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 mr1543 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
vg1200200887 sf1200199887 12 200887 5.62E-09 NA
vg0123839187 sf0123838143 1 23839187 6.77E-09 NA
vg0142033067 sf0142032024 1 42033067 1.90E-08 NA
vg0141992653 sf0141991610 1 41992653 4.47E-08 NA
vg0826637879 sf0826635165 8 26637879 5.05E-08 NA
vg0136579622 sf0136578579 1 36579622 2.99E-06 NA
vg0812796308 sf0812794133 8 12796308 6.76E-06 NA
vg0104468017 sf0104467017 1 4468017 NA 5.63E-06