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 mr1697 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
vg0505612533 sf0505612471 5 5612533 7.28E-16 1.59E-13
vg0505480283 sf0505480261 5 5480283 2.64E-15 4.58E-14
vg0505633755 sf0505633693 5 5633755 2.66E-14 5.70E-14
vg0202071611 sf0202071611 2 2071611 1.30E-09 NA
vg0611017308 sf0611016309 6 11017308 2.95E-09 NA
vg0202081722 sf0202081722 2 2081722 3.06E-09 9.50E-07
vg0209673998 sf0209673996 2 9673998 1.16E-08 NA
vg0207562985 sf0207562985 2 7562985 1.19E-08 7.52E-07
vg0403738024 sf0403733630 4 3738024 3.85E-07 2.20E-06
vg0610808854 sf0610807855 6 10808854 4.04E-07 4.51E-06
vg0302570584 sf0302569580 3 2570584 4.16E-07 1.42E-06
vg0611018738 sf0611017739 6 11018738 1.28E-06 2.76E-06
vg0109411370 sf0109410346 1 9411370 1.50E-06 4.06E-06
vg0905652760 sf0905651760 9 5652760 1.82E-06 7.52E-07
vg0621438164 sf0621437167 6 21438164 3.75E-06 1.44E-06
vg0115873074 sf0115872048 1 15873074 7.86E-06 1.07E-06
vg0716356793 sf0716355800 7 16356793 7.91E-06 NA
vg0625093787 sf0625092790 6 25093787 NA 1.53E-07
vg0808770697 sf0808769701 8 8770697 NA 4.26E-06
vg0413452048 sf0413442762 4 13452048 NA 8.09E-06