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 mr1686 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
vg0724440186 sf0724439192 7 24440186 8.48E-22 2.45E-07
vg0136902608 sf0136901565 1 36902608 4.60E-19 7.02E-06
vg0136902523 sf0136901480 1 36902523 1.69E-18 3.66E-06
vg0618903529 sf0618902532 6 18903529 2.02E-18 NA
vg0705436484 sf0705435485 7 5436484 5.25E-18 NA
vg0721760138 sf0721759145 7 21760138 5.38E-18 NA
vg0626091811 sf0626090814 6 26091811 9.46E-18 3.74E-06
vg0611842145 sf0611841146 6 11842145 3.54E-16 NA
vg1111313699 sf1111308016 11 11313699 NA 2.34E-07
vg0607146332 sf0607145333 6 7146332 NA 8.39E-06