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 mr1346 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
vg1121965345 sf1121499216 11 21965345 1.01E-07 1.01E-07
vg1017929024 sf1017857796 10 17929024 4.07E-07 4.07E-07
vg0907773561 sf0907772561 9 7773561 2.35E-06 2.35E-06
vg0715473397 sf0715472404 7 15473397 3.22E-06 3.22E-06
vg0800762876 sf0800761878 8 762876 3.32E-06 3.33E-06
vg1124423034 sf1123956874 11 24423034 4.66E-06 4.66E-06