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 mr1981 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
vg0228468795 sf0228462926 2 28468795 5.82E-08 5.83E-08
vg0909829640 sf0909828639 9 9829640 1.01E-06 1.01E-06
vg0810665700 sf0810664704 8 10665700 1.01E-06 1.02E-06
vg0808580570 sf0808579574 8 8580570 2.81E-06 2.81E-06
vg0101962916 sf0101961916 1 1962916 3.21E-06 3.21E-06
vg0802219193 sf0802218196 8 2219193 3.77E-06 3.77E-06
vg0519574200 sf0519511684 5 19574200 3.91E-06 3.91E-06
vg0514011016 sf0513953560 5 14011016 4.19E-06 4.19E-06
vg0616930764 sf0616929767 6 16930764 4.35E-06 4.34E-06
vg0316549548 sf0316548193 3 16549548 4.55E-06 4.55E-06
vg0626826472 sf0626825475 6 26826472 4.70E-06 4.70E-06
vg0518597457 sf0518534940 5 18597457 4.98E-06 4.98E-06