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 mr1408 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
vg0719067465 sf0719066472 7 19067465 3.01E-13 1.61E-11
vg1213429246 sf1213426584 12 13429246 3.96E-10 6.51E-08
vg1100694812 sf1100693815 11 694812 4.66E-10 5.59E-08
vg0218591225 sf0218585356 2 18591225 2.21E-09 5.03E-07
vg0324882835 sf0324880914 3 24882835 2.54E-09 5.99E-07
vg1117099141 sf1116632993 11 17099141 9.09E-09 1.43E-06
vg0406192421 sf0406187861 4 6192421 1.35E-08 3.17E-06
vg0818421321 sf0818418608 8 18421321 1.81E-08 2.81E-06
vg1017997693 sf1017926465 10 17997693 2.32E-08 4.10E-07
vg0827974117 sf0827971403 8 27974117 2.59E-08 3.34E-06
vg0112839994 sf0112838968 1 12839994 5.95E-08 3.40E-06
vg0719065500 sf0719064507 7 19065500 NA 9.07E-10
vg0422276479 sf0422091361 4 22276479 NA 6.84E-07
vg0410109116 sf0410099814 4 10109116 NA 7.48E-07