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 mr1865 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
vg0922422731 sf0922422250 9 22422731 1.32E-121 2.84E-25
vg0917708805 sf0917707804 9 17708805 8.16E-103 7.76E-07
vg0914742822 sf0914741821 9 14742822 1.90E-98 NA
vg0304916745 sf0304915747 3 4916745 4.29E-97 NA
vg1013524041 sf1013452811 10 13524041 1.74E-94 NA
vg0922428117 sf0922427636 9 22428117 NA 1.95E-28
vg0922427838 sf0922427357 9 22427838 NA 2.61E-17
vg0922451431 sf0922450950 9 22451431 NA 7.95E-12
vg0922636537 sf0922636056 9 22636537 NA 6.37E-11
vg0922506851 sf0922506370 9 22506851 NA 4.16E-10
vg0922202326 sf0922201845 9 22202326 NA 1.10E-08
vg1202557972 sf1202556974 12 2557972 NA 2.85E-07
vg0922541714 sf0922541233 9 22541714 NA 2.44E-06
vg0922392672 sf0922392191 9 22392672 NA 2.62E-06
vg0922186621 sf0922186140 9 22186621 NA 2.66E-06
vg0312651219 sf0312649937 3 12651219 NA 3.23E-06
vg0407212383 sf0407207653 4 7212383 NA 3.59E-06
vg0120818869 sf0120817824 1 20818869 NA 3.98E-06
vg0723622803 sf0723621810 7 23622803 NA 4.16E-06
vg0723567969 sf0723566976 7 23567969 NA 4.26E-06
vg0922577989 sf0922577508 9 22577989 NA 4.44E-06