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 mr1483 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
vg0619802728 sf0619801731 6 19802728 2.00E-08 2.99E-06
vg0801744528 sf0801743531 8 1744528 3.41E-08 8.92E-07
vg0801775717 sf0801774720 8 1775717 1.66E-07 NA
vg0226753616 sf0226747747 2 26753616 2.86E-07 1.36E-06
vg1205322151 sf1205321137 12 5322151 4.66E-07 4.05E-06
vg0525550165 sf0525487586 5 25550165 2.00E-06 1.82E-06
vg0306447900 sf0306446900 3 6447900 5.76E-06 NA