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 mr1503 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
vg0222742146 sf0222736277 2 22742146 1.22E-27 6.59E-19
vg0222742213 sf0222736344 2 22742213 2.55E-27 5.11E-19
vg1009144392 sf1009073253 10 9144392 1.50E-13 NA
vg0223818027 sf0223812158 2 23818027 5.93E-12 2.06E-10
vg0912077331 sf0912076330 9 12077331 2.79E-11 NA
vg0133338750 sf0133337706 1 33338750 2.81E-11 NA
vg1009133770 sf1009062631 10 9133770 5.54E-11 2.41E-09
vg1008002204 sf1008042033 10 8002204 1.95E-10 4.53E-09
vg0209237133 sf0209237131 2 9237133 3.36E-10 7.48E-08
vg1006488269 sf1006503892 10 6488269 5.77E-10 6.93E-09
vg1006304251 sf1006319874 10 6304251 9.31E-10 NA
vg0202692022 sf0202692020 2 2692022 4.55E-09 NA
vg0528707749 sf0528645104 5 28707749 1.16E-08 1.81E-06
vg0222681985 sf0222676116 2 22681985 1.36E-08 4.91E-08
vg0224275719 sf0224269850 2 24275719 1.09E-07 1.75E-06
vg0526754630 sf0504919094 5 26754630 3.79E-07 NA
vg0117137382 sf0117136336 1 17137382 1.34E-06 NA
vg0810919840 sf0810918845 8 10919840 NA 1.15E-06
vg1120378562 sf1119912487 11 20378562 NA 1.44E-06
vg0807842592 sf0807841596 8 7842592 NA 1.50E-06
vg0222858831 sf0222852962 2 22858831 NA 2.64E-06
vg0317168413 sf0317167223 3 17168413 NA 2.78E-06
vg0317037719 sf0317036593 3 17037719 NA 3.25E-06
vg1116351931 sf1115886807 11 16351931 NA 3.90E-06
vg1217214923 sf1217208878 12 17214923 NA 4.50E-06
vg1012832290 sf1012761105 10 12832290 NA 4.68E-06
vg1214403070 sf1214400411 12 14403070 NA 4.80E-06
vg0813873814 sf0813871100 8 13873814 NA 4.81E-06