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 mr1137 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
vg0604350087 sf0604349088 6 4350087 7.10E-36 8.35E-22
vg0207150816 sf0207150816 2 7150816 9.45E-18 1.10E-06
vg0808781519 sf0808780523 8 8781519 1.38E-16 4.34E-06
vg1021124595 sf1021053074 10 21124595 8.06E-16 NA
vg0128528170 sf0128527125 1 28528170 3.35E-15 NA
vg1116506738 sf1116041615 11 16506738 2.46E-14 4.14E-06
vg0604757294 sf0604756295 6 4757294 8.87E-11 2.53E-06
vg0604356746 sf0604355747 6 4356746 4.22E-09 1.99E-11