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 mr1396 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
vg0130163180 sf0130162135 1 30163180 1.46E-08 1.57E-06
vg1104978992 sf1104974803 11 4978992 3.62E-08 3.85E-06
vg0300249514 sf0300248514 3 249514 7.09E-07 9.50E-07
vg0229918162 sf0229912293 2 29918162 2.85E-06 NA
vg0324205491 sf0324203570 3 24205491 7.08E-06 3.17E-06
vg1125773021 sf1125306860 11 25773021 7.18E-06 NA