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 mr1621 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
vg1117790476 sf1117324332 11 17790476 8.82E-09 2.19E-06
vg1117802458 sf1117336314 11 17802458 1.41E-08 1.73E-06
vg0528650875 sf0528588230 5 28650875 5.51E-08 2.62E-06
vg0140395650 sf0140394607 1 40395650 6.84E-08 5.96E-06
vg0801700429 sf0801699432 8 1700429 8.00E-08 6.63E-06
vg0724505923 sf0724504929 7 24505923 1.08E-07 2.94E-07
vg0419536798 sf0419364836 4 19536798 1.69E-06 4.90E-06
vg0724516480 sf0724515486 7 24516480 1.77E-06 3.18E-08
vg0907959783 sf0907958783 9 7959783 2.21E-06 3.56E-06
vg0103583289 sf0103582289 1 3583289 4.41E-06 3.10E-06