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 mr1077 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
vg0222742146 sf0222736277 2 22742146 6.46E-35 1.65E-20
vg0222738038 sf0222732169 2 22738038 1.30E-34 5.45E-22
vg0223683609 sf0223677740 2 23683609 4.31E-15 9.69E-08
vg0222624829 sf0222618960 2 22624829 1.47E-14 5.33E-10
vg0222620162 sf0222614293 2 22620162 1.04E-13 5.43E-09
vg0224233917 sf0224228048 2 24233917 3.23E-13 3.37E-07
vg0229592697 sf0229586828 2 29592697 5.43E-12 NA
vg1112606104 sf1112142307 11 12606104 5.67E-12 NA
vg0222857256 sf0222851387 2 22857256 1.36E-10 7.79E-07
vg1112909023 sf1112445344 11 12909023 3.15E-10 3.57E-06
vg0221905933 sf0221900064 2 21905933 4.31E-10 5.03E-07
vg0221650044 sf0221644175 2 21650044 6.97E-10 3.21E-06
vg0222671915 sf0222666046 2 22671915 7.48E-08 4.63E-09
vg0114102698 sf0114101672 1 14102698 1.37E-07 NA
vg0410406461 sf0410397160 4 10406461 2.70E-06 NA
vg0905341973 sf0905340973 9 5341973 NA 3.47E-06
vg0620398180 sf0620397183 6 20398180 NA 4.21E-06