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 mr1704 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
vg0426020064 sf0425834939 4 26020064 2.35E-08 2.21E-06
vg0415198238 sf0415188953 4 15198238 3.60E-06 NA
vg0630809492 sf0630808494 6 30809492 4.77E-06 1.66E-06
vg0620348476 sf0620347479 6 20348476 5.87E-06 7.22E-06
vg0910939326 sf0910938325 9 10939326 9.12E-06 4.66E-06
vg0813705372 sf0813702658 8 13705372 NA 4.40E-06