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 mr1502 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
vg1121671958 sf1121205835 11 21671958 4.17E-08 3.47E-06
vg0417573231 sf0417401273 4 17573231 7.05E-08 NA
vg0224248945 sf0224243076 2 24248945 7.49E-08 NA
vg0619422571 sf0619421574 6 19422571 3.38E-07 4.37E-06
vg0904311002 sf0904310002 9 4311002 4.13E-07 1.20E-06
vg0718406689 sf0718405696 7 18406689 4.54E-06 NA
vg0904007553 sf0904006553 9 4007553 5.81E-06 2.46E-06