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 mr1671 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
vg0717180842 sf0717179849 7 17180842 1.41E-68 NA
vg0334580690 sf0334573560 3 34580690 2.84E-68 NA
vg0305155579 sf0305154581 3 5155579 1.34E-67 9.46E-06
vg0706828581 sf0706827586 7 6828581 2.13E-67 NA
vg0204210973 sf0204210970 2 4210973 7.63E-67 NA
vg0122073422 sf0122072377 1 22073422 2.07E-65 4.43E-06
vg0334633999 sf0334626869 3 34633999 7.31E-60 6.79E-10
vg0324945119 sf0324943199 3 24945119 NA 6.17E-08
vg0334580739 sf0334573609 3 34580739 NA 8.97E-08
vg0132886037 sf0132884993 1 32886037 NA 3.24E-07
vg0132918542 sf0132917498 1 32918542 NA 3.53E-07
vg0311534838 sf0311533556 3 11534838 NA 5.47E-07
vg0306466083 sf0306465083 3 6466083 NA 1.29E-06
vg1000570465 sf1000569441 10 570465 NA 1.89E-06
vg0304303829 sf0304302831 3 4303829 NA 2.83E-06
vg0716996805 sf0716995812 7 16996805 NA 4.58E-06