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 mr1287 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
vg0712648528 sf0712647535 7 12648528 1.08E-07 1.08E-07
vg1002941120 sf1002940097 10 2941120 3.72E-07 3.72E-07
vg1111043318 sf1111037635 11 11043318 5.99E-07 5.99E-07
vg0406883539 sf0406878798 4 6883539 9.12E-07 9.12E-07
vg1116473187 sf1116008064 11 16473187 9.63E-07 9.64E-07
vg1119100956 sf1118634644 11 19100956 1.07E-06 1.07E-06
vg0327981236 sf0327974290 3 27981236 1.70E-06 1.70E-06
vg1122446629 sf1121980500 11 22446629 2.45E-06 2.45E-06
vg0406888783 sf0406884042 4 6888783 3.01E-06 3.01E-06
vg0715817404 sf0715816411 7 15817404 3.05E-06 3.05E-06
vg1114873399 sf1114409713 11 14873399 3.48E-06 3.48E-06
vg0607657176 sf0607656177 6 7657176 3.83E-06 3.83E-06
vg0722504959 sf0722503966 7 22504959 3.89E-06 3.89E-06
vg1001392057 sf1001391034 10 1392057 4.15E-06 4.15E-06
vg0411387439 sf0411378142 4 11387439 4.23E-06 4.23E-06
vg0910768444 sf0910767443 9 10768444 4.25E-06 4.25E-06