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 mr1210 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
vg0325696417 sf0325694435 3 25696417 3.67E-39 8.09E-33
vg1121970827 sf1121504698 11 21970827 7.84E-15 3.45E-09
vg0400345487 sf0400344487 4 345487 3.42E-14 4.66E-09
vg1002067295 sf1002066272 10 2067295 1.09E-13 2.52E-09
vg1004789770 sf1004806307 10 4789770 3.60E-13 1.49E-09
vg1006011150 sf1006027688 10 6011150 3.62E-12 1.40E-07
vg0202731072 sf0202731070 2 2731072 6.78E-12 4.68E-09
vg0318271847 sf0318270629 3 18271847 1.16E-11 8.37E-09
vg1012888857 sf1012817672 10 12888857 1.66E-11 4.41E-11
vg1222644507 sf1222610946 12 22644507 5.14E-11 7.87E-08
vg0416712669 sf0416540713 4 16712669 6.86E-11 1.69E-08
vg0327423375 sf0327416428 3 27423375 1.02E-10 2.57E-08
vg0609841754 sf0609840755 6 9841754 1.03E-10 3.68E-08
vg0304415129 sf0304414131 3 4415129 1.13E-10 5.72E-09
vg0315495912 sf0315494559 3 15495912 1.37E-10 6.78E-08
vg0220048340 sf0220042472 2 20048340 1.61E-10 7.25E-08
vg0322820996 sf0322819485 3 22820996 2.49E-10 1.67E-09
vg0415028838 sf0415019552 4 15028838 5.59E-10 4.84E-09
vg1212987580 sf1212984919 12 12987580 1.14E-09 8.47E-08
vg0203127408 sf0203127406 2 3127408 2.57E-06 NA
vg0907836758 sf0907835758 9 7836758 NA 6.31E-08