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 mr1129 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
vg0130732040 sf0130730996 1 30732040 1.12E-10 4.73E-07
vg0222145560 sf0222139691 2 22145560 7.78E-10 9.84E-06
vg0216763637 sf0216757767 2 16763637 1.60E-09 3.46E-06
vg0710231860 sf0710230866 7 10231860 2.22E-09 NA
vg0132278599 sf0132277555 1 32278599 3.34E-09 5.41E-06
vg1011966171 sf1011894986 10 11966171 5.47E-08 1.65E-07
vg0418899218 sf0418727261 4 18899218 1.39E-07 1.52E-06
vg0222439621 sf0222433752 2 22439621 1.70E-07 4.64E-06
vg0215878891 sf0215873021 2 15878891 4.78E-07 3.74E-06
vg0426128634 sf0425943508 4 26128634 5.75E-07 1.03E-06
vg0709360843 sf0709359849 7 9360843 8.31E-07 1.53E-06
vg1205501586 sf1205500572 12 5501586 1.16E-06 3.63E-06
vg1123808197 sf1123342067 11 23808197 1.92E-06 2.67E-06
vg0714142387 sf0714141394 7 14142387 3.33E-06 4.61E-06
vg1203702115 sf1203701114 12 3702115 NA 4.15E-06