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 mr1054 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
vg1002941120 sf1002940097 10 2941120 8.47E-08 8.47E-08
vg0712648528 sf0712647535 7 12648528 1.10E-07 1.10E-07
vg0406883539 sf0406878798 4 6883539 3.11E-07 3.11E-07
vg0411387439 sf0411378142 4 11387439 9.86E-07 9.86E-07
vg0406888783 sf0406884042 4 6888783 1.31E-06 1.31E-06
vg0715817404 sf0715816411 7 15817404 1.38E-06 1.38E-06
vg0910768444 sf0910767443 9 10768444 1.73E-06 1.73E-06
vg1114873399 sf1114409713 11 14873399 2.20E-06 2.20E-06
vg0406987146 sf0406982417 4 6987146 2.39E-06 2.39E-06
vg0327981236 sf0327974290 3 27981236 2.78E-06 2.78E-06
vg1122446629 sf1121980500 11 22446629 3.10E-06 3.10E-06
vg0208267128 sf0208267127 2 8267128 3.68E-06 3.68E-06
vg0208850397 sf0208850395 2 8850397 4.74E-06 4.74E-06
vg0722504959 sf0722503966 7 22504959 4.84E-06 4.84E-06
vg1119100956 sf1118634644 11 19100956 4.96E-06 4.96E-06