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 mr1201 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
vg1117163869 sf1116697721 11 17163869 2.02E-09 9.62E-07
vg0916716723 sf0916715722 9 16716723 5.04E-09 4.00E-06
vg0401488518 sf0401484068 4 1488518 1.43E-08 1.46E-06
vg0401488173 sf0401483723 4 1488173 1.97E-08 6.00E-07
vg1010137144 sf1010065965 10 10137144 6.57E-08 8.14E-07
vg1218194292 sf1218165728 12 18194292 6.97E-08 2.08E-06
vg1104497863 sf1104493765 11 4497863 1.32E-07 3.95E-06
vg0808194223 sf0808193227 8 8194223 1.54E-07 1.79E-06
vg0602650491 sf0602649492 6 2650491 2.27E-07 4.58E-06
vg0140818805 sf0140817762 1 40818805 2.28E-07 3.98E-06
vg1110030990 sf1110025567 11 10030990 4.47E-07 5.15E-06
vg0137912876 sf0137911833 1 37912876 5.76E-07 4.13E-06
vg1110030699 sf1110025276 11 10030699 6.98E-07 3.34E-06
vg0104825126 sf0104824126 1 4825126 1.05E-06 1.21E-06
vg0122013494 sf0122012449 1 22013494 2.41E-06 1.52E-06
vg1003100708 sf1003099685 10 3100708 3.20E-06 4.69E-06
vg1218161219 sf1218132655 12 18161219 NA 4.64E-06
vg0106766299 sf0106765299 1 6766299 NA 5.85E-06