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 mr1469 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
vg0623833223 sf0623832226 6 23833223 5.96E-08 5.96E-08
vg0406863365 sf0406858810 4 6863365 6.48E-07 6.48E-07
vg1001246161 sf1001245138 10 1246161 1.00E-06 1.00E-06
vg0131923446 sf0131922402 1 31923446 3.78E-06 3.78E-06
vg0222194170 sf0222188301 2 22194170 3.88E-06 3.88E-06