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 mr1736 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
vg0316269128 sf0316267775 3 16269128 1.43E-08 1.36E-06
vg0917430047 sf0917429046 9 17430047 1.52E-08 6.34E-06
vg0919040682 sf0919040271 9 19040682 1.59E-08 4.98E-06
vg0432267846 sf0432082739 4 32267846 1.96E-08 NA
vg0820402725 sf0820400012 8 20402725 2.21E-08 5.41E-06
vg0316664724 sf0316663369 3 16664724 2.56E-08 NA
vg0133432014 sf0133430970 1 33432014 1.55E-06 3.16E-06
vg0228498409 sf0228492540 2 28498409 1.64E-06 3.42E-06
vg0917087568 sf0917086567 9 17087568 7.74E-06 NA
vg0709984451 sf0709983457 7 9984451 NA 4.87E-06