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 mr1242 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 1.61E-17 2.69E-12
vg0305235129 sf0305234129 3 5235129 1.92E-13 5.34E-07
vg0727970899 sf0727969906 7 27970899 6.56E-13 8.38E-08
vg0336193973 sf0336186899 3 36193973 1.13E-12 1.14E-09
vg0626383263 sf0626382266 6 26383263 1.78E-12 3.36E-06
vg1126461419 sf1125989832 11 26461419 5.67E-12 3.62E-08
vg1001348300 sf1001347277 10 1348300 4.22E-11 5.13E-07
vg1219134304 sf1219105740 12 19134304 6.01E-11 1.73E-07
vg1016339056 sf1016267832 10 16339056 6.19E-11 4.22E-07
vg1004727190 sf1004743727 10 4727190 7.17E-11 3.00E-08
vg0328369698 sf0328362751 3 28369698 8.60E-11 7.91E-07
vg1014514985 sf1014443751 10 14514985 1.79E-10 3.81E-07
vg1201867679 sf1201866676 12 1867679 1.94E-10 1.11E-07
vg1204507349 sf1204506337 12 4507349 3.36E-10 8.73E-07
vg0504952991 sf0504952969 5 4952991 5.80E-10 5.00E-08
vg1002008736 sf1002007713 10 2008736 1.53E-09 1.24E-06
vg1117137503 sf1116671355 11 17137503 1.72E-09 1.82E-08
vg0819366916 sf0819364203 8 19366916 8.27E-09 6.77E-07
vg0219292377 sf0219286509 2 19292377 4.14E-08 7.83E-08
vg0714480545 sf0714479552 7 14480545 4.99E-08 2.61E-07
vg0812050496 sf0812049501 8 12050496 4.14E-07 4.55E-06
vg1208630676 sf1208628083 12 8630676 NA 8.46E-07
vg0812003263 sf0812002268 8 12003263 NA 1.22E-06