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 mr1159 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
vg0912250067 sf0912249066 9 12250067 4.70E-09 2.53E-07
vg0630468525 sf0630467527 6 30468525 1.18E-06 4.80E-06
vg1224523683 sf1224490137 12 24523683 1.39E-06 3.40E-07
vg0330777536 sf0330770423 3 30777536 5.21E-06 9.32E-07
vg0402902417 sf0402898022 4 2902417 9.43E-06 NA
vg0408330841 sf0407269371 4 8330841 NA 3.94E-06