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 mr1401 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
vg0313058915 sf0313057633 3 13058915 1.09E-10 NA
vg0728265516 sf0728264524 7 28265516 1.14E-10 NA
vg1115925850 sf1115460720 11 15925850 1.73E-10 NA
vg1102677343 sf1102673247 11 2677343 2.36E-10 2.67E-06
vg1019690763 sf1019619264 10 19690763 3.82E-10 NA
vg0125628571 sf0125627527 1 25628571 7.46E-10 1.74E-06
vg0920272507 sf0920272026 9 20272507 1.01E-09 3.71E-06
vg0818034083 sf0818031370 8 18034083 5.84E-09 NA