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 mr1099 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
vg0220960199 sf0220954331 2 20960199 7.83E-09 7.83E-09
vg0222833455 sf0222827586 2 22833455 8.20E-09 8.20E-09
vg0627929341 sf0627928343 6 27929341 1.43E-08 1.43E-08
vg0108533994 sf0108532994 1 8533994 9.45E-08 9.45E-08
vg0727090466 sf0727089472 7 27090466 3.87E-07 3.87E-07
vg0709675216 sf0709674222 7 9675216 7.44E-07 7.44E-07
vg0402996405 sf0402992011 4 2996405 9.37E-07 9.37E-07
vg0416966079 sf0416794121 4 16966079 1.94E-06 1.94E-06
vg0220849802 sf0220843934 2 20849802 2.09E-06 2.09E-06
vg0228145108 sf0228139239 2 28145108 2.16E-06 2.16E-06
vg0805855827 sf0805854830 8 5855827 2.54E-06 2.54E-06
vg0628759426 sf0628758428 6 28759426 2.84E-06 2.84E-06
vg1002659326 sf1002658303 10 2659326 2.99E-06 2.99E-06
vg0223741023 sf0223735154 2 23741023 3.30E-06 3.30E-06
vg0224228628 sf0224222759 2 24228628 3.31E-06 3.31E-06
vg0625603773 sf0625602776 6 25603773 4.99E-06 4.99E-06