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 mr1979 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
vg0331716906 sf0331709783 3 31716906 1.55E-10 NA
vg0322677970 sf0322676459 3 22677970 3.59E-10 NA
vg0613080964 sf0613079965 6 13080964 2.01E-09 NA
vg0909006841 sf0909005840 9 9006841 2.59E-09 NA
vg1117647726 sf1117181582 11 17647726 3.13E-09 NA
vg0631246670 sf0631245672 6 31246670 9.15E-09 NA
vg0301371740 sf0301370738 3 1371740 2.77E-08 1.69E-06
vg1217862215 sf1217833649 12 17862215 NA 4.63E-06