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 mr1850 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
vg1126776659 sf1126305046 11 26776659 6.83E-08 6.83E-08
vg0611125168 sf0611124169 6 11125168 4.50E-07 4.50E-07
vg1122736186 sf1122270057 11 22736186 1.19E-06 1.19E-06
vg0431783464 sf0431598357 4 31783464 1.26E-06 1.26E-06
vg1104144721 sf1104140623 11 4144721 1.35E-06 1.35E-06
vg1121198117 sf1120731995 11 21198117 2.85E-06 2.85E-06
vg0312158508 sf0312157226 3 12158508 3.73E-06 3.73E-06
vg0134200751 sf0134199707 1 34200751 4.21E-06 4.21E-06
vg0624774901 sf0624773904 6 24774901 4.38E-06 4.38E-06