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 mr1099 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
vg0222739831 sf0222733962 2 22739831 9.76E-60 5.88E-48
vg0224678499 sf0224672630 2 24678499 2.36E-13 4.17E-09
vg0222879623 sf0222873754 2 22879623 6.64E-13 1.92E-14
vg0223006301 sf0223000432 2 23006301 3.29E-11 NA
vg0224664402 sf0224658533 2 24664402 8.22E-11 2.72E-11
vg0224238625 sf0224232756 2 24238625 1.77E-10 1.37E-08
vg0222817468 sf0222811599 2 22817468 7.13E-10 1.07E-10
vg0222672641 sf0222666772 2 22672641 1.94E-08 8.38E-07
vg0224788519 sf0224782650 2 24788519 2.49E-08 3.70E-06
vg0224835947 sf0224830078 2 24835947 2.59E-08 7.09E-10
vg1112606104 sf1112142307 11 12606104 6.09E-08 1.02E-06
vg0222735022 sf0222729153 2 22735022 2.66E-07 2.49E-06
vg0222857256 sf0222851387 2 22857256 6.21E-07 2.01E-06
vg0224239569 sf0224233700 2 24239569 2.44E-06 3.65E-07
vg0430202848 sf0430017721 4 30202848 3.57E-06 NA
vg0220758243 sf0220752375 2 20758243 4.52E-06 4.27E-06
vg0222041029 sf0222035160 2 22041029 5.02E-06 1.35E-06
vg0221953494 sf0221947625 2 21953494 5.55E-06 3.65E-06
vg0912905423 sf0912904422 9 12905423 6.43E-06 NA
vg0224793596 sf0224787727 2 24793596 NA 6.28E-08
vg0610640917 sf0610639918 6 10640917 NA 1.09E-07
vg0222546189 sf0222540320 2 22546189 NA 1.40E-07
vg0222271516 sf0222265647 2 22271516 NA 2.23E-07
vg0224480783 sf0224474914 2 24480783 NA 7.95E-07
vg0524972451 sf0524909866 5 24972451 NA 2.39E-06
vg0223039697 sf0223033828 2 23039697 NA 4.53E-06
vg0524970300 sf0524907715 5 24970300 NA 5.19E-06