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 mr1576 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
vg0426777183 sf0426592060 4 26777183 4.33E-09 3.12E-06
vg0500771205 sf0500771187 5 771205 7.00E-09 1.33E-07
vg0500807732 sf0500807714 5 807732 1.60E-08 5.30E-07
vg0220752536 sf0220746668 2 20752536 2.29E-08 1.73E-06
vg0220789608 sf0220783740 2 20789608 2.87E-08 1.54E-06
vg0329269593 sf0329262633 3 29269593 3.52E-08 NA
vg0105937313 sf0105936313 1 5937313 4.60E-08 2.56E-06
vg0603938076 sf0603937077 6 3938076 2.32E-07 NA