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 mr1327 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
vg0139621602 sf0139620559 1 39621602 3.31E-24 1.85E-07
vg0139032129 sf0139031086 1 39032129 9.06E-24 1.65E-08
vg0141763237 sf0141762194 1 41763237 5.41E-19 2.94E-06
vg0136150523 sf0136149480 1 36150523 1.64E-18 NA
vg0133305734 sf0133304690 1 33305734 7.66E-18 NA
vg0820872354 sf0820869641 8 20872354 1.41E-14 NA
vg0130771526 sf0130770482 1 30771526 1.77E-13 NA
vg0232694354 sf0232688485 2 32694354 8.98E-10 NA
vg1004671078 sf1004687615 10 4671078 1.26E-08 2.61E-07
vg1108503240 sf1108497850 11 8503240 NA 1.18E-06