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 mr1051 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
vg0921457375 sf0921456894 9 21457375 4.45E-11 1.45E-07
vg0921543752 sf0921543271 9 21543752 2.52E-10 4.68E-09
vg0328947114 sf0328940166 3 28947114 9.60E-10 8.07E-07
vg0205319579 sf0205319578 2 5319579 2.17E-09 2.19E-06
vg0626417085 sf0626416088 6 26417085 3.31E-09 NA
vg0328911258 sf0328904310 3 28911258 6.05E-09 1.32E-07
vg0328953433 sf0328946485 3 28953433 6.43E-09 3.12E-07
vg0134815001 sf0134813958 1 34815001 7.00E-09 NA
vg0133208220 sf0133207176 1 33208220 5.07E-08 2.17E-06
vg0133599398 sf0133598354 1 33599398 2.04E-06 2.29E-06
vg0215099729 sf0215093859 2 15099729 4.36E-06 4.80E-06
vg1103462067 sf1103457970 11 3462067 NA 1.98E-06
vg0504038203 sf0504038180 5 4038203 NA 2.37E-06