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 mr1462 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 5.67E-09 5.67E-09
vg0901840944 sf0901839944 9 1840944 1.45E-07 1.45E-07
vg1224577767 sf1224544221 12 24577767 6.42E-07 6.42E-07
vg0915814038 sf0915813037 9 15814038 1.52E-06 1.52E-06
vg0324094127 sf0324092206 3 24094127 2.11E-06 2.11E-06
vg0201504554 sf0201504554 2 1504554 2.57E-06 2.57E-06
vg1218040492 sf1218011928 12 18040492 3.95E-06 3.95E-06
vg0714404540 sf0714403547 7 14404540 4.69E-06 4.69E-06
vg0319345137 sf0319343648 3 19345137 6.31E-06 6.31E-06