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 mr1383 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
vg0140491505 sf0140490462 1 40491505 6.81E-09 NA
vg0134353171 sf0134352128 1 34353171 7.08E-09 NA
vg0726218255 sf0726217261 7 26218255 1.27E-08 NA
vg0701030912 sf0701029912 7 1030912 2.31E-08 NA
vg0232319126 sf0232313257 2 32319126 2.79E-08 NA
vg1111496910 sf1111491227 11 11496910 5.99E-08 2.07E-06
vg0202324015 sf0202324013 2 2324015 1.66E-07 NA
vg0631157534 sf0631156536 6 31157534 4.73E-07 NA
vg1224504289 sf1224470743 12 24504289 1.09E-06 NA
vg1125297477 sf1124831317 11 25297477 5.71E-06 NA
vg1000105874 sf1000104874 10 105874 NA 1.58E-06