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 mr1434 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
vg0620348476 sf0620347479 6 20348476 2.29E-08 7.45E-07
vg0320864432 sf0320862942 3 20864432 6.46E-08 NA
vg0323504883 sf0323503057 3 23504883 9.48E-08 NA
vg0500592706 sf0500592706 5 592706 1.20E-06 NA
vg0316608593 sf0316607238 3 16608593 4.75E-06 NA
vg0402100710 sf0402096304 4 2100710 NA 1.77E-06
vg0819258196 sf0819255483 8 19258196 NA 2.26E-06