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 mr1263 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
vg0300249514 sf0300248514 3 249514 2.15E-09 5.40E-09
vg1106375766 sf1106371518 11 6375766 4.96E-08 9.51E-08
vg0726847020 sf0726846026 7 26847020 3.44E-07 4.46E-06
vg0128962067 sf0128961022 1 28962067 1.64E-06 3.80E-06
vg0322468242 sf0322466731 3 22468242 1.80E-06 2.68E-06
vg1204560575 sf1204559563 12 4560575 4.10E-06 2.93E-06
vg0718582884 sf0718581891 7 18582884 6.06E-06 NA