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 1.28E-15 3.74E-11
vg0336193973 sf0336186899 3 36193973 1.27E-13 2.08E-09
vg0727970899 sf0727969906 7 27970899 3.43E-13 1.36E-08
vg0308535729 sf0308534667 3 8535729 4.78E-13 6.52E-08
vg0728000317 sf0727999324 7 28000317 7.04E-13 1.05E-08
vg0504687974 sf0504687951 5 4687974 8.20E-13 1.01E-07
vg1016339056 sf1016267832 10 16339056 1.96E-12 6.92E-08
vg0700863821 sf0700862821 7 863821 2.87E-12 4.07E-07
vg0625443240 sf0625442243 6 25443240 1.20E-11 5.85E-08
vg0136191693 sf0136190650 1 36191693 1.73E-11 5.29E-09
vg1117137503 sf1116671355 11 17137503 1.82E-11 1.51E-10
vg0424049928 sf0423864789 4 24049928 5.16E-11 2.47E-07
vg1001348300 sf1001347277 10 1348300 8.89E-11 3.59E-07
vg0222717674 sf0222711805 2 22717674 1.41E-10 2.70E-07
vg0224173859 sf0224167990 2 24173859 4.91E-10 8.69E-08
vg0139756098 sf0139755055 1 39756098 1.21E-09 2.60E-08
vg0432825867 sf0432640753 4 32825867 1.19E-08 1.88E-07
vg0432345183 sf0432160072 4 32345183 6.78E-08 5.56E-08
vg0222906648 sf0222900779 2 22906648 1.24E-07 2.18E-09
vg0432799553 sf0432614439 4 32799553 4.54E-07 NA
vg0714480545 sf0714479552 7 14480545 1.13E-06 1.64E-07
vg0409745188 sf0409735886 4 9745188 3.55E-06 NA
vg1105604343 sf1105600095 11 5604343 3.73E-06 2.33E-07