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 mr1137 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
vg0216865447 sf0216859577 2 16865447 1.05E-08 3.16E-08
vg1204312554 sf1204311542 12 4312554 7.78E-08 1.04E-07
vg0809643286 sf0809642290 8 9643286 4.20E-07 2.03E-06
vg0809848736 sf0809847740 8 9848736 1.67E-06 4.69E-06
vg0612902521 sf0612901522 6 12902521 2.55E-06 1.98E-06
vg0709322081 sf0709321087 7 9322081 3.85E-06 4.31E-06
vg1107338652 sf1107334397 11 7338652 6.28E-06 2.51E-06
vg0601078672 sf0601077673 6 1078672 9.62E-06 2.53E-06
vg0817961039 sf0817958326 8 17961039 NA 2.95E-06
vg0307715785 sf0307714723 3 7715785 NA 3.29E-06
vg0318735765 sf0318734525 3 18735765 NA 6.16E-06