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 mr1699 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
vg0331059172 sf0331052059 3 31059172 3.10E-17 4.58E-12
vg0331278847 sf0331271732 3 31278847 7.59E-17 8.67E-13
vg0107138250 sf0107137250 1 7138250 8.70E-14 2.93E-08
vg0107072026 sf0107071026 1 7072026 1.10E-13 5.30E-09
vg0825014347 sf0825011633 8 25014347 1.33E-12 3.13E-08
vg0619498874 sf0619497877 6 19498874 5.12E-12 2.61E-06
vg0825151824 sf0825149110 8 25151824 3.67E-11 2.01E-08
vg0825099366 sf0825096652 8 25099366 6.05E-11 4.50E-09
vg0824769690 sf0824766976 8 24769690 4.30E-10 1.24E-06
vg0433338500 sf0433153390 4 33338500 1.31E-07 2.16E-06
vg0107103607 sf0107102607 1 7103607 7.41E-06 1.23E-07
vg0107047840 sf0107046840 1 7047840 NA 3.09E-06
vg0227382414 sf0227376545 2 27382414 NA 3.86E-06
vg0714912592 sf0714911599 7 14912592 NA 4.21E-06