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 mr1585 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
vg1010118225 sf1010047046 10 10118225 2.45E-17 1.87E-08
vg1010713156 sf1010641977 10 10713156 8.57E-17 1.43E-10
vg0202719681 sf0202719679 2 2719681 2.63E-16 6.06E-09
vg0628049712 sf0628048714 6 28049712 6.44E-16 4.55E-08
vg0216955961 sf0216950091 2 16955961 5.31E-15 8.23E-07
vg0400367677 sf0400366676 4 367677 7.82E-15 4.86E-10
vg1007924793 sf1007940403 10 7924793 2.83E-14 2.02E-13
vg1005387575 sf1005404112 10 5387575 6.33E-14 8.13E-14
vg0317021688 sf0317020670 3 17021688 7.03E-13 1.63E-09
vg0217437409 sf0217431539 2 17437409 6.26E-12 2.02E-09
vg0400388457 sf0400387455 4 388457 2.32E-11 2.01E-09
vg1205876728 sf1205875710 12 5876728 2.65E-11 1.50E-06
vg0327424324 sf0327417377 3 27424324 7.09E-11 4.20E-13
vg0229396054 sf0229390185 2 29396054 1.01E-10 1.13E-09
vg0220315567 sf0220309699 2 20315567 2.91E-09 1.39E-08
vg0208695804 sf0208695803 2 8695804 7.76E-09 2.72E-08
vg0400995844 sf0400991396 4 995844 9.61E-09 2.81E-07
vg1011003755 sf1010932575 10 11003755 1.36E-08 4.00E-10
vg0324795678 sf0324793757 3 24795678 1.78E-08 5.63E-09
vg1010655649 sf1010584470 10 10655649 3.84E-08 1.10E-09
vg0628029397 sf0628028399 6 28029397 5.66E-08 2.84E-08
vg0711698103 sf0711697109 7 11698103 2.19E-07 1.70E-06
vg0327425445 sf0327418498 3 27425445 NA 4.27E-10
vg0221854079 sf0221848210 2 21854079 NA 1.17E-09
vg0229470684 sf0229464815 2 29470684 NA 7.39E-09
vg0911132200 sf0911131199 9 11132200 NA 1.51E-07
vg0324228701 sf0324226780 3 24228701 NA 1.85E-07
vg0217542009 sf0217536139 2 17542009 NA 4.15E-06