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 mr1611 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
vg0726964336 sf0726963342 7 26964336 3.35E-11 NA
vg0123685482 sf0123684438 1 23685482 2.01E-10 NA
vg1104966222 sf1104962033 11 4966222 1.73E-09 NA
vg1217606407 sf1217600362 12 17606407 5.46E-09 NA
vg0131535738 sf0131534694 1 31535738 6.54E-09 NA
vg0431655631 sf0431470524 4 31655631 3.59E-07 4.68E-06
vg1116933718 sf1116468597 11 16933718 1.08E-06 2.10E-06
vg0412512389 sf0412503099 4 12512389 1.77E-06 NA
vg1106375766 sf1106371518 11 6375766 4.38E-06 5.53E-07
vg1102449959 sf1102445863 11 2449959 7.46E-06 NA