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 mr1305 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
vg1005695540 sf1005712078 10 5695540 1.34E-33 5.19E-10
vg0335000939 sf0334993809 3 35000939 9.49E-31 2.62E-11
vg0434732193 sf0434547084 4 34732193 3.21E-29 9.30E-07
vg1010636917 sf1010565738 10 10636917 3.76E-29 2.15E-06
vg1021187693 sf1021116171 10 21187693 4.72E-28 1.48E-06
vg1010713156 sf1010641977 10 10713156 2.47E-26 2.00E-09
vg0400388457 sf0400387455 4 388457 3.72E-24 3.09E-08
vg0703681415 sf0703680416 7 3681415 1.82E-21 NA
vg1005384319 sf1005400856 10 5384319 NA 5.81E-13
vg0400367677 sf0400366676 4 367677 NA 4.55E-12
vg0327425445 sf0327418498 3 27425445 NA 1.70E-11
vg1008640554 sf1008569416 10 8640554 NA 3.35E-11
vg0327424324 sf0327417377 3 27424324 NA 7.81E-11
vg0202735231 sf0202735229 2 2735231 NA 1.70E-10
vg0605613230 sf0605612231 6 5613230 NA 6.63E-10
vg0202722002 sf0202722000 2 2722002 NA 1.17E-09
vg0317023117 sf0317021991 3 17023117 NA 2.03E-09
vg0628049712 sf0628048714 6 28049712 NA 5.83E-09
vg0628029397 sf0628028399 6 28029397 NA 6.82E-09
vg0324795678 sf0324793757 3 24795678 NA 1.33E-08
vg0627986717 sf0627985719 6 27986717 NA 3.68E-08
vg0221859377 sf0221853508 2 21859377 NA 5.43E-08
vg0307990876 sf0307989814 3 7990876 NA 7.77E-08
vg0220315567 sf0220309699 2 20315567 NA 1.22E-07
vg0323665466 sf0323663640 3 23665466 NA 1.59E-07
vg1118772186 sf1118305994 11 18772186 NA 2.55E-06