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 mr1431 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
vg1114877299 sf1114413613 11 14877299 2.11E-18 NA
vg0327442246 sf0327435299 3 27442246 2.68E-18 NA
vg1218194091 sf1218165527 12 18194091 3.04E-18 NA
vg0819137940 sf0819135227 8 19137940 9.06E-18 NA
vg0129977795 sf0129976750 1 29977795 2.70E-17 NA
vg1216039002 sf1216036298 12 16039002 1.44E-16 2.02E-06
vg1216054938 sf1216052234 12 16054938 4.18E-16 5.34E-06
vg1215566706 sf1215564003 12 15566706 4.04E-14 9.10E-07