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 mr1937 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
vg1216059532 sf1216056828 12 16059532 1.65E-08 7.20E-06
vg0601266368 sf0601265369 6 1266368 6.38E-08 NA
vg0919996493 sf0919996012 9 19996493 9.66E-07 NA
vg1125888962 sf1125422881 11 25888962 1.70E-06 NA
vg1215106968 sf1215104305 12 15106968 NA 7.57E-07