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 mr1338 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
vg1209423376 sf1209420785 12 9423376 1.31E-08 5.47E-07
vg1212217499 sf1212214837 12 12217499 3.13E-08 5.66E-06
vg0122915621 sf0122914577 1 22915621 5.68E-08 NA
vg0414176233 sf0414166949 4 14176233 7.65E-08 NA
vg0328828515 sf0328821569 3 28828515 9.53E-08 7.03E-06