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 mr1405 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
vg0419217910 sf0419045948 4 19217910 5.23E-12 4.80E-09
vg1217967699 sf1217939135 12 17967699 2.90E-08 NA
vg1009637244 sf1009566065 10 9637244 3.05E-08 1.66E-07
vg0810825523 sf0810824528 8 10825523 5.73E-08 NA
vg1122531132 sf1122065003 11 22531132 8.15E-08 NA
vg0116027186 sf0116026160 1 16027186 1.13E-07 3.48E-06