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 mr1406 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
vg0102430888 sf0102429888 1 2430888 6.91E-08 6.92E-08
vg1214863744 sf1214861085 12 14863744 1.77E-07 1.78E-07
vg0915238489 sf0915237488 9 15238489 3.90E-07 3.90E-07
vg0724559906 sf0724558912 7 24559906 1.10E-06 1.10E-06
vg0118887296 sf0118886251 1 18887296 1.17E-06 1.17E-06
vg0505815242 sf0505815180 5 5815242 1.22E-06 1.22E-06
vg1102677343 sf1102673247 11 2677343 2.45E-06 2.46E-06
vg0715512638 sf0715511645 7 15512638 2.55E-06 2.55E-06