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 mr1478 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
vg0234350385 sf0234344516 2 34350385 7.96E-16 2.07E-07
vg0306337186 sf0306336186 3 6337186 1.39E-13 NA
vg0600459723 sf0600458724 6 459723 1.14E-12 NA
vg0300353676 sf0300352674 3 353676 1.93E-12 NA
vg0610849825 sf0610848826 6 10849825 2.44E-12 1.00E-06
vg0620630387 sf0620629390 6 20630387 2.24E-10 1.45E-06
vg0400640863 sf0400639862 4 640863 NA 3.10E-06
vg0234328298 sf0234322429 2 34328298 NA 4.97E-06