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 mr1117 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
vg0421387824 sf0421215877 4 21387824 7.42E-21 2.40E-16
vg0728000317 sf0727999324 7 28000317 1.69E-17 4.34E-12
vg0336193973 sf0336186899 3 36193973 6.05E-17 1.13E-12
vg0308535729 sf0308534667 3 8535729 6.15E-16 1.27E-10
vg1001348300 sf1001347277 10 1348300 1.15E-14 4.81E-10
vg1117137503 sf1116671355 11 17137503 3.29E-14 7.92E-13
vg1016339056 sf1016267832 10 16339056 8.19E-14 3.12E-09
vg1204507349 sf1204506337 12 4507349 7.18E-12 3.83E-08
vg1201867679 sf1201866676 12 1867679 1.15E-11 6.41E-08
vg0504952991 sf0504952969 5 4952991 1.31E-11 7.86E-09
vg0918474400 sf0918473399 9 18474400 1.81E-11 2.13E-08
vg0222717674 sf0222711805 2 22717674 5.71E-11 3.93E-08
vg1227451463 sf1227417863 12 27451463 1.34E-10 9.75E-10
vg0136191693 sf0136190650 1 36191693 4.83E-10 7.73E-08
vg0819366916 sf0819364203 8 19366916 6.04E-10 4.42E-08
vg0139756098 sf0139755055 1 39756098 1.05E-09 3.41E-08
vg0714480545 sf0714479552 7 14480545 2.05E-09 9.54E-10
vg0819421680 sf0819418967 8 19421680 1.76E-08 2.04E-08
vg0907480791 sf0907479791 9 7480791 2.44E-07 8.78E-08
vg1208630676 sf1208628083 12 8630676 NA 4.29E-08