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 mr1321 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
vg0300375981 sf0300374979 3 375981 2.13E-11 NA
vg1125556816 sf1125090655 11 25556816 2.39E-10 1.84E-06
vg1125556483 sf1125090322 11 25556483 3.19E-10 2.79E-06
vg0406510363 sf0406505806 4 6510363 8.20E-10 NA
vg0111347703 sf0111346679 1 11347703 8.54E-10 NA
vg0232556186 sf0232550317 2 32556186 1.15E-09 4.54E-06
vg1124647337 sf1124181177 11 24647337 2.77E-09 1.70E-06
vg0623036613 sf0623035616 6 23036613 2.94E-09 3.45E-06
vg0319113443 sf0319112203 3 19113443 5.11E-09 1.02E-06
vg0307765595 sf0307764533 3 7765595 7.81E-09 1.27E-06
vg0628648301 sf0628647303 6 28648301 9.51E-09 3.28E-07
vg0912243494 sf0912242493 9 12243494 2.03E-08 1.06E-06
vg1120489837 sf1120023762 11 20489837 2.52E-08 1.39E-06
vg0219483986 sf0219478118 2 19483986 6.16E-08 3.63E-06
vg1117637145 sf1117171001 11 17637145 9.64E-08 3.79E-06
vg0226906255 sf0226900386 2 26906255 1.40E-07 NA
vg0623042453 sf0623041456 6 23042453 NA 4.58E-06