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 mr1138 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
vg0918447666 sf0918446665 9 18447666 7.45E-16 2.08E-09
vg0916795852 sf0916794851 9 16795852 3.36E-15 2.11E-10
vg0916858916 sf0916857915 9 16858916 1.18E-13 1.77E-07
vg0918467471 sf0918466470 9 18467471 2.28E-12 2.47E-07
vg0430281846 sf0430096718 4 30281846 1.20E-09 NA
vg1203687735 sf1203686734 12 3687735 1.69E-09 NA
vg0217984068 sf0217978199 2 17984068 5.74E-09 1.28E-06
vg0218080379 sf0218074510 2 18080379 1.03E-08 8.55E-07
vg0217968982 sf0217963113 2 17968982 1.98E-08 1.03E-06
vg0315920143 sf0315918790 3 15920143 3.59E-07 4.52E-06
vg1105813718 sf1105809470 11 5813718 2.98E-06 NA
vg0431405060 sf0431219958 4 31405060 3.29E-06 2.22E-06
vg0315164123 sf0315162770 3 15164123 4.71E-06 NA
vg0431397443 sf0431212341 4 31397443 8.88E-06 7.76E-06
vg0331292031 sf0331284916 3 31292031 8.96E-06 NA
vg0800596392 sf0800595392 8 596392 NA 1.10E-10
vg1009597003 sf1009525824 10 9597003 NA 1.01E-06
vg0420360464 sf0420188508 4 20360464 NA 3.95E-06
vg0217792236 sf0217786367 2 17792236 NA 4.43E-06