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
vg0226816599 sf0226810730 2 26816599 7.63E-08 5.89E-07
vg0501390670 sf0501390654 5 1390670 5.62E-07 3.60E-06
vg0620348476 sf0620347479 6 20348476 1.18E-06 4.22E-06
vg0622463129 sf0622462132 6 22463129 2.26E-06 3.52E-06
vg0329917563 sf0329910602 3 29917563 4.58E-06 2.19E-06
vg0612586822 sf0612585823 6 12586822 9.94E-06 2.75E-06