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 mr1760 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
vg0805826839 sf0805825842 8 5826839 1.28E-08 1.28E-08
vg1124705653 sf1124239493 11 24705653 2.93E-07 2.93E-07
vg0131848160 sf0131847116 1 31848160 3.37E-07 3.37E-07
vg0421030366 sf0420858419 4 21030366 1.05E-06 1.05E-06
vg0629854146 sf0629853148 6 29854146 2.42E-06 2.42E-06
vg0628634575 sf0628633577 6 28634575 2.84E-06 2.84E-06
vg0412497804 sf0412488519 4 12497804 2.91E-06 2.91E-06
vg1225484489 sf1225450884 12 25484489 2.92E-06 2.91E-06
vg0515278523 sf0515221064 5 15278523 3.17E-06 3.17E-06
vg0134561221 sf0134560178 1 34561221 3.59E-06 3.59E-06