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 mr1571 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
vg0609920649 sf0609919650 6 9920649 2.45E-09 1.72E-10
vg0610683293 sf0610682294 6 10683293 5.17E-09 1.02E-08
vg1224474357 sf1224440811 12 24474357 6.09E-09 1.81E-06
vg0922309029 sf0922308548 9 22309029 7.82E-09 1.85E-06
vg0141749941 sf0141748898 1 41749941 1.32E-08 9.51E-06
vg0820872709 sf0820869996 8 20872709 8.76E-08 1.68E-06
vg0609889743 sf0609888744 6 9889743 2.89E-07 8.39E-13
vg1202051271 sf1202050269 12 2051271 5.86E-07 3.78E-06
vg1207928379 sf1207925785 12 7928379 4.27E-06 8.89E-07
vg0128909956 sf0128908911 1 28909956 5.35E-06 NA
vg0914521598 sf0914520597 9 14521598 8.20E-06 NA
vg0610585258 sf0610584259 6 10585258 NA 1.16E-06
vg1112803368 sf1112339689 11 12803368 NA 1.80E-06
vg0610002915 sf0610001916 6 10002915 NA 4.12E-06