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 mr1670 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
vg0400416361 sf0400415359 4 416361 7.78E-14 7.78E-14
vg0400034660 sf0400033660 4 34660 4.65E-08 4.65E-08
vg0138176410 sf0138175367 1 38176410 8.88E-08 8.88E-08
vg0400557049 sf0400556048 4 557049 9.72E-08 9.72E-08
vg0138169040 sf0138167997 1 38169040 9.86E-08 9.86E-08
vg0135810780 sf0135809737 1 35810780 3.84E-06 3.84E-06