10 16339056 5.00E-11 2.29E-07
vg1219134304 sf1219105740 12 19134304 8.74E-11 6.82E-08
vg1204507349 sf1204506337 12 4507349 1.55E-10 1.66E-07
vg0504952991 sf0504952969 5 4952991 4.61E-10 2.08E-08
vg0334827866 sf0334820736 3 34827866 7.49E-10 3.93E-07
vg0906313471 sf0906312471 9 6313471 1.45E-09 7.33E-08
vg1002009944 sf1002008921 10 2009944 1.64E-09 4.03E-07
vg0819366916 sf0819364203 8 19366916 2.35E-09 6.18E-08
vg1117137503 sf1116671355 11 17137503 5.08E-09 1.12E-08
vg1004727190 sf1004743727 10 4727190 7.93E-09 3.04E-07
vg0819421680 sf0819418967 8 19421680 2.15E-08 1.56E-08
vg0219292377 sf0219286509 2 19292377 6.42E-07 3.74E-07
vg1002768715 sf1002767692 10 2768715 1.27E-06 NA
vg0714252447 sf0714251454 7 14252447 1.71E-06 4.78E-07
vg0812050496 sf0812049501 8 12050496 4.39E-06 NA
vg0812003263 sf0812002268 8 12003263 NA 4.21E-07