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 mr1369 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
vg0329703696 sf0329696736 3 29703696 4.38E-07 4.38E-07
vg0335289141 sf0335282010 3 35289141 6.04E-07 6.04E-07
vg0206578247 sf0206578247 2 6578247 1.23E-06 1.23E-06
vg0826077942 sf0826075228 8 26077942 1.49E-06 1.49E-06
vg0805946030 sf0805945033 8 5946030 1.61E-06 1.61E-06
vg0804905723 sf0804904726 8 4905723 2.13E-06 2.13E-06
vg0223518691 sf0223512822 2 23518691 2.99E-06 2.99E-06
vg0825726642 sf0825723928 8 25726642 3.70E-06 3.70E-06
vg0724377253 sf0724376259 7 24377253 4.22E-06 4.22E-06
vg0226808043 sf0226802174 2 26808043 4.56E-06 4.56E-06