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 mr1603 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
vg0216770681 sf0216764811 2 16770681 4.22E-09 4.22E-09
vg0216600070 sf0216594200 2 16600070 1.42E-08 1.42E-08
vg0521338739 sf0521276180 5 21338739 2.52E-07 2.52E-07
vg1011651673 sf1011580488 10 11651673 6.48E-07 6.48E-07
vg0803690368 sf0803689371 8 3690368 1.04E-06 1.04E-06
vg0216903126 sf0216897256 2 16903126 1.24E-06 1.24E-06
vg1004248992 sf1004265530 10 4248992 1.56E-06 1.56E-06
vg0308205423 sf0308204361 3 8205423 1.58E-06 1.58E-06
vg0502967614 sf0502967590 5 2967614 2.04E-06 2.04E-06
vg0700897980 sf0700896980 7 897980 2.39E-06 2.39E-06
vg0625654852 sf0625653855 6 25654852 3.00E-06 3.00E-06
vg0432668084 sf0432482973 4 32668084 3.27E-06 3.28E-06
vg0212535742 sf0212535738 2 12535742 3.49E-06 3.49E-06
vg0316513657 sf0316512302 3 16513657 3.82E-06 3.82E-06
vg0825901790 sf0825899076 8 25901790 4.11E-06 4.11E-06
vg1020448314 sf1020376793 10 20448314 4.27E-06 4.27E-06