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 mr1289 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
vg0335297514 sf0335290383 3 35297514 8.92E-10 3.80E-07
vg0134802811 sf0134801768 1 34802811 2.83E-09 8.73E-07
vg0528836237 sf0528773592 5 28836237 2.95E-09 1.19E-06
vg0107647549 sf0107646549 1 7647549 1.20E-08 5.17E-06
vg0714523532 sf0714522539 7 14523532 1.23E-08 3.26E-06
vg0805992743 sf0805991746 8 5992743 1.56E-08 3.49E-06
vg0207699992 sf0207699991 2 7699992 2.79E-08 4.76E-06
vg1214763854 sf1214761195 12 14763854 2.11E-07 1.03E-06
vg1127933245 sf1127461631 11 27933245 3.11E-07 1.12E-06
vg0525550165 sf0525487586 5 25550165 NA 1.55E-06