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 mr1335 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
vg0423899143 sf0423714001 4 23899143 8.15E-09 2.89E-06
vg1218168835 sf1218140271 12 18168835 1.22E-08 3.95E-07
vg0101042259 sf0101041259 1 1042259 4.77E-08 NA
vg1108636902 sf1108631512 11 8636902 7.56E-08 1.60E-06
vg1218120371 sf1218091807 12 18120371 3.68E-07 7.30E-07
vg0315818553 sf0315817200 3 15818553 2.04E-06 3.35E-06
vg1207248243 sf1207245650 12 7248243 2.68E-06 1.05E-06
vg1200731266 sf1200730266 12 731266 NA 2.23E-06