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 mr1615 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
vg1210400634 sf1210398047 12 10400634 8.49E-08 8.49E-08
vg0137651074 sf0137650031 1 37651074 1.18E-07 1.18E-07
vg0805969903 sf0805968906 8 5969903 1.34E-07 1.34E-07
vg0806098917 sf0806097922 8 6098917 4.73E-07 4.73E-07
vg0527394004 sf0527331360 5 27394004 9.12E-07 9.12E-07
vg0819195560 sf0819192847 8 19195560 9.23E-07 9.24E-07
vg0808474802 sf0808473806 8 8474802 3.34E-06 3.34E-06
vg0128444492 sf0128443447 1 28444492 4.23E-06 4.23E-06
vg0141766196 sf0141765153 1 41766196 4.91E-06 4.91E-06