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 mr1749 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
vg0142259031 sf0142257987 1 42259031 2.41E-09 NA
vg0518852740 sf0518790224 5 18852740 1.90E-08 NA
vg1223091848 sf1223058308 12 23091848 2.21E-08 NA
vg0607313745 sf0607312746 6 7313745 2.24E-08 NA
vg0624880130 sf0624879133 6 24880130 3.11E-08 NA
vg1002941211 sf1002940188 10 2941211 3.74E-06 2.06E-06
vg0113805813 sf0113804787 1 13805813 8.78E-06 8.05E-07