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 mr1453 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
vg0335289141 sf0335282010 3 35289141 1.91E-07 1.91E-07
vg0329703696 sf0329696736 3 29703696 6.52E-07 6.52E-07
vg0805055173 sf0805054176 8 5055173 7.80E-07 7.80E-07
vg0223518691 sf0223512822 2 23518691 1.07E-06 1.07E-06
vg0206578247 sf0206578247 2 6578247 1.57E-06 1.57E-06
vg0826077942 sf0826075228 8 26077942 1.91E-06 1.91E-06
vg0805005643 sf0805004646 8 5005643 2.04E-06 2.04E-06
vg0630441706 sf0630440708 6 30441706 2.78E-06 2.78E-06
vg0226808649 sf0226802780 2 26808649 2.92E-06 2.92E-06
vg0724377253 sf0724376259 7 24377253 2.97E-06 2.97E-06
vg0228320179 sf0228314310 2 28320179 3.72E-06 3.72E-06
vg0805183407 sf0805182410 8 5183407 4.76E-06 4.76E-06
vg0825726642 sf0825723928 8 25726642 4.85E-06 4.85E-06