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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 mr1581 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
vg0224541248 sf0224535379 2 24541248 2.87E-07 2.87E-07
vg1110088127 sf1110082704 11 10088127 6.11E-07 6.11E-07
vg0315183809 sf0315182456 3 15183809 1.60E-06 1.60E-06
vg0522134829 sf0522072271 5 22134829 1.64E-06 1.64E-06
vg0816866494 sf0816863780 8 16866494 2.53E-06 2.53E-06
vg0318074722 sf0318073504 3 18074722 2.56E-06 2.56E-06
vg1115149972 sf1114686286 11 15149972 3.34E-06 3.34E-06
vg0213822496 sf0213816626 2 13822496 3.88E-06 3.88E-06