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 mr1306 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
vg0726847020 sf0726846026 7 26847020 3.13E-08 NA
vg0125906058 sf0125905014 1 25906058 3.59E-08 NA
vg0131535738 sf0131534694 1 31535738 7.98E-08 NA
vg0300249514 sf0300248514 3 249514 1.64E-07 1.13E-06
vg0431655631 sf0431470524 4 31655631 9.67E-07 3.99E-06
vg1109530326 sf1109524903 11 9530326 1.58E-06 1.56E-06
vg1217659093 sf1217653048 12 17659093 2.47E-06 NA
vg0324647482 sf0324645561 3 24647482 3.65E-06 1.34E-06
vg1204560575 sf1204559563 12 4560575 9.09E-06 4.88E-06
vg1106375766 sf1106371518 11 6375766 9.28E-06 6.51E-07