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 mr1205 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
vg0915815139 sf0915814138 9 15815139 1.40E-12 2.74E-07
vg0230082625 sf0230076756 2 30082625 9.17E-12 NA
vg0722226606 sf0722225613 7 22226606 2.24E-11 3.83E-06
vg1219503084 sf1219474554 12 19503084 2.71E-11 NA
vg0225156203 sf0225150334 2 25156203 3.11E-11 NA
vg1219919758 sf1219891228 12 19919758 6.40E-10 NA
vg0410044585 sf0410035282 4 10044585 1.41E-09 2.58E-06
vg0432280842 sf0432095735 4 32280842 1.01E-08 2.78E-06