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 mr1247 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
vg1008520987 sf1008449849 10 8520987 8.78E-15 2.94E-11
vg1005827020 sf1005843558 10 5827020 1.77E-12 1.23E-09
vg0407825687 sf0407820955 4 7825687 1.93E-12 3.04E-08
vg0407826743 sf0407822011 4 7826743 4.31E-12 1.84E-08
vg1216843502 sf1216837456 12 16843502 1.77E-11 1.42E-08
vg0709229134 sf0709228140 7 9229134 3.47E-11 2.83E-07
vg0716828374 sf0716827381 7 16828374 6.34E-11 9.86E-08
vg0813089324 sf0813086954 8 13089324 5.31E-10 1.76E-07
vg0528707749 sf0528645104 5 28707749 5.52E-10 7.35E-07
vg1005441451 sf1005457988 10 5441451 7.30E-10 7.61E-07
vg0122848570 sf0122847526 1 22848570 1.34E-09 7.38E-07
vg0905249361 sf0905248361 9 5249361 2.14E-09 4.36E-06
vg1107416561 sf1107412306 11 7416561 9.49E-09 1.42E-06
vg0609747066 sf0609746067 6 9747066 1.52E-08 3.11E-06
vg1202107668 sf1202106666 12 2107668 4.62E-08 1.53E-06
vg0403205910 sf0403201513 4 3205910 8.16E-08 4.50E-06
vg1006647778 sf1006663401 10 6647778 9.89E-08 1.51E-06
vg0216716103 sf0216710233 2 16716103 4.00E-07 2.95E-06
vg0617480222 sf0617479225 6 17480222 2.70E-06 1.83E-06
vg0222730246 sf0222724377 2 22730246 3.88E-06 4.99E-09