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 mr1383 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
vg1000080974 sf1000079974 10 80974 7.89E-33 3.94E-08
vg1111746885 sf1111741202 11 11746885 2.06E-29 3.20E-06
vg1113876908 sf1113413229 11 13876908 9.55E-29 8.60E-07
vg1115260526 sf1114796840 11 15260526 1.13E-28 NA
vg0820742977 sf0820740264 8 20742977 1.35E-28 NA
vg0207488696 sf0207488696 2 7488696 2.89E-28 NA
vg0517802565 sf0517742051 5 17802565 1.06E-25 8.94E-06
vg1113936658 sf1113472979 11 13936658 3.78E-25 NA
vg0113613619 sf0113612593 1 13613619 NA 9.43E-10
vg0700266518 sf0700265518 7 266518 NA 1.15E-08
vg0700096792 sf0700095792 7 96792 NA 1.73E-08
vg0700217039 sf0700216039 7 217039 NA 2.16E-08
vg1206606922 sf1206605812 12 6606922 NA 7.68E-07
vg0311227346 sf0311226064 3 11227346 NA 9.59E-07
vg0206503587 sf0206503587 2 6503587 NA 7.51E-06