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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 mr1447 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
vg0434764872 sf0434579763 4 34764872 6.79E-07 6.79E-07
vg0808232376 sf0808231380 8 8232376 1.11E-06 1.11E-06
vg0706215718 sf0706214719 7 6215718 2.85E-06 2.85E-06
vg0519675004 sf0519612488 5 19675004 3.92E-06 3.92E-06
vg0725152187 sf0725151193 7 25152187 4.78E-06 4.78E-06
vg0704603367 sf0704602368 7 4603367 5.00E-06 5.00E-06