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 mr1609 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
vg1124965681 sf1124499521 11 24965681 3.74E-16 2.73E-11
vg1009709699 sf1009638520 10 9709699 1.03E-10 NA
vg0516125319 sf0516067803 5 16125319 1.33E-10 NA
vg1124305277 sf1123839147 11 24305277 1.65E-10 NA
vg0205948332 sf0205948332 2 5948332 6.97E-10 NA
vg1124468452 sf1124002292 11 24468452 1.97E-08 4.93E-07
vg1107386372 sf1107382117 11 7386372 6.08E-07 NA
vg1124078152 sf1123612022 11 24078152 8.41E-07 9.38E-07
vg1123834004 sf1123367874 11 23834004 4.79E-06 NA